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galaxy.schema package¶

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

Bases: BaseModel

email: Optional[str]¶

preferences: Dict[str, str]¶

all_roles() → list[source]¶

class galaxy.schema.ValueFilterQueryParams(*, q: Optional[Union[List[str], str]] = None, qv: Optional[Union[List[str], str]] = None)[source]¶

Bases: BaseModel

Allows filtering/querying elements by value like q=<property>-<operator>&qv=<value>

Multiple q/qv queries can be concatenated.

q: Optional[Union[List[str], str]]¶

qv: Optional[Union[List[str], str]]¶

class galaxy.schema.PaginationQueryParams(*, offset: Optional[ConstrainedIntValue] = 0, limit: Optional[ConstrainedIntValue] = None)[source]¶

Bases: BaseModel

Used to paginate a the request results by limiting and offsetting.

offset: Optional[int]¶

limit: Optional[int]¶

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

Bases: ValueFilterQueryParams, PaginationQueryParams

Contains full filtering options to query elements, paginate and order them.

order: Optional[str]¶

class galaxy.schema.SerializationParams(*, view: Optional[str] = None, keys: Optional[List[str]] = None, default_view: Optional[str] = None)[source]¶

Bases: BaseModel

Contains common parameters for customizing model serialization.

view: Optional[str]¶

keys: Optional[List[str]]¶

default_view: Optional[str]¶

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

Bases: str, Enum

An enumeration.

invocation_report = 'invocation_report'¶

page = 'page'¶

class galaxy.schema.APIKeyModel(*, key: str, create_time: datetime)[source]¶

Bases: BaseModel

key: str¶

create_time: datetime¶

Submodules¶

galaxy.schema.fetch_data module¶

class galaxy.schema.fetch_data.FetchBaseModel[source]¶

Bases: Model

class Config[source]¶

Bases: object

allow_population_by_field_name = True¶

class galaxy.schema.fetch_data.ElementsFromType(value)[source]¶

Bases: str, Enum

An enumeration.

archive = 'archive'¶

bagit = 'bagit'¶

bagit_archive = 'bagit_archive'¶

directory = 'directory'¶

class galaxy.schema.fetch_data.BaseFetchDataTarget(*, auto_decompress: bool = False)[source]¶

Bases: FetchBaseModel

auto_decompress: bool¶

class galaxy.schema.fetch_data.ItemsFromSrc(value)[source]¶

Bases: str, Enum

An enumeration.

url = 'url'¶

files = 'files'¶

path = 'path'¶

ftp_import = 'ftp_import'¶

server_dir = 'server_dir'¶

class galaxy.schema.fetch_data.Src(value)[source]¶

Bases: str, Enum

An enumeration.

url = 'url'¶

pasted = 'pasted'¶

files = 'files'¶

path = 'path'¶

composite = 'composite'¶

ftp_import = 'ftp_import'¶

server_dir = 'server_dir'¶

class galaxy.schema.fetch_data.DestinationType(value)[source]¶

Bases: str, Enum

An enumeration.

library = 'library'¶

library_folder = 'library_folder'¶

hdcas = 'hdcas'¶

hdas = 'hdas'¶

class galaxy.schema.fetch_data.HdaDestination(*, type: typing_extensions.Literal[hdas])[source]¶

Bases: FetchBaseModel

type: typing_extensions.Literal[hdas]¶

class galaxy.schema.fetch_data.HdcaDestination(*, type: typing_extensions.Literal[hdca])[source]¶

Bases: FetchBaseModel

type: typing_extensions.Literal[hdca]¶

class galaxy.schema.fetch_data.LibraryFolderDestination(*, type: typing_extensions.Literal[library_folder], library_folder_id: DecodedDatabaseIdField)[source]¶

Bases: FetchBaseModel

type: typing_extensions.Literal[library_folder]¶

library_folder_id: DecodedDatabaseIdField¶

class galaxy.schema.fetch_data.BaseCollectionTarget(*, auto_decompress: bool = False, destination: HdcaDestination, collection_type: Optional[str] = None, tags: Optional[List[str]] = None, name: Optional[str] = None)[source]¶

Bases: BaseFetchDataTarget

destination: HdcaDestination¶

collection_type: Optional[str]¶

tags: Optional[List[str]]¶

name: Optional[str]¶

class galaxy.schema.fetch_data.LibraryDestination(*, type: typing_extensions.Literal[library], name: str, description: Optional[str] = None, synopsis: Optional[str] = None)[source]¶

Bases: FetchBaseModel

type: typing_extensions.Literal[library]¶

name: str¶

description: Optional[str]¶

synopsis: Optional[str]¶

class galaxy.schema.fetch_data.ExtraFiles(*, items_from: Optional[str] = None, src: Src, fuzzy_root: Optional[bool] = True)[source]¶

Bases: FetchBaseModel

items_from: Optional[str]¶

src: Src¶

fuzzy_root: Optional[bool]¶

class galaxy.schema.fetch_data.BaseDataElement(*, name: Optional[str] = None, dbkey: str = '?', info: Optional[str] = None, ext: str = 'auto', space_to_tab: bool = False, to_posix_lines: bool = False, deferred: bool = False, tags: Optional[List[str]] = None, created_from_basename: Optional[str] = None, extra_files: Optional[ExtraFiles] = None, auto_decompress: bool = False, elements_from: Optional[ElementsFromType] = None, collection_type: Optional[str] = None, MD5: Optional[str] = None, description: Optional[str] = None)[source]¶

Bases: FetchBaseModel

name: Optional[str]¶

dbkey: str¶

info: Optional[str]¶

ext: str¶

space_to_tab: bool¶

to_posix_lines: bool¶

deferred: bool¶

tags: Optional[List[str]]¶

created_from_basename: Optional[str]¶

extra_files: Optional[ExtraFiles]¶

auto_decompress: bool¶

items_from: Optional[ElementsFromType]¶

collection_type: Optional[str]¶

MD5: Optional[str]¶

description: Optional[str]¶

class Config[source]¶

Bases: object

extra = 'forbid'¶

class galaxy.schema.fetch_data.FileDataElement(*, name: Optional[str] = None, dbkey: str = '?', info: Optional[str] = None, ext: str = 'auto', space_to_tab: bool = False, to_posix_lines: bool = False, deferred: bool = False, tags: Optional[List[str]] = None, created_from_basename: Optional[str] = None, extra_files: Optional[ExtraFiles] = None, auto_decompress: bool = False, elements_from: Optional[ElementsFromType] = None, collection_type: Optional[str] = None, MD5: Optional[str] = None, description: Optional[str] = None, src: typing_extensions.Literal[files])[source]¶

Bases: BaseDataElement

src: typing_extensions.Literal[files]¶

class galaxy.schema.fetch_data.PastedDataElement(*, name: Optional[str] = None, dbkey: str = '?', info: Optional[str] = None, ext: str = 'auto', space_to_tab: bool = False, to_posix_lines: bool = False, deferred: bool = False, tags: Optional[List[str]] = None, created_from_basename: Optional[str] = None, extra_files: Optional[ExtraFiles] = None, auto_decompress: bool = False, elements_from: Optional[ElementsFromType] = None, collection_type: Optional[str] = None, MD5: Optional[str] = None, description: Optional[str] = None, src: typing_extensions.Literal[pasted], paste_content: str)[source]¶

Bases: BaseDataElement

src: typing_extensions.Literal[pasted]¶

paste_content: str¶

class galaxy.schema.fetch_data.UrlDataElement(*, name: Optional[str] = None, dbkey: str = '?', info: Optional[str] = None, ext: str = 'auto', space_to_tab: bool = False, to_posix_lines: bool = False, deferred: bool = False, tags: Optional[List[str]] = None, created_from_basename: Optional[str] = None, extra_files: Optional[ExtraFiles] = None, auto_decompress: bool = False, elements_from: Optional[ElementsFromType] = None, collection_type: Optional[str] = None, MD5: Optional[str] = None, description: Optional[str] = None, src: typing_extensions.Literal[url], url: str)[source]¶

Bases: BaseDataElement

src: typing_extensions.Literal[url]¶

url: str¶

class galaxy.schema.fetch_data.ServerDirElement(*, name: Optional[str] = None, dbkey: str = '?', info: Optional[str] = None, ext: str = 'auto', space_to_tab: bool = False, to_posix_lines: bool = False, deferred: bool = False, tags: Optional[List[str]] = None, created_from_basename: Optional[str] = None, extra_files: Optional[ExtraFiles] = None, auto_decompress: bool = False, elements_from: Optional[ElementsFromType] = None, collection_type: Optional[str] = None, MD5: Optional[str] = None, description: Optional[str] = None, src: typing_extensions.Literal[server_dir], server_dir: str, link_data_only: Optional[bool] = None)[source]¶

Bases: BaseDataElement

src: typing_extensions.Literal[server_dir]¶

server_dir: str¶

link_data_only: Optional[bool]¶

class galaxy.schema.fetch_data.FtpImportElement(*, name: Optional[str] = None, dbkey: str = '?', info: Optional[str] = None, ext: str = 'auto', space_to_tab: bool = False, to_posix_lines: bool = False, deferred: bool = False, tags: Optional[List[str]] = None, created_from_basename: Optional[str] = None, extra_files: Optional[ExtraFiles] = None, auto_decompress: bool = False, elements_from: Optional[ElementsFromType] = None, collection_type: Optional[str] = None, MD5: Optional[str] = None, description: Optional[str] = None, src: typing_extensions.Literal[ftp_import], ftp_path: str)[source]¶

Bases: BaseDataElement

src: typing_extensions.Literal[ftp_import]¶

ftp_path: str¶

items_from: Optional[ElementsFromType]¶

name: Optional[str]¶

collection_type: Optional[str]¶

class galaxy.schema.fetch_data.ItemsFromModel(*, src: ItemsFromSrc, path: Optional[str] = None, ftp_path: Optional[str] = None, server_dir: Optional[str] = None, url: Optional[str] = None)[source]¶

Bases: Model

src: ItemsFromSrc¶

path: Optional[str]¶

ftp_path: Optional[str]¶

server_dir: Optional[str]¶

url: Optional[str]¶

class galaxy.schema.fetch_data.FtpImportTarget(*, auto_decompress: bool = False, destination: HdcaDestination, collection_type: Optional[str] = None, tags: Optional[List[str]] = None, name: Optional[str] = None, src: typing_extensions.Literal[ftp_import], ftp_path: str, elements_from: Optional[ElementsFromType] = None)[source]¶

Bases: BaseCollectionTarget

src: typing_extensions.Literal[ftp_import]¶

ftp_path: str¶

items_from: Optional[ElementsFromType]¶

class galaxy.schema.fetch_data.PathDataElement(*, name: Optional[str] = None, dbkey: str = '?', info: Optional[str] = None, ext: str = 'auto', space_to_tab: bool = False, to_posix_lines: bool = False, deferred: bool = False, tags: Optional[List[str]] = None, created_from_basename: Optional[str] = None, extra_files: Optional[ExtraFiles] = None, auto_decompress: bool = False, elements_from: Optional[ElementsFromType] = None, collection_type: Optional[str] = None, MD5: Optional[str] = None, description: Optional[str] = None, src: typing_extensions.Literal[path], path: str, link_data_only: Optional[bool] = None)[source]¶

Bases: BaseDataElement

src: typing_extensions.Literal[path]¶

path: str¶

items_from: Optional[ElementsFromType]¶

link_data_only: Optional[bool]¶

class galaxy.schema.fetch_data.CompositeDataElement(*, name: Optional[str] = None, dbkey: str = '?', info: Optional[str] = None, ext: str = 'auto', space_to_tab: bool = False, to_posix_lines: bool = False, deferred: bool = False, tags: Optional[List[str]] = None, created_from_basename: Optional[str] = None, extra_files: Optional[ExtraFiles] = None, auto_decompress: bool = False, elements_from: Optional[ElementsFromType] = None, collection_type: Optional[str] = None, MD5: Optional[str] = None, description: Optional[str] = None, src: typing_extensions.Literal[composite], composite: CompositeItems)[source]¶

Bases: BaseDataElement

src: typing_extensions.Literal[composite]¶

composite: CompositeItems¶

class galaxy.schema.fetch_data.CompositeItems(*, elements: List[Union[FileDataElement, PastedDataElement, UrlDataElement, PathDataElement, ServerDirElement, FtpImportElement]])[source]¶

Bases: FetchBaseModel

items: List[Union[FileDataElement, PastedDataElement, UrlDataElement, PathDataElement, ServerDirElement, FtpImportElement]]¶

class galaxy.schema.fetch_data.NestedElement(*, name: Optional[str] = None, dbkey: str = '?', info: Optional[str] = None, ext: str = 'auto', space_to_tab: bool = False, to_posix_lines: bool = False, deferred: bool = False, tags: Optional[List[str]] = None, created_from_basename: Optional[str] = None, extra_files: Optional[ExtraFiles] = None, auto_decompress: bool = False, elements_from: Optional[ElementsFromType] = None, collection_type: Optional[str] = None, MD5: Optional[str] = None, description: Optional[str] = None, elements: List[Union[AnyElement, NestedElement]])[source]¶

Bases: BaseDataElement

class galaxy.schema.fetch_data.BaseDataTarget(*, auto_decompress: bool = False, destination: Union[HdaDestination, LibraryFolderDestination, LibraryDestination])[source]¶

Bases: BaseFetchDataTarget

destination: Union[HdaDestination, LibraryFolderDestination, LibraryDestination]¶

Bases: BaseDataTarget

class galaxy.schema.fetch_data.DataElementsFromTarget(*, src: ItemsFromSrc, path: Optional[str] = None, ftp_path: Optional[str] = None, server_dir: Optional[str] = None, url: Optional[str] = None, auto_decompress: bool = False, destination: Union[HdaDestination, LibraryFolderDestination, LibraryDestination], elements_from: ElementsFromType)[source]¶

Bases: BaseDataTarget, ItemsFromModel

items_from: ElementsFromType¶

class galaxy.schema.fetch_data.HdcaDataItemsTarget(*, auto_decompress: bool = False, destination: HdcaDestination, collection_type: Optional[str] = None, tags: Optional[List[str]] = None, name: Optional[str] = None, elements: List[Union[Union[galaxy.schema.fetch_data.FileDataElement, galaxy.schema.fetch_data.PastedDataElement, galaxy.schema.fetch_data.UrlDataElement, galaxy.schema.fetch_data.PathDataElement, galaxy.schema.fetch_data.ServerDirElement, galaxy.schema.fetch_data.FtpImportElement, galaxy.schema.fetch_data.CompositeDataElement][Union[FileDataElement, PastedDataElement, UrlDataElement, PathDataElement, ServerDirElement, FtpImportElement, CompositeDataElement]], NestedElement]])[source]¶

Bases: BaseCollectionTarget

class galaxy.schema.fetch_data.HdcaDataItemsFromTarget(*, src: ItemsFromSrc, path: Optional[str] = None, ftp_path: Optional[str] = None, server_dir: Optional[str] = None, url: Optional[str] = None, auto_decompress: bool = False, destination: HdcaDestination, collection_type: Optional[str] = None, tags: Optional[List[str]] = None, name: Optional[str] = None, elements_from: ElementsFromType)[source]¶

Bases: BaseCollectionTarget, ItemsFromModel

items_from: ElementsFromType¶

class galaxy.schema.fetch_data.FilesPayload(*, filename: str, local_filename: str)[source]¶

Bases: Model

filename: str¶

local_filename: str¶

class galaxy.schema.fetch_data.BaseDataPayload(*, history_id: DecodedDatabaseIdField, **extra_data: Any)[source]¶

Bases: FetchBaseModel

history_id: DecodedDatabaseIdField¶

class Config[source]¶

Bases: object

extra = 'allow'¶

classmethod targets_string_to_json(v)[source]¶

class galaxy.schema.fetch_data.FetchDataPayload(*, history_id: DecodedDatabaseIdField, targets: List[Union[DataElementsTarget, HdcaDataItemsTarget, DataElementsFromTarget, HdcaDataItemsFromTarget, FtpImportTarget]], **extra_data: Any)[source]¶

Bases: BaseDataPayload

targets: List[Union[DataElementsTarget, HdcaDataItemsTarget, DataElementsFromTarget, HdcaDataItemsFromTarget, FtpImportTarget]]¶

class galaxy.schema.fetch_data.FetchDataFormPayload(*, history_id: DecodedDatabaseIdField, targets: Union[JsonWrapperValue, List[Union[DataElementsTarget, HdcaDataItemsTarget, DataElementsFromTarget, HdcaDataItemsFromTarget, FtpImportTarget]]], **extra_data: Any)[source]¶

Bases: BaseDataPayload

targets: Union[JsonWrapperValue, List[Union[DataElementsTarget, HdcaDataItemsTarget, DataElementsFromTarget, HdcaDataItemsFromTarget, FtpImportTarget]]]¶

galaxy.schema.fields module¶

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

Bases: object

Database ID validation.

security: IdEncodingHelper¶

classmethod validate(v)[source]¶

classmethod ensure_valid(v: str)[source]¶

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

Bases: int, BaseDatabaseIdField

classmethod validate(v)[source]¶

classmethod encode(v) → str[source]¶

security: IdEncodingHelper¶

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

Bases: str, BaseDatabaseIdField

classmethod validate(v)[source]¶

classmethod decode(v) → int[source]¶

security: IdEncodingHelper¶

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

Bases: int, BaseDatabaseIdField

classmethod validate(v)[source]¶

classmethod encode(v) → str[source]¶

security: IdEncodingHelper¶

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

Bases: str, BaseDatabaseIdField

classmethod validate(v)[source]¶

classmethod decode(v: str) → int[source]¶

security: IdEncodingHelper¶

galaxy.schema.fields.literal_to_value(arg)[source]¶

galaxy.schema.fields.ModelClassField(default_value=Ellipsis)[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.remote_files module¶

class galaxy.schema.remote_files.RemoteFilesTarget(value)[source]¶

Bases: str, Enum

An enumeration.

ftpdir = 'ftpdir'¶

userdir = 'userdir'¶

importdir = 'importdir'¶

class galaxy.schema.remote_files.RemoteFilesFormat(value)[source]¶

Bases: str, Enum

An enumeration.

flat = 'flat'¶

jstree = 'jstree'¶

uri = 'uri'¶

class galaxy.schema.remote_files.RemoteFilesDisableMode(value)[source]¶

Bases: str, Enum

An enumeration.

folders = 'folders'¶

files = 'files'¶

class galaxy.schema.remote_files.FilesSourcePlugin(*, id: str, type: str, uri_root: Optional[str] = None, label: str, doc: str, writable: bool, requires_roles: Optional[str] = None, requires_groups: Optional[str] = None, **extra_data: Any)[source]¶

Bases: Model

id: str¶

type: str¶

uri_root: Optional[str]¶

label: str¶

doc: str¶

writable: bool¶

requires_roles: Optional[str]¶

requires_groups: Optional[str]¶

class Config[source]¶

Bases: object

extra = 'allow'¶

class galaxy.schema.remote_files.FilesSourcePluginList(*, __root__: List[FilesSourcePlugin] = [])[source]¶: Bases: Model

galaxy.schema.schema module¶

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

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

Bases: str, Enum

An enumeration.

NEW = 'new'¶

UPLOAD = 'upload'¶

QUEUED = 'queued'¶

RUNNING = 'running'¶

OK = 'ok'¶

EMPTY = 'empty'¶

ERROR = 'error'¶

PAUSED = 'paused'¶

SETTING_METADATA = 'setting_metadata'¶

FAILED_METADATA = 'failed_metadata'¶

DEFERRED = 'deferred'¶

DISCARDED = 'discarded'¶

classmethod values()[source]¶

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

Bases: str, Enum

An enumeration.

NEW = 'new'¶

RESUBMITTED = 'resubmitted'¶

UPLOAD = 'upload'¶

WAITING = 'waiting'¶

QUEUED = 'queued'¶

RUNNING = 'running'¶

OK = 'ok'¶

ERROR = 'error'¶

FAILED = 'failed'¶

PAUSED = 'paused'¶

DELETING = 'deleting'¶

DELETED = 'deleted'¶

STOPPING = 'stop'¶

STOPPED = 'stopped'¶

SKIPPED = 'skipped'¶

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

Bases: str, Enum

An enumeration.

NEW = 'new'¶

OK = 'ok'¶

FAILED = 'failed'¶

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

Bases: 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¶

json_encoders = {<class 'galaxy.schema.fields.DecodedDatabaseIdField'>: <function Model.Config.<lambda>>, <class 'galaxy.schema.fields.LibraryFolderDatabaseIdField'>: <function Model.Config.<lambda>>}¶

static schema_extra(schema: Dict[str, Any], model) → None[source]¶

class galaxy.schema.schema.UserModel(*, id: DecodedDatabaseIdField, username: str, email: str, active: bool, deleted: bool, last_password_change: Optional[datetime] = None, model_class: typing_extensions.Literal[User] = 'User')[source]¶

Bases: Model

User in a transaction context.

id: DecodedDatabaseIdField¶

username: str¶

email: str¶

active: bool¶

deleted: bool¶

last_password_change: Optional[datetime]¶

model_class: typing_extensions.Literal[User]¶

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

Bases: Model

User group model

model_class: typing_extensions.Literal[Group]¶

id: DecodedDatabaseIdField¶

name: str¶

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

Bases: str, 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

Available types of History contents.

dataset = 'dataset'¶

dataset_collection = 'dataset_collection'¶

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

Bases: str, Enum

Available types of History archive sources.

url = 'url'¶

file = 'file'¶

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

Bases: str, Enum

Available types of dataset collection elements.

hda = 'hda'¶

dataset_collection = 'dataset_collection'¶

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

Bases: str, Enum

An enumeration.

hda = 'hda'¶

ldda = 'ldda'¶

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

Bases: str, Enum

An enumeration.

hda = 'hda'¶

ldda = 'ldda'¶

hdca = 'hdca'¶

new_collection = 'new_collection'¶

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

Bases: str, Enum

An enumeration.

hda = 'hda'¶

hdca = 'hdca'¶

library = 'library'¶

library_folder = 'library_folder'¶

new_collection = 'new_collection'¶

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

Bases: ConstrainedStr

regex = re.compile('^([^\\s.:])+(.[^\\s.:]+)*(:[^\\s.:]+)?$')¶

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

Bases: Model

Represents the collection of tags associated with an item.

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

Bases: Model

Metadata file associated with a dataset.

file_type: str¶

download_url: str¶

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

Bases: Model

Role-based permissions for accessing and managing a dataset.

manage: List[DecodedDatabaseIdField]¶

access: List[DecodedDatabaseIdField]¶

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

Bases: Model

Represents some text with an Hyperlink.

target: str¶

href: AnyUrl¶

text: str¶

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

Bases: Model

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

label: str¶

links: List[Hyperlink]¶

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

Bases: Model

class Config[source]¶

Bases: object

extra = 'allow'¶

class galaxy.schema.schema.HistoryItemBase(*, id: DecodedDatabaseIdField, name: Optional[str] = None, history_id: DecodedDatabaseIdField, hid: int, history_content_type: HistoryContentType, deleted: bool, visible: bool)[source]¶

Bases: Model

Basic information provided by items contained in a History.

id: DecodedDatabaseIdField¶

name: Optional[str]¶

history_id: DecodedDatabaseIdField¶

hid: int¶

history_content_type: HistoryContentType¶

deleted: bool¶

visible: bool¶

class galaxy.schema.schema.HistoryItemCommon(*, id: DecodedDatabaseIdField, name: Optional[str] = None, history_id: DecodedDatabaseIdField, hid: int, history_content_type: HistoryContentType, deleted: bool, visible: bool, type_id: Optional[str] = None, type: str, create_time: Optional[datetime] = None, update_time: Optional[datetime] = None, url: str, tags: TagCollection, **extra_data: Any)[source]¶

Bases: HistoryItemBase

Common information provided by items contained in a History.

class Config[source]¶

Bases: object

extra = 'allow'¶

type_id: Optional[str]¶

type: str¶

create_time: Optional[datetime]¶

update_time: Optional[datetime]¶

url: str¶

tags: TagCollection¶

class galaxy.schema.schema.HDASummary(*, id: DecodedDatabaseIdField, name: Optional[str] = None, history_id: DecodedDatabaseIdField, hid: int, history_content_type: HistoryContentType, deleted: bool, visible: bool, type_id: Optional[str] = None, type: str, create_time: Optional[datetime] = None, update_time: Optional[datetime] = None, url: str, tags: TagCollection, dataset_id: DecodedDatabaseIdField, state: DatasetState, extension: str, purged: bool, **extra_data: Any)[source]¶

Bases: HistoryItemCommon

History Dataset Association summary information.

dataset_id: DecodedDatabaseIdField¶

state: DatasetState¶

extension: str¶

purged: bool¶

class galaxy.schema.schema.HDAInaccessible(*, id: DecodedDatabaseIdField, name: Optional[str] = None, history_id: DecodedDatabaseIdField, hid: int, history_content_type: HistoryContentType, deleted: bool, visible: bool, accessible: bool, state: DatasetState)[source]¶

Bases: HistoryItemBase

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

accessible: bool¶

state: DatasetState¶

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

Bases: str, Enum

An enumeration.

UNKNOWN = 'unknown'¶

INVALID = 'invalid'¶

OK = 'ok'¶

class galaxy.schema.schema.HDADetailed(*, id: DecodedDatabaseIdField, name: Optional[str] = None, history_id: DecodedDatabaseIdField, hid: int, history_content_type: HistoryContentType, deleted: bool, visible: bool, type_id: Optional[str] = None, type: typing_extensions.Literal[file][typing_extensions.Literal[file]] = 'file', create_time: Optional[datetime] = None, update_time: Optional[datetime] = None, url: str, tags: TagCollection, dataset_id: DecodedDatabaseIdField, state: DatasetState, extension: str, purged: bool, model_class: typing_extensions.Literal[HistoryDatasetAssociation][typing_extensions.Literal[HistoryDatasetAssociation]], hda_ldda: DatasetSourceType = DatasetSourceType.hda, accessible: bool, genome_build: Optional[str] = '?', misc_info: Optional[str] = None, misc_blurb: Optional[str] = None, file_ext: str, file_size: int, resubmitted: bool, metadata: Optional[Any] = None, metadata_dbkey: Optional[str] = '?', metadata_data_lines: int = 0, meta_files: List[MetadataFile], data_type: str, peek: Optional[str] = None, creating_job: str, rerunnable: bool, uuid: UUID4, permissions: DatasetPermissions, file_name: Optional[str] = None, display_apps: List[DisplayApp], display_types: List[DisplayApp], visualizations: List[Visualization], validated_state: DatasetValidatedState, validated_state_message: Optional[str], annotation: Optional[str], download_url: str, api_type: typing_extensions.Literal[file][typing_extensions.Literal[file]] = 'file', created_from_basename: Optional[str] = None, **extra_data: Any)[source]¶

Bases: HDASummary

History Dataset Association detailed information.

model_class: typing_extensions.Literal[HistoryDatasetAssociation][typing_extensions.Literal[HistoryDatasetAssociation]]¶

hda_ldda: DatasetSourceType¶

accessible: bool¶

genome_build: Optional[str]¶

misc_info: Optional[str]¶

misc_blurb: Optional[str]¶

file_ext: str¶

file_size: int¶

resubmitted: bool¶

metadata: Optional[Any]¶

metadata_dbkey: Optional[str]¶

metadata_data_lines: int¶

meta_files: List[MetadataFile]¶

data_type: str¶

peek: Optional[str]¶

creating_job: str¶

rerunnable: bool¶

uuid: UUID4¶

permissions: DatasetPermissions¶

file_name: Optional[str]¶

display_apps: List[DisplayApp]¶

display_types: List[DisplayApp]¶

visualizations: List[Visualization]¶

validated_state: DatasetValidatedState¶

validated_state_message: Optional[str]¶

annotation: Optional[str]¶

download_url: str¶

type: typing_extensions.Literal[file][typing_extensions.Literal[file]]¶

api_type: typing_extensions.Literal[file][typing_extensions.Literal[file]]¶

created_from_basename: Optional[str]¶

class galaxy.schema.schema.HDAExtended(*, id: DecodedDatabaseIdField, name: Optional[str] = None, history_id: DecodedDatabaseIdField, hid: int, history_content_type: HistoryContentType, deleted: bool, visible: bool, type_id: Optional[str] = None, type: typing_extensions.Literal[file][typing_extensions.Literal[file]] = 'file', create_time: Optional[datetime] = None, update_time: Optional[datetime] = None, url: str, tags: TagCollection, dataset_id: DecodedDatabaseIdField, state: DatasetState, extension: str, purged: bool, model_class: typing_extensions.Literal[HistoryDatasetAssociation][typing_extensions.Literal[HistoryDatasetAssociation]], hda_ldda: DatasetSourceType = DatasetSourceType.hda, accessible: bool, genome_build: Optional[str] = '?', misc_info: Optional[str] = None, misc_blurb: Optional[str] = None, file_ext: str, file_size: int, resubmitted: bool, metadata: Optional[Any] = None, metadata_dbkey: Optional[str] = '?', metadata_data_lines: int = 0, meta_files: List[MetadataFile], data_type: str, peek: Optional[str] = None, creating_job: str, rerunnable: bool, uuid: UUID4, permissions: DatasetPermissions, file_name: Optional[str] = None, display_apps: List[DisplayApp], display_types: List[DisplayApp], visualizations: List[Visualization], validated_state: DatasetValidatedState, validated_state_message: Optional[str], annotation: Optional[str], download_url: str, api_type: typing_extensions.Literal[file][typing_extensions.Literal[file]] = 'file', created_from_basename: Optional[str] = None, tool_version: str, parent_id: Optional[DecodedDatabaseIdField] = None, designation: Optional[str] = None, **extra_data: Any)[source]¶

Bases: HDADetailed

History Dataset Association extended information.

tool_version: str¶

parent_id: Optional[DecodedDatabaseIdField]¶

designation: Optional[str]¶

class galaxy.schema.schema.DCSummary(*, model_class: typing_extensions.Literal[DatasetCollection] = 'DatasetCollection', id: DecodedDatabaseIdField, create_time: datetime, update_time: datetime, collection_type: str, populated_state: DatasetCollectionPopulatedState, populated_state_message: Optional[str] = None, element_count: Optional[int] = None)[source]¶

Bases: Model

Dataset Collection summary information.

model_class: typing_extensions.Literal[DatasetCollection]¶

id: DecodedDatabaseIdField¶

create_time: datetime¶

update_time: datetime¶

collection_type: str¶

populated_state: DatasetCollectionPopulatedState¶

populated_state_message: Optional[str]¶

element_count: Optional[int]¶

class galaxy.schema.schema.HDAObject(*, id: DecodedDatabaseIdField, model_class: typing_extensions.Literal[HistoryDatasetAssociation] = 'HistoryDatasetAssociation', state: DatasetState, hda_ldda: DatasetSourceType = DatasetSourceType.hda, history_id: DecodedDatabaseIdField, tags: List[str], **extra_data: Any)[source]¶

Bases: Model

History Dataset Association Object

id: DecodedDatabaseIdField¶

model_class: typing_extensions.Literal[HistoryDatasetAssociation]¶

state: DatasetState¶

hda_ldda: DatasetSourceType¶

history_id: DecodedDatabaseIdField¶

tags: List[str]¶

class Config[source]¶

Bases: object

extra = 'allow'¶

class galaxy.schema.schema.DCObject(*, id: DecodedDatabaseIdField, model_class: typing_extensions.Literal[DatasetCollection] = 'DatasetCollection', collection_type: str, populated: Optional[bool] = None, element_count: Optional[int] = None, contents_url: Optional[str] = None, elements: List[DCESummary] = [])[source]¶

Bases: Model

Dataset Collection Object

id: DecodedDatabaseIdField¶

model_class: typing_extensions.Literal[DatasetCollection]¶

collection_type: str¶

populated: Optional[bool]¶

element_count: Optional[int]¶

contents_url: Optional[str]¶

elements: List[DCESummary]¶

class galaxy.schema.schema.DCESummary(*, id: DecodedDatabaseIdField, model_class: typing_extensions.Literal[DatasetCollectionElement] = 'DatasetCollectionElement', element_index: int, element_identifier: str, element_type: DCEType, object: Union[HDAObject, HDADetailed, DCObject])[source]¶

Bases: Model

Dataset Collection Element summary information.

id: DecodedDatabaseIdField¶

model_class: typing_extensions.Literal[DatasetCollectionElement]¶

element_index: int¶

element_identifier: str¶

element_type: DCEType¶

object: Union[HDAObject, HDADetailed, DCObject]¶

class galaxy.schema.schema.DCDetailed(*, model_class: typing_extensions.Literal[DatasetCollection] = 'DatasetCollection', id: DecodedDatabaseIdField, create_time: datetime, update_time: datetime, collection_type: str, populated_state: DatasetCollectionPopulatedState, populated_state_message: Optional[str] = None, element_count: Optional[int] = None, populated: bool, elements: List[DCESummary] = [])[source]¶

Bases: DCSummary

Dataset Collection detailed information.

populated: bool¶

elements: List[DCESummary]¶

class galaxy.schema.schema.HDCJobStateSummary(*, all_jobs: int = 0, new: int = 0, waiting: int = 0, running: int = 0, error: int = 0, paused: int = 0, skipped: 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: Model

Overview of the job states working inside a dataset collection.

all_jobs: int¶

new: int¶

waiting: int¶

running: int¶

error: int¶

paused: int¶

skipped: int¶

deleted_new: int¶

resubmitted: int¶

queued: int¶

ok: int¶

failed: int¶

deleted: int¶

upload: int¶

class galaxy.schema.schema.HDCASummary(*, id: DecodedDatabaseIdField, name: Optional[str] = None, history_id: DecodedDatabaseIdField, hid: int, history_content_type: HistoryContentType, deleted: bool, visible: bool, type_id: Optional[str] = None, type: typing_extensions.Literal[collection][typing_extensions.Literal[collection]] = 'collection', create_time: Optional[datetime] = None, update_time: Optional[datetime] = None, url: str, tags: TagCollection, model_class: typing_extensions.Literal[HistoryDatasetCollectionAssociation] = 'HistoryDatasetCollectionAssociation', collection_type: str, populated_state: DatasetCollectionPopulatedState, populated_state_message: Optional[str] = None, element_count: Optional[int] = None, job_source_id: Optional[DecodedDatabaseIdField] = None, job_source_type: Optional[JobSourceType] = None, job_state_summary: Optional[HDCJobStateSummary] = None, contents_url: str, collection_id: DecodedDatabaseIdField, **extra_data: Any)[source]¶

Bases: HistoryItemCommon

History Dataset Collection Association summary information.

model_class: typing_extensions.Literal[HistoryDatasetCollectionAssociation]¶

type: typing_extensions.Literal[collection][typing_extensions.Literal[collection]]¶

collection_type: str¶

populated_state: DatasetCollectionPopulatedState¶

populated_state_message: Optional[str]¶

element_count: Optional[int]¶

job_source_id: Optional[DecodedDatabaseIdField]¶

job_source_type: Optional[JobSourceType]¶

job_state_summary: Optional[HDCJobStateSummary]¶

contents_url: str¶

collection_id: DecodedDatabaseIdField¶

class galaxy.schema.schema.HDCADetailed(*, id: DecodedDatabaseIdField, name: Optional[str] = None, history_id: DecodedDatabaseIdField, hid: int, history_content_type: HistoryContentType, deleted: bool, visible: bool, type_id: Optional[str] = None, type: typing_extensions.Literal[collection][typing_extensions.Literal[collection]] = 'collection', create_time: Optional[datetime] = None, update_time: Optional[datetime] = None, url: str, tags: TagCollection, model_class: typing_extensions.Literal[HistoryDatasetCollectionAssociation] = 'HistoryDatasetCollectionAssociation', collection_type: str, populated_state: DatasetCollectionPopulatedState, populated_state_message: Optional[str] = None, element_count: Optional[int] = None, job_source_id: Optional[DecodedDatabaseIdField] = None, job_source_type: Optional[JobSourceType] = None, job_state_summary: Optional[HDCJobStateSummary] = None, contents_url: str, collection_id: DecodedDatabaseIdField, populated: bool, elements: List[DCESummary] = [], elements_datatypes: Set[str], **extra_data: Any)[source]¶

Bases: HDCASummary

History Dataset Collection Association detailed information.

populated: bool¶

elements: List[DCESummary]¶

elements_datatypes: Set[str]¶

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

Bases: Model

Provides basic configuration for all the History models.

class Config[source]¶

Bases: object

extra = 'allow'¶

class galaxy.schema.schema.HistoryContentItemBase(*, history_content_type: HistoryContentType)[source]¶

Bases: Model

Identifies a dataset or collection contained in a History.

history_content_type: HistoryContentType¶

class galaxy.schema.schema.HistoryContentItem(*, history_content_type: HistoryContentType, id: DecodedDatabaseIdField)[source]¶

Bases: HistoryContentItemBase

id: DecodedDatabaseIdField¶

class galaxy.schema.schema.EncodedHistoryContentItem(*, history_content_type: HistoryContentType, id: EncodedDatabaseIdField)[source]¶

Bases: HistoryContentItemBase

id: EncodedDatabaseIdField¶

class galaxy.schema.schema.UpdateContentItem(*, history_content_type: HistoryContentType, id: DecodedDatabaseIdField, **extra_data: Any)[source]¶

Bases: HistoryContentItem

Used for updating a particular history item. All fields are optional.

class Config[source]¶

Bases: object

use_enum_values = True¶

extra = 'allow'¶

id: DecodedDatabaseIdField¶

history_content_type: HistoryContentType¶

class galaxy.schema.schema.UpdateHistoryContentsBatchPayload(*, items: List[UpdateContentItem], **extra_data: Any)[source]¶

Bases: HistoryBase

Contains property values that will be updated for all the history items provided.

items: List[UpdateContentItem]¶

class Config[source]¶

Bases: object

schema_extra = {'example': {'items': [{'history_content_type': 'dataset', 'id': 'string'}], 'visible': False}}¶

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

Bases: str, Enum

An enumeration.

hide = 'hide'¶

unhide = 'unhide'¶

delete = 'delete'¶

undelete = 'undelete'¶

purge = 'purge'¶

change_datatype = 'change_datatype'¶

change_dbkey = 'change_dbkey'¶

add_tags = 'add_tags'¶

remove_tags = 'remove_tags'¶

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

Bases: Model

type: str¶

class galaxy.schema.schema.ChangeDatatypeOperationParams(*, type: typing_extensions.Literal[change_datatype], datatype: str)[source]¶

Bases: BulkOperationParams

type: typing_extensions.Literal[change_datatype]¶

datatype: str¶

class galaxy.schema.schema.ChangeDbkeyOperationParams(*, type: typing_extensions.Literal[change_dbkey], dbkey: str)[source]¶

Bases: BulkOperationParams

type: typing_extensions.Literal[change_dbkey]¶

dbkey: str¶

class galaxy.schema.schema.TagOperationParams(*, type: Union[typing_extensions.Literal[add_tags], typing_extensions.Literal[remove_tags]], tags: List[str])[source]¶

Bases: BulkOperationParams

type: Union[typing_extensions.Literal[add_tags], typing_extensions.Literal[remove_tags]]¶

tags: List[str]¶

class galaxy.schema.schema.HistoryContentBulkOperationPayload(*, operation: HistoryContentItemOperation, items: Optional[List[HistoryContentItem]] = None, params: Optional[Union[ChangeDatatypeOperationParams, ChangeDbkeyOperationParams, TagOperationParams]] = None)[source]¶

Bases: Model

operation: HistoryContentItemOperation¶

items: Optional[List[HistoryContentItem]]¶

params: Optional[Union[ChangeDatatypeOperationParams, ChangeDbkeyOperationParams, TagOperationParams]]¶

class galaxy.schema.schema.BulkOperationItemError(*, item: EncodedHistoryContentItem, error: str)[source]¶

Bases: Model

item: EncodedHistoryContentItem¶

error: str¶

class galaxy.schema.schema.HistoryContentBulkOperationResult(*, success_count: int, errors: List[BulkOperationItemError])[source]¶

Bases: Model

success_count: int¶

errors: List[BulkOperationItemError]¶

class galaxy.schema.schema.UpdateHistoryContentsPayload(*, name: Optional[str] = None, deleted: Optional[bool] = None, visible: Optional[bool] = None, annotation: Optional[str] = None, tags: Optional[TagCollection] = None, **extra_data: Any)[source]¶

Bases: HistoryBase

Can contain arbitrary/dynamic fields that will be updated for a particular history item.

name: Optional[str]¶

deleted: Optional[bool]¶

visible: Optional[bool]¶

annotation: Optional[str]¶

tags: Optional[TagCollection]¶

class Config[source]¶

Bases: object

schema_extra = {'example': {'annotation': 'Test', 'visible': False}}¶

class galaxy.schema.schema.HistorySummary(*, model_class: typing_extensions.Literal[History] = 'History', id: DecodedDatabaseIdField, name: str, deleted: bool, purged: bool, archived: bool, url: str, published: bool, count: int, annotation: Optional[str], tags: TagCollection, update_time: datetime, preferred_object_store_id: Optional[str] = None, **extra_data: Any)[source]¶

Bases: HistoryBase

History summary information.

model_class: typing_extensions.Literal[History]¶

id: DecodedDatabaseIdField¶

name: str¶

deleted: bool¶

purged: bool¶

archived: bool¶

url: str¶

published: bool¶

count: int¶

annotation: Optional[str]¶

tags: TagCollection¶

update_time: datetime¶

preferred_object_store_id: Optional[str]¶

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

Bases: 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: typing_extensions.Literal[History] = 'History', id: DecodedDatabaseIdField, name: str, deleted: bool, purged: bool, archived: bool, url: str, published: bool, count: int, annotation: Optional[str], tags: TagCollection, update_time: datetime, preferred_object_store_id: Optional[str] = None, contents_url: str, size: int, user_id: DecodedDatabaseIdField, create_time: datetime, importable: bool, slug: Optional[str] = None, username_and_slug: Optional[str] = None, genome_build: Optional[str] = '?', state: DatasetState, state_ids: Dict[DatasetState, List[DecodedDatabaseIdField]], state_details: Dict[DatasetState, int], **extra_data: Any)[source]¶

Bases: HistorySummary

History detailed information.

contents_url: str¶

size: int¶

user_id: DecodedDatabaseIdField¶

create_time: datetime¶

importable: bool¶

slug: Optional[str]¶

username_and_slug: Optional[str]¶

genome_build: Optional[str]¶

state: DatasetState¶

state_ids: Dict[DatasetState, List[DecodedDatabaseIdField]]¶

state_details: Dict[DatasetState, int]¶

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

Bases: 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.WorkflowIndexQueryPayload(*, show_deleted: bool = False, show_hidden: bool = False, show_published: Optional[bool] = None, show_shared: Optional[bool] = None, sort_by: Optional[typing_extensions.Literal[create_time, update_time, name]] = None, sort_desc: Optional[bool] = None, limit: Optional[ConstrainedIntValue] = None, offset: Optional[int] = 0, search: Optional[str] = None, skip_step_counts: bool = False)[source]¶

Bases: Model

show_deleted: bool¶

show_hidden: bool¶

show_published: Optional[bool]¶

show_shared: Optional[bool]¶

sort_by: Optional[typing_extensions.Literal[create_time, update_time, name]]¶

sort_desc: Optional[bool]¶

limit: Optional[int]¶

offset: Optional[int]¶

search: Optional[str]¶

skip_step_counts: bool¶

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

Bases: str, Enum

An enumeration.

create_time = 'create_time'¶

update_time = 'update_time'¶

class galaxy.schema.schema.JobIndexQueryPayload(*, states: Optional[List[str]] = None, user_details: bool = False, user_id: Optional[DecodedDatabaseIdField] = None, tool_ids: Optional[List[str]] = None, tool_ids_like: Optional[List[str]] = None, date_range_min: Optional[Union[OffsetNaiveDatetime, date]] = None, date_range_max: Optional[Union[OffsetNaiveDatetime, date]] = None, history_id: Optional[DecodedDatabaseIdField] = None, workflow_id: Optional[DecodedDatabaseIdField] = None, invocation_id: Optional[DecodedDatabaseIdField] = None, order_by: JobIndexSortByEnum = JobIndexSortByEnum.update_time, search: Optional[str] = None, limit: int = 500, offset: int = 0)[source]¶

Bases: Model

states: Optional[List[str]]¶

user_details: bool¶

user_id: Optional[DecodedDatabaseIdField]¶

tool_ids: Optional[List[str]]¶

tool_ids_like: Optional[List[str]]¶

date_range_min: Optional[Union[OffsetNaiveDatetime, date]]¶

date_range_max: Optional[Union[OffsetNaiveDatetime, date]]¶

history_id: Optional[DecodedDatabaseIdField]¶

workflow_id: Optional[DecodedDatabaseIdField]¶

invocation_id: Optional[DecodedDatabaseIdField]¶

order_by: JobIndexSortByEnum¶

search: Optional[str]¶

limit: int¶

offset: int¶

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

Bases: str, Enum

An enumeration.

create_time = 'create_time'¶

update_time = 'update_time'¶

none = 'None'¶

class galaxy.schema.schema.InvocationIndexQueryPayload(*, workflow_id: Optional[DecodedDatabaseIdField] = None, history_id: Optional[DecodedDatabaseIdField] = None, job_id: Optional[DecodedDatabaseIdField] = None, user_id: Optional[DecodedDatabaseIdField] = None, sort_by: Optional[InvocationSortByEnum] = None, sort_desc: bool = False, include_terminal: bool = True, limit: Optional[ConstrainedIntValue] = 100, offset: Optional[int] = 0)[source]¶

Bases: Model

workflow_id: Optional[DecodedDatabaseIdField]¶

history_id: Optional[DecodedDatabaseIdField]¶

job_id: Optional[DecodedDatabaseIdField]¶

user_id: Optional[DecodedDatabaseIdField]¶

sort_by: Optional[InvocationSortByEnum]¶

sort_desc: bool¶

include_terminal: bool¶

limit: Optional[int]¶

offset: Optional[int]¶

class galaxy.schema.schema.PageIndexQueryPayload(*, deleted: bool = False, show_published: Optional[bool] = None, show_shared: Optional[bool] = None, user_id: Optional[DecodedDatabaseIdField] = None, sort_by: typing_extensions.Literal[update_time, title, username] = 'update_time', sort_desc: Optional[bool] = False, search: Optional[str] = None, limit: Optional[ConstrainedIntValue] = 100, offset: Optional[int] = 0)[source]¶

Bases: Model

deleted: bool¶

show_published: Optional[bool]¶

show_shared: Optional[bool]¶

user_id: Optional[DecodedDatabaseIdField]¶

sort_by: typing_extensions.Literal[update_time, title, username]¶

sort_desc: Optional[bool]¶

search: Optional[str]¶

limit: Optional[int]¶

offset: Optional[int]¶

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

Bases: Model

name: Optional[str]¶

history_id: Optional[DecodedDatabaseIdField]¶

all_datasets: Optional[bool]¶

archive_source: Optional[str]¶

archive_type: Optional[HistoryImportArchiveSourceType]¶

archive_file: Optional[Any]¶

class galaxy.schema.schema.CollectionElementIdentifier(*, name: Optional[str] = None, src: ColletionSourceType, id: Optional[DecodedDatabaseIdField] = None, collection_type: Optional[str] = None, element_identifiers: Optional[List[CollectionElementIdentifier]] = None, tags: Optional[List[str]] = None)[source]¶

Bases: Model

name: Optional[str]¶

src: ColletionSourceType¶

id: Optional[DecodedDatabaseIdField]¶

collection_type: Optional[str]¶

element_identifiers: Optional[List[CollectionElementIdentifier]]¶

tags: Optional[List[str]]¶

class galaxy.schema.schema.CreateNewCollectionPayload(*, collection_type: Optional[str] = None, element_identifiers: Optional[List[CollectionElementIdentifier]] = None, name: Optional[str] = None, hide_source_items: Optional[bool] = False, copy_elements: Optional[bool] = True, instance_type: Optional[typing_extensions.Literal[history, library]] = 'history', history_id: Optional[DecodedDatabaseIdField] = None, folder_id: Optional[LibraryFolderDatabaseIdField] = None)[source]¶

Bases: Model

collection_type: Optional[str]¶

element_identifiers: Optional[List[CollectionElementIdentifier]]¶

name: Optional[str]¶

hide_source_items: Optional[bool]¶

copy_elements: Optional[bool]¶

instance_type: Optional[typing_extensions.Literal[history, library]]¶

history_id: Optional[DecodedDatabaseIdField]¶

folder_id: Optional[LibraryFolderDatabaseIdField]¶

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

Bases: str, Enum

Available types of model stores for export.

TGZ = 'tgz'¶

TAR = 'tar'¶

TAR_DOT_GZ = 'tar.gz'¶

BAG_DOT_ZIP = 'bag.zip'¶

BAG_DOT_TAR = 'bag.tar'¶

BAG_DOT_TGZ = 'bag.tgz'¶

ROCRATE_ZIP = 'rocrate.zip'¶

BCO_JSON = 'bco.json'¶

classmethod is_compressed(value: ModelStoreFormat)[source]¶

classmethod is_bag(value: ModelStoreFormat)[source]¶

class galaxy.schema.schema.StoreContentSource(*, store_content_uri: Optional[str] = None, store_dict: Optional[Dict[str, Any]] = None, model_store_format: Optional[ModelStoreFormat] = None)[source]¶

Bases: Model

store_content_uri: Optional[str]¶

store_dict: Optional[Dict[str, Any]]¶

model_store_format: Optional[ModelStoreFormat]¶

class galaxy.schema.schema.CreateHistoryFromStore(*, store_content_uri: Optional[str] = None, store_dict: Optional[Dict[str, Any]] = None, model_store_format: Optional[ModelStoreFormat] = None)[source]¶

Bases: StoreContentSource

store_content_uri: Optional[str]¶

store_dict: Optional[Dict[str, Any]]¶

model_store_format: Optional[ModelStoreFormat]¶

class galaxy.schema.schema.StoreExportPayload(*, model_store_format: ModelStoreFormat = ModelStoreFormat.TAR_DOT_GZ, include_files: bool = True, include_deleted: bool = False, include_hidden: bool = False)[source]¶

Bases: Model

model_store_format: ModelStoreFormat¶

include_files: bool¶

include_deleted: bool¶

include_hidden: bool¶

class galaxy.schema.schema.ShortTermStoreExportPayload(*, model_store_format: ModelStoreFormat = ModelStoreFormat.TAR_DOT_GZ, include_files: bool = True, include_deleted: bool = False, include_hidden: bool = False, short_term_storage_request_id: UUID, duration: Optional[Union[int, float]] = None)[source]¶

Bases: StoreExportPayload

short_term_storage_request_id: UUID¶

duration: Optional[Union[int, float]]¶

class galaxy.schema.schema.BcoGenerationParametersMixin(*, bco_merge_history_metadata: bool = False, bco_override_environment_variables: Optional[Dict[str, str]] = None, bco_override_empirical_error: Optional[Dict[str, str]] = None, bco_override_algorithmic_error: Optional[Dict[str, str]] = None, bco_override_xref: Optional[List[XrefItem]] = None)[source]¶

Bases: BaseModel

bco_merge_history_metadata: bool¶

bco_override_environment_variables: Optional[Dict[str, str]]¶

bco_override_empirical_error: Optional[Dict[str, str]]¶

bco_override_algorithmic_error: Optional[Dict[str, str]]¶

bco_override_xref: Optional[List[XrefItem]]¶

class galaxy.schema.schema.WriteStoreToPayload(*, model_store_format: ModelStoreFormat = ModelStoreFormat.TAR_DOT_GZ, include_files: bool = True, include_deleted: bool = False, include_hidden: bool = False, target_uri: str)[source]¶

Bases: StoreExportPayload

target_uri: str¶

class galaxy.schema.schema.ObjectExportResponseBase(*, id: EncodedDatabaseIdField, ready: bool, preparing: bool, up_to_date: bool)[source]¶

Bases: Model

id: EncodedDatabaseIdField¶

ready: bool¶

preparing: bool¶

up_to_date: bool¶

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

Bases: ObjectExportResponseBase

job_id: EncodedDatabaseIdField¶

download_url: str¶

external_download_latest_url: AnyUrl¶

external_download_permanent_url: AnyUrl¶

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

Bases: str, Enum

Types of objects that can be exported.

HISTORY = 'history'¶

INVOCATION = 'invocation'¶

class galaxy.schema.schema.ExportObjectRequestMetadata(*, object_id: EncodedDatabaseIdField, object_type: ExportObjectType, user_id: Optional[EncodedDatabaseIdField] = None, payload: Union[WriteStoreToPayload, ShortTermStoreExportPayload])[source]¶

Bases: Model

object_id: EncodedDatabaseIdField¶

object_type: ExportObjectType¶

user_id: Optional[EncodedDatabaseIdField]¶

payload: Union[WriteStoreToPayload, ShortTermStoreExportPayload]¶

class galaxy.schema.schema.ExportObjectResultMetadata(*, success: bool, error: Optional[str] = None)[source]¶

Bases: Model

success: bool¶

error: Optional[str]¶

class galaxy.schema.schema.ExportObjectMetadata(*, request_data: ExportObjectRequestMetadata, result_data: Optional[ExportObjectResultMetadata] = None)[source]¶

Bases: Model

request_data: ExportObjectRequestMetadata¶

result_data: Optional[ExportObjectResultMetadata]¶

is_short_term()[source]¶: Whether the export is a short term export.

is_ready()[source]¶: Whether the export has finished and it’s ready to be used.

class galaxy.schema.schema.ObjectExportTaskResponse(*, id: EncodedDatabaseIdField, ready: bool, preparing: bool, up_to_date: bool, task_uuid: UUID4, create_time: datetime, export_metadata: Optional[ExportObjectMetadata] = None)[source]¶

Bases: ObjectExportResponseBase

task_uuid: UUID4¶

create_time: datetime¶

export_metadata: Optional[ExportObjectMetadata]¶

class galaxy.schema.schema.JobExportHistoryArchiveListResponse(*, __root__: List[JobExportHistoryArchiveModel])[source]¶: Bases: Model

class galaxy.schema.schema.ExportTaskListResponse(*, __root__: List[ObjectExportTaskResponse])[source]¶: Bases: Model

class galaxy.schema.schema.ArchiveHistoryRequestPayload(*, archive_export_id: Optional[DecodedDatabaseIdField] = None, purge_history: bool = False)[source]¶

Bases: Model

archive_export_id: Optional[DecodedDatabaseIdField]¶

purge_history: bool¶

class galaxy.schema.schema.ExportRecordData(*, model_store_format: ModelStoreFormat = ModelStoreFormat.TAR_DOT_GZ, include_files: bool = True, include_deleted: bool = False, include_hidden: bool = False, target_uri: str)[source]¶

Bases: WriteStoreToPayload

Data of an export record associated with a history that was archived.

target_uri: str¶

model_store_format: ModelStoreFormat¶

include_files: bool¶

include_deleted: bool¶

include_hidden: bool¶

class galaxy.schema.schema.ExportAssociationData(*, export_record_data: Optional[ExportRecordData] = None)[source]¶

Bases: Model

export_record_data: Optional[ExportRecordData]¶

class galaxy.schema.schema.ArchivedHistorySummary(*, export_record_data: Optional[ExportRecordData] = None, model_class: typing_extensions.Literal[History] = 'History', id: DecodedDatabaseIdField, name: str, deleted: bool, purged: bool, archived: bool, url: str, published: bool, count: int, annotation: Optional[str], tags: TagCollection, update_time: datetime, preferred_object_store_id: Optional[str] = None, **extra_data: Any)[source]¶

Bases: HistorySummary, ExportAssociationData

model_class: typing_extensions.Literal[History]¶

id: DecodedDatabaseIdField¶

name: str¶

deleted: bool¶

purged: bool¶

archived: bool¶

url: str¶

published: bool¶

count: int¶

annotation: Optional[str]¶

tags: TagCollection¶

update_time: datetime¶

preferred_object_store_id: Optional[str]¶

class galaxy.schema.schema.ArchivedHistoryDetailed(*, export_record_data: Optional[ExportRecordData] = None, model_class: typing_extensions.Literal[History] = 'History', id: DecodedDatabaseIdField, name: str, deleted: bool, purged: bool, archived: bool, url: str, published: bool, count: int, annotation: Optional[str], tags: TagCollection, update_time: datetime, preferred_object_store_id: Optional[str] = None, contents_url: str, size: int, user_id: DecodedDatabaseIdField, create_time: datetime, importable: bool, slug: Optional[str] = None, username_and_slug: Optional[str] = None, genome_build: Optional[str] = '?', state: DatasetState, state_ids: Dict[DatasetState, List[DecodedDatabaseIdField]], state_details: Dict[DatasetState, int], **extra_data: Any)[source]¶

Bases: HistoryDetailed, ExportAssociationData

contents_url: str¶

size: int¶

user_id: DecodedDatabaseIdField¶

create_time: datetime¶

importable: bool¶

slug: Optional[str]¶

username_and_slug: Optional[str]¶

genome_build: Optional[str]¶

state: DatasetState¶

state_ids: Dict[DatasetState, List[DecodedDatabaseIdField]]¶

state_details: Dict[DatasetState, int]¶

model_class: typing_extensions.Literal[History]¶

id: DecodedDatabaseIdField¶

name: str¶

deleted: bool¶

purged: bool¶

archived: bool¶

url: str¶

published: bool¶

count: int¶

annotation: Optional[str]¶

tags: TagCollection¶

update_time: datetime¶

preferred_object_store_id: Optional[str]¶

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

Bases: Model

Generic Label/Value pair model.

label: str¶

value: str¶

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

Bases: Model

installed_builds: List[LabelValuePair]¶

fasta_hdas: List[LabelValuePair]¶

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

Bases: Model

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

job_id: EncodedDatabaseIdField¶

class galaxy.schema.schema.JobBaseModel(*, id: DecodedDatabaseIdField, model_class: typing_extensions.Literal[Job] = 'Job', tool_id: str, history_id: Optional[DecodedDatabaseIdField] = None, state: JobState, exit_code: Optional[int] = None, create_time: datetime, update_time: datetime, galaxy_version: str)[source]¶

Bases: Model

id: DecodedDatabaseIdField¶

model_class: typing_extensions.Literal[Job]¶

tool_id: str¶

history_id: Optional[DecodedDatabaseIdField]¶

state: JobState¶

exit_code: Optional[int]¶

create_time: datetime¶

update_time: datetime¶

galaxy_version: str¶

class galaxy.schema.schema.JobImportHistoryResponse(*, id: DecodedDatabaseIdField, model_class: typing_extensions.Literal[Job] = 'Job', tool_id: str, history_id: Optional[DecodedDatabaseIdField] = None, state: JobState, exit_code: Optional[int] = None, create_time: datetime, update_time: datetime, galaxy_version: str, message: str)[source]¶

Bases: JobBaseModel

message: str¶

class galaxy.schema.schema.ItemStateSummary(*, id: DecodedDatabaseIdField, populated_state: DatasetCollectionPopulatedState, states: Dict[JobState, int] = {})[source]¶

Bases: Model

id: DecodedDatabaseIdField¶

populated_state: DatasetCollectionPopulatedState¶

states: Dict[JobState, int]¶

class galaxy.schema.schema.JobStateSummary(*, id: DecodedDatabaseIdField, populated_state: DatasetCollectionPopulatedState, states: Dict[JobState, int] = {}, model: typing_extensions.Literal[Job] = 'Job')[source]¶

Bases: ItemStateSummary

model: typing_extensions.Literal[Job]¶

class galaxy.schema.schema.ImplicitCollectionJobsStateSummary(*, id: DecodedDatabaseIdField, populated_state: DatasetCollectionPopulatedState, states: Dict[JobState, int] = {}, model: typing_extensions.Literal[ImplicitCollectionJobs] = 'ImplicitCollectionJobs')[source]¶

Bases: ItemStateSummary

model: typing_extensions.Literal[ImplicitCollectionJobs]¶

class galaxy.schema.schema.WorkflowInvocationStateSummary(*, id: DecodedDatabaseIdField, populated_state: DatasetCollectionPopulatedState, states: Dict[JobState, int] = {}, model: typing_extensions.Literal[WorkflowInvocation] = 'WorkflowInvocation')[source]¶

Bases: ItemStateSummary

model: typing_extensions.Literal[WorkflowInvocation]¶

class galaxy.schema.schema.JobSummary(*, id: DecodedDatabaseIdField, model_class: typing_extensions.Literal[Job] = 'Job', tool_id: str, history_id: Optional[DecodedDatabaseIdField] = None, state: JobState, exit_code: Optional[int] = None, create_time: datetime, update_time: datetime, galaxy_version: str, external_id: Optional[str] = None, command_line: Optional[str] = None, user_email: Optional[str] = None)[source]¶

Bases: JobBaseModel

Basic information about a job.

external_id: Optional[str]¶

command_line: Optional[str]¶

user_email: Optional[str]¶

class galaxy.schema.schema.DatasetSourceIdBase(*, src: DatasetSourceType)[source]¶

Bases: Model

src: DatasetSourceType¶

class galaxy.schema.schema.DatasetSourceId(*, src: DatasetSourceType, id: DecodedDatabaseIdField)[source]¶

Bases: DatasetSourceIdBase

id: DecodedDatabaseIdField¶

class galaxy.schema.schema.EncodedDatasetSourceId(*, src: DatasetSourceType, id: EncodedDatabaseIdField)[source]¶

Bases: DatasetSourceIdBase

id: EncodedDatabaseIdField¶

class galaxy.schema.schema.DatasetJobInfo(*, src: DatasetSourceType, id: DecodedDatabaseIdField, uuid: UUID4)[source]¶

Bases: DatasetSourceId

uuid: UUID4¶

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

Bases: JobSummary

command_version: str¶

params: Any¶

inputs: Dict[str, DatasetJobInfo]¶

outputs: Dict[str, DatasetJobInfo]¶

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

Bases: 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[JobMetric] = [])[source]¶

Bases: Model

Represents a collection of metrics associated with a Job.

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

Bases: JobDetails

tool_stdout: str¶

tool_stderr: str¶

job_stdout: str¶

job_stderr: str¶

stdout: str¶

stderr: str¶

job_messages: List[str]¶

job_metrics: Optional[JobMetricCollection]¶

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

Bases: Model

id: DecodedDatabaseIdField¶

model_class: typing_extensions.Literal[StoredWorkflow]¶

create_time: datetime¶

update_time: datetime¶

name: str¶

url: str¶

published: bool¶

annotations: List[str]¶

tags: TagCollection¶

deleted: bool¶

hidden: bool¶

owner: str¶

latest_workflow_uuid: UUID4¶

number_of_steps: int¶

show_in_tool_panel: bool¶

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

Bases: Model

label: str¶

value: str¶

uuid: UUID4¶

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

Bases: Model

label: Optional[str]¶

output_name: str¶

uuid: Optional[UUID4]¶

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

Bases: Model

source_step: int¶

step_output: str¶

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

Bases: str, 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: WorkflowModuleType, annotation: Optional[str], input_steps: Dict[str, InputStep])[source]¶

Bases: Model

id: int¶

type: WorkflowModuleType¶

annotation: Optional[str]¶

input_steps: Dict[str, InputStep]¶

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

Bases: WorkflowStepBase

tool_id: Optional[str]¶

tool_version: Optional[str]¶

tool_inputs: Any¶

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

Bases: ToolBasedWorkflowStep

type: WorkflowModuleType¶

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

Bases: ToolBasedWorkflowStep

type: WorkflowModuleType¶

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

Bases: ToolBasedWorkflowStep

type: WorkflowModuleType¶

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

Bases: WorkflowStepBase

type: WorkflowModuleType¶

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

Bases: ToolBasedWorkflowStep

type: WorkflowModuleType¶

class galaxy.schema.schema.SubworkflowStep(*, id: int, type: WorkflowModuleType = WorkflowModuleType.subworkflow, annotation: Optional[str], input_steps: Dict[str, InputStep], workflow_id: DecodedDatabaseIdField)[source]¶

Bases: WorkflowStepBase

type: WorkflowModuleType¶

workflow_id: DecodedDatabaseIdField¶

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

Bases: Model

class_: str¶

name: str¶

address: Optional[str]¶

alternate_name: Optional[str]¶

email: Optional[str]¶

fax_number: Optional[str]¶

identifier: Optional[str]¶

image: Optional[AnyHttpUrl]¶

telephone: Optional[str]¶

url: Optional[AnyHttpUrl]¶

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

Bases: Creator

class_: str¶

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

Bases: Creator

class_: str¶

family_name: Optional[str]¶

givenName: Optional[str]¶

honorific_prefix: Optional[str]¶

honorific_suffix: Optional[str]¶

job_title: Optional[str]¶

class galaxy.schema.schema.StoredWorkflowDetailed(*, id: DecodedDatabaseIdField, model_class: typing_extensions.Literal[StoredWorkflow] = 'StoredWorkflow', create_time: datetime, update_time: datetime, name: str, url: str, published: bool, annotations: List[str], tags: TagCollection, deleted: bool, hidden: bool, owner: str, latest_workflow_uuid: UUID4, number_of_steps: int, show_in_tool_panel: bool, annotation: Optional[str], license: Optional[str] = None, version: int, inputs: Dict[int, WorkflowInput] = {}, creator: Optional[List[Union[Person, Organization]]] = None, steps: Dict[int, Union[InputDataStep, InputDataCollectionStep, InputParameterStep, PauseStep, ToolStep, SubworkflowStep]] = {})[source]¶

Bases: StoredWorkflowSummary

annotation: Optional[str]¶

license: Optional[str]¶

version: int¶

inputs: Dict[int, WorkflowInput]¶

creator: Optional[List[Union[Person, Organization]]]¶

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

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

Bases: Model

name: str¶

description: str¶

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

Bases: Model

name: str¶

type: str¶

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

Bases: Model

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: Model

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: Optional[str], tool_id: Optional[str] = None, uuid: UUID4, label: Optional[str] = None, inputs: List[Input], outputs: List[Output], input_connections: Dict[str, InputConnection] = {}, position: WorkflowStepLayoutPosition, workflow_outputs: List[WorkflowOutput] = [])[source]¶

Bases: Model

id: int¶

type: str¶

name: str¶

annotation: Optional[str]¶

tool_id: Optional[str]¶

uuid: UUID4¶

label: Optional[str]¶

inputs: List[Input]¶

outputs: List[Output]¶

input_connections: Dict[str, InputConnection]¶

position: WorkflowStepLayoutPosition¶

workflow_outputs: List[WorkflowOutput]¶

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

Bases: WorkflowStepToExportBase

content_id: Optional[str]¶

tool_version: Optional[str]¶

tool_state: Json¶

errors: Optional[str]¶

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

Bases: Model

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: Model

action_type: str¶

output_name: str¶

action_arguments: Dict[str, Any]¶

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

Bases: WorkflowStepToExportBase

tool_shed_repository: ToolShedRepositorySummary¶

post_job_actions: Dict[str, PostJobAction]¶

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

Bases: WorkflowStepToExportBase

subworkflow: WorkflowToExport¶

class galaxy.schema.schema.WorkflowToExport(*, a_galaxy_workflow: str = 'true', format_version: str = '0.1', name: str, annotation: Optional[str], tags: TagCollection, uuid: Optional[UUID4] = None, creator: Optional[List[Union[Person, Organization]]] = None, license: Optional[str] = None, version: int, steps: Dict[int, Union[SubworkflowStepToExport, WorkflowToolStepToExport, WorkflowStepToExport]] = {})[source]¶

Bases: Model

a_galaxy_workflow: str¶

format_version: str¶

name: str¶

annotation: Optional[str]¶

tags: TagCollection¶

uuid: Optional[UUID4]¶

creator: Optional[List[Union[Person, Organization]]]¶

license: Optional[str]¶

version: int¶

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

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

Bases: Model

id: EncodedDatabaseIdField¶

name: str¶

type: str¶

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

Bases: BasicRoleModel

description: Optional[str]¶

url: str¶

model_class: typing_extensions.Literal[Role]¶

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

Bases: Model

name: str¶

description: str¶

user_ids: Optional[List[DecodedDatabaseIdField]]¶

group_ids: Optional[List[DecodedDatabaseIdField]]¶

class galaxy.schema.schema.RoleListResponse(*, __root__: List[RoleModelResponse])[source]¶: Bases: Model

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

Bases: Model

id: EncodedDatabaseIdField¶

name: str¶

url: str¶

class galaxy.schema.schema.GroupRoleListResponse(*, __root__: List[GroupRoleResponse])[source]¶: Bases: Model

class galaxy.schema.schema.GroupUserResponse(*, id: EncodedDatabaseIdField, email: str, url: str)[source]¶

Bases: Model

id: EncodedDatabaseIdField¶

email: str¶

url: str¶

class galaxy.schema.schema.GroupUserListResponse(*, __root__: List[GroupUserResponse])[source]¶: Bases: Model

class galaxy.schema.schema.ImportToolDataBundleUriSource(*, src: typing_extensions.Literal[uri], uri: str)[source]¶

Bases: Model

src: typing_extensions.Literal[uri]¶

uri: str¶

class galaxy.schema.schema.ImportToolDataBundleDatasetSource(*, src: typing_extensions.Literal[hda, ldda], id: DecodedDatabaseIdField)[source]¶

Bases: Model

src: typing_extensions.Literal[hda, ldda]¶

id: DecodedDatabaseIdField¶

class galaxy.schema.schema.ToolShedRepository(*, tool_shed_url: str = 'https://toolshed.g2.bx.psu.edu/', name: str, owner: str)[source]¶

Bases: Model

tool_shed_url: str¶

name: str¶

owner: str¶

class galaxy.schema.schema.ToolShedRepositoryChangeset(*, tool_shed_url: str = 'https://toolshed.g2.bx.psu.edu/', name: str, owner: str, changeset_revision: str)[source]¶

Bases: ToolShedRepository

changeset_revision: str¶

class galaxy.schema.schema.InstalledRepositoryToolShedStatus(*, latest_installable_revision: Optional[str] = None, revision_update: str, revision_upgrade: Optional[str] = None, repository_deprecated: Optional[str] = None)[source]¶

Bases: Model

latest_installable_revision: Optional[str]¶

revision_update: str¶

revision_upgrade: Optional[str]¶

repository_deprecated: Optional[str]¶

class galaxy.schema.schema.InstalledToolShedRepository(*, model_class: typing_extensions.Literal[ToolShedRepository] = 'ToolShedRepository', id: EncodedDatabaseIdField, status: str, name: str, owner: str, deleted: bool, ctx_rev: Optional[str] = None, error_message: str = 'Installation error message, the empty string means no error was recorded', installed_changeset_revision: str, tool_shed: str, dist_to_shed: bool, uninstalled: bool, changeset_revision: str, tool_shed_status: Optional[InstalledRepositoryToolShedStatus] = None)[source]¶

Bases: Model

model_class: typing_extensions.Literal[ToolShedRepository]¶

id: EncodedDatabaseIdField¶

status: str¶

name: str¶

owner: str¶

deleted: bool¶

ctx_rev: Optional[str]¶

error_message: str¶

installed_changeset_revision: str¶

tool_shed: str¶

dist_to_shed: bool¶

uninstalled: bool¶

changeset_revision: str¶

tool_shed_status: Optional[InstalledRepositoryToolShedStatus]¶

class galaxy.schema.schema.InstalledToolShedRepositories(*, __root__: List[InstalledToolShedRepository])[source]¶: Bases: Model

class galaxy.schema.schema.CheckForUpdatesResponse(*, status: typing_extensions.Literal[ok, error], message: str)[source]¶

Bases: Model

status: typing_extensions.Literal[ok, error]¶

message: str¶

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

Bases: str, Enum

An enumeration.

current = 'current'¶

available = 'available'¶

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

Bases: Model

model_class: typing_extensions.Literal[Library]¶

id: EncodedDatabaseIdField¶

name: str¶

description: Optional[str]¶

synopsis: Optional[str]¶

root_folder_id: EncodedLibraryFolderDatabaseIdField¶

create_time: datetime¶

deleted: bool¶

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

Bases: 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[LibrarySummary] = [])[source]¶: Bases: Model

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

Bases: Model

name: str¶

description: Optional[str]¶

synopsis: Optional[str]¶

class galaxy.schema.schema.CreateLibrariesFromStore(*, store_content_uri: Optional[str] = None, store_dict: Optional[Dict[str, Any]] = None, model_store_format: Optional[ModelStoreFormat] = None)[source]¶

Bases: StoreContentSource

store_content_uri: Optional[str]¶

store_dict: Optional[Dict[str, Any]]¶

model_store_format: Optional[ModelStoreFormat]¶

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

Bases: Model

name: Optional[str]¶

description: Optional[str]¶

synopsis: Optional[str]¶

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

Bases: Model

undelete: bool¶

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

Bases: Model

access_library_role_list: List[List[str]]¶

modify_library_role_list: List[List[str]]¶

manage_library_role_list: List[List[str]]¶

add_library_item_role_list: List[List[str]]¶

class galaxy.schema.schema.LegacyLibraryPermissionsPayload(*, LIBRARY_ACCESS_in: Optional[Union[List[DecodedDatabaseIdField], DecodedDatabaseIdField]] = [], LIBRARY_MODIFY_in: Optional[Union[List[DecodedDatabaseIdField], DecodedDatabaseIdField]] = [], LIBRARY_ADD_in: Optional[Union[List[DecodedDatabaseIdField], DecodedDatabaseIdField]] = [], LIBRARY_MANAGE_in: Optional[Union[List[DecodedDatabaseIdField], DecodedDatabaseIdField]] = [])[source]¶

Bases: Model

LIBRARY_ACCESS_in: Optional[Union[List[DecodedDatabaseIdField], DecodedDatabaseIdField]]¶

LIBRARY_MODIFY_in: Optional[Union[List[DecodedDatabaseIdField], DecodedDatabaseIdField]]¶

LIBRARY_ADD_in: Optional[Union[List[DecodedDatabaseIdField], DecodedDatabaseIdField]]¶

LIBRARY_MANAGE_in: Optional[Union[List[DecodedDatabaseIdField], DecodedDatabaseIdField]]¶

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

Bases: str, Enum

An enumeration.

set_permissions = 'set_permissions'¶

remove_restrictions = 'remove_restrictions'¶

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

Bases: str, 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[DecodedDatabaseIdField], DecodedDatabaseIdField]] = [], manage_ids: Optional[Union[List[DecodedDatabaseIdField], DecodedDatabaseIdField]] = [], modify_ids: Optional[Union[List[DecodedDatabaseIdField], DecodedDatabaseIdField]] = [])[source]¶

Bases: Model

add_ids: Optional[Union[List[DecodedDatabaseIdField], DecodedDatabaseIdField]]¶

manage_ids: Optional[Union[List[DecodedDatabaseIdField], DecodedDatabaseIdField]]¶

modify_ids: Optional[Union[List[DecodedDatabaseIdField], DecodedDatabaseIdField]]¶

class galaxy.schema.schema.LibraryPermissionsPayload(*, add_ids: Optional[Union[List[DecodedDatabaseIdField], DecodedDatabaseIdField]] = [], manage_ids: Optional[Union[List[DecodedDatabaseIdField], DecodedDatabaseIdField]] = [], modify_ids: Optional[Union[List[DecodedDatabaseIdField], DecodedDatabaseIdField]] = [], action: Optional[LibraryPermissionAction], access_ids: Optional[Union[List[DecodedDatabaseIdField], DecodedDatabaseIdField]] = [])[source]¶

Bases: LibraryPermissionsPayloadBase

action: Optional[LibraryPermissionAction]¶

access_ids: Optional[Union[List[DecodedDatabaseIdField], DecodedDatabaseIdField]]¶

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

Bases: str, Enum

An enumeration.

set_permissions = 'set_permissions'¶

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

Bases: LibraryPermissionsPayloadBase

action: Optional[LibraryFolderPermissionAction]¶

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

Bases: Model

model_class: typing_extensions.Literal[LibraryFolder]¶

id: LibraryFolderDatabaseIdField¶

name: str¶

description: Optional[str]¶

item_count: int¶

parent_library_id: DecodedDatabaseIdField¶

parent_id: Optional[LibraryFolderDatabaseIdField]¶

genome_build: Optional[str]¶

update_time: datetime¶

deleted: bool¶

library_path: List[str]¶

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

Bases: Model

name: str¶

description: Optional[str]¶

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

Bases: Model

name: Optional[str]¶

description: Optional[str]¶

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

Bases: Model

roles: List[BasicRoleModel]¶

page: int¶

page_limit: int¶

total: int¶

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

Bases: Model

modify_folder_role_list: List[List[str]]¶

manage_folder_role_list: List[List[str]]¶

add_library_item_role_list: List[List[str]]¶

class galaxy.schema.schema.LibraryFolderContentsIndexQueryPayload(*, limit: int = 10, offset: int = 0, search_text: Optional[str] = None, include_deleted: Optional[bool] = None, order_by: typing_extensions.Literal[name, description, type, size, update_time] = 'name', sort_desc: Optional[bool] = False)[source]¶

Bases: Model

limit: int¶

offset: int¶

search_text: Optional[str]¶

include_deleted: Optional[bool]¶

order_by: typing_extensions.Literal[name, description, type, size, update_time]¶

sort_desc: Optional[bool]¶

class galaxy.schema.schema.LibraryFolderItemBase(*, name: str, type: str, create_time: datetime, update_time: datetime, can_manage: bool, deleted: bool)[source]¶

Bases: Model

name: str¶

type: str¶

create_time: datetime¶

update_time: datetime¶

can_manage: bool¶

deleted: bool¶

class galaxy.schema.schema.FolderLibraryFolderItem(*, name: str, type: typing_extensions.Literal[folder], create_time: datetime, update_time: datetime, can_manage: bool, deleted: bool, id: EncodedLibraryFolderDatabaseIdField, can_modify: bool, description: Optional[str] = '')[source]¶

Bases: LibraryFolderItemBase

id: EncodedLibraryFolderDatabaseIdField¶

type: typing_extensions.Literal[folder]¶

can_modify: bool¶

description: Optional[str]¶

class galaxy.schema.schema.FileLibraryFolderItem(*, name: str, type: typing_extensions.Literal[file], create_time: datetime, update_time: datetime, can_manage: bool, deleted: bool, id: EncodedDatabaseIdField, file_ext: str, date_uploaded: datetime, is_unrestricted: bool, is_private: bool, state: DatasetState, file_size: str, raw_size: int, ldda_id: EncodedDatabaseIdField, tags: TagCollection, message: Optional[str] = None)[source]¶

Bases: LibraryFolderItemBase

id: EncodedDatabaseIdField¶

type: typing_extensions.Literal[file]¶

file_ext: str¶

date_uploaded: datetime¶

is_unrestricted: bool¶

is_private: bool¶

state: DatasetState¶

file_size: str¶

raw_size: int¶

ldda_id: EncodedDatabaseIdField¶

tags: TagCollection¶

message: Optional[str]¶

class galaxy.schema.schema.LibraryFolderMetadata(*, parent_library_id: EncodedDatabaseIdField, folder_name: str, folder_description: str, total_rows: int, can_modify_folder: bool, can_add_library_item: bool, full_path: List[List[str]])[source]¶

Bases: Model

parent_library_id: EncodedDatabaseIdField¶

folder_name: str¶

folder_description: str¶

total_rows: int¶

can_modify_folder: bool¶

can_add_library_item: bool¶

full_path: List[List[str]]¶

class galaxy.schema.schema.LibraryFolderContentsIndexResult(*, metadata: LibraryFolderMetadata, folder_contents: List[Union[galaxy.schema.schema.FileLibraryFolderItem, galaxy.schema.schema.FolderLibraryFolderItem][Union[FileLibraryFolderItem, FolderLibraryFolderItem]]])[source]¶

Bases: Model

metadata: LibraryFolderMetadata¶

folder_contents: List[Union[galaxy.schema.schema.FileLibraryFolderItem, galaxy.schema.schema.FolderLibraryFolderItem][Union[FileLibraryFolderItem, FolderLibraryFolderItem]]]¶

class galaxy.schema.schema.CreateLibraryFilePayload(*, from_hda_id: Optional[DecodedDatabaseIdField] = None, from_hdca_id: Optional[DecodedDatabaseIdField] = None, ldda_message: Optional[str] = '')[source]¶

Bases: Model

from_hda_id: Optional[DecodedDatabaseIdField]¶

from_hdca_id: Optional[DecodedDatabaseIdField]¶

ldda_message: Optional[str]¶

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

Bases: Model

access_dataset_roles: List[List[str]]¶

manage_dataset_roles: List[List[str]]¶

modify_item_roles: List[List[str]]¶

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

Bases: Model

action: Optional[DatasetPermissionAction]¶

access_ids: Optional[Union[List[DecodedDatabaseIdField], DecodedDatabaseIdField]]¶

manage_ids: Optional[Union[List[DecodedDatabaseIdField], DecodedDatabaseIdField]]¶

modify_ids: Optional[Union[List[DecodedDatabaseIdField], DecodedDatabaseIdField]]¶

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

Bases: Model

Can contain any serializable property of the item.

Allows arbitrary custom keys to be specified in the serialization parameters without a particular view (predefined set of keys).

class Config[source]¶

Bases: object

extra = 'allow'¶

class galaxy.schema.schema.DeleteHistoryContentPayload(*, purge: bool = False, recursive: bool = False, stop_job: bool = False)[source]¶

Bases: Model

purge: bool¶

recursive: bool¶

stop_job: bool¶

class galaxy.schema.schema.DeleteHistoryContentResult(*, id: DecodedDatabaseIdField, deleted: bool, purged: Optional[bool] = None, **extra_data: Any)[source]¶

Bases: CustomHistoryItem

Contains minimum information about the deletion state of a history item.

Can also contain any other properties of the item.

id: DecodedDatabaseIdField¶

deleted: bool¶

purged: Optional[bool]¶

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

Bases: Model

Contains a collection of filepath/filename entries that represent the contents that would have been included in the archive. This is returned when the dry_run flag is active when creating an archive with the contents of the history.

This is used for debugging purposes.

class galaxy.schema.schema.HistoryContentStats(*, total_matches: int)[source]¶

Bases: Model

total_matches: int¶

class galaxy.schema.schema.HistoryContentsResult(*, __root__: List[Union[HDADetailed, HDASummary, HDCADetailed, HDCASummary, CustomHistoryItem]])[source]¶

Bases: Model

List of history content items. Can contain different views and kinds of items.

class galaxy.schema.schema.HistoryContentsWithStatsResult(*, stats: HistoryContentStats, contents: List[Union[HDADetailed, HDASummary, HDCADetailed, HDCASummary, CustomHistoryItem]])[source]¶

Bases: Model

Includes stats with items counting

stats: HistoryContentStats¶

contents: List[Union[HDADetailed, HDASummary, HDCADetailed, HDCASummary, CustomHistoryItem]]¶

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

Bases: str, Enum

Options for sharing resources that may have restricted access to all or part of their contents.

make_public = 'make_public'¶

make_accessible_to_shared = 'make_accessible_to_shared'¶

no_changes = 'no_changes'¶

class galaxy.schema.schema.ShareWithExtra(*, can_share: bool = False, **extra_data: Any)[source]¶

Bases: Model

can_share: bool¶

class Config[source]¶

Bases: object

extra = 'allow'¶

class galaxy.schema.schema.ShareWithPayload(*, user_ids: List[Union[DecodedDatabaseIdField, str]], share_option: Optional[SharingOptions] = None)[source]¶

Bases: Model

user_ids: List[Union[DecodedDatabaseIdField, str]]¶

share_option: Optional[SharingOptions]¶

class galaxy.schema.schema.SetSlugPayload(*, new_slug: str)[source]¶

Bases: Model

new_slug: str¶

class galaxy.schema.schema.UserEmail(*, id: DecodedDatabaseIdField, email: str)[source]¶

Bases: Model

id: DecodedDatabaseIdField¶

email: str¶

class galaxy.schema.schema.UserBeaconSetting(*, enabled: bool)[source]¶

Bases: Model

enabled: bool¶

class galaxy.schema.schema.SharingStatus(*, id: DecodedDatabaseIdField, title: str, importable: bool, published: bool, users_shared_with: List[UserEmail] = [], email_hash: Optional[str] = None, username: Optional[str] = None, username_and_slug: Optional[str] = None)[source]¶

Bases: Model

id: DecodedDatabaseIdField¶

title: str¶

importable: bool¶

published: bool¶

users_shared_with: List[UserEmail]¶

email_hash: Optional[str]¶

username: Optional[str]¶

username_and_slug: Optional[str]¶

class galaxy.schema.schema.ShareWithStatus(*, id: DecodedDatabaseIdField, title: str, importable: bool, published: bool, users_shared_with: List[UserEmail] = [], email_hash: Optional[str] = None, username: Optional[str] = None, username_and_slug: Optional[str] = None, errors: List[str] = [], extra: Optional[ShareWithExtra] = None)[source]¶

Bases: SharingStatus

errors: List[str]¶

extra: Optional[ShareWithExtra]¶

class galaxy.schema.schema.HDABasicInfo(*, id: DecodedDatabaseIdField, name: str)[source]¶

Bases: Model

id: DecodedDatabaseIdField¶

name: str¶

class galaxy.schema.schema.ShareHistoryExtra(*, can_share: bool = False, can_change: List[HDABasicInfo] = [], cannot_change: List[HDABasicInfo] = [], accessible_count: int = 0, **extra_data: Any)[source]¶

Bases: ShareWithExtra

can_change: List[HDABasicInfo]¶

cannot_change: List[HDABasicInfo]¶

accessible_count: int¶

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

Bases: str, Enum

An enumeration.

markdown = 'markdown'¶

html = 'html'¶

class galaxy.schema.schema.PageSummaryBase(*, title: str, slug: ConstrainedStrValue)[source]¶

Bases: Model

title: str¶

slug: str¶

class galaxy.schema.schema.MaterializeDatasetInstanceAPIRequest(*, source: DatasetSourceType, content: DecodedDatabaseIdField)[source]¶

Bases: Model

source: DatasetSourceType¶

content: DecodedDatabaseIdField¶

class galaxy.schema.schema.MaterializeDatasetInstanceRequest(*, source: DatasetSourceType, content: DecodedDatabaseIdField, history_id: DecodedDatabaseIdField)[source]¶

Bases: MaterializeDatasetInstanceAPIRequest

history_id: DecodedDatabaseIdField¶

class galaxy.schema.schema.CreatePagePayload(*, title: str, slug: ConstrainedStrValue, content_format: PageContentFormat = PageContentFormat.html, content: Optional[str] = '', annotation: Optional[str] = None, invocation_id: Optional[DecodedDatabaseIdField] = None, **extra_data: Any)[source]¶

Bases: PageSummaryBase

content_format: PageContentFormat¶

content: Optional[str]¶

annotation: Optional[str]¶

invocation_id: Optional[DecodedDatabaseIdField]¶

class Config[source]¶

Bases: object

use_enum_values = True¶

extra = 'allow'¶

class galaxy.schema.schema.AsyncTaskResultSummary(*, id: str, ignored: bool, name: Optional[str] = None, queue: Optional[str] = None)[source]¶

Bases: Model

id: str¶

ignored: bool¶

name: Optional[str]¶

queue: Optional[str]¶

class galaxy.schema.schema.AsyncFile(*, storage_request_id: UUID, task: AsyncTaskResultSummary)[source]¶

Bases: Model

storage_request_id: UUID¶

task: AsyncTaskResultSummary¶

class galaxy.schema.schema.PageSummary(*, title: str, slug: ConstrainedStrValue, id: DecodedDatabaseIdField, model_class: typing_extensions.Literal[Page] = 'Page', username: str, email_hash: str, published: bool, importable: bool, deleted: bool, latest_revision_id: DecodedDatabaseIdField, revision_ids: List[DecodedDatabaseIdField], create_time: Optional[datetime] = None, update_time: Optional[datetime] = None, tags: TagCollection)[source]¶

Bases: PageSummaryBase

id: DecodedDatabaseIdField¶

model_class: typing_extensions.Literal[Page]¶

username: str¶

email_hash: str¶

published: bool¶

importable: bool¶

deleted: bool¶

latest_revision_id: DecodedDatabaseIdField¶

revision_ids: List[DecodedDatabaseIdField]¶

create_time: Optional[datetime]¶

update_time: Optional[datetime]¶

tags: TagCollection¶

class galaxy.schema.schema.PageDetails(*, title: str, slug: ConstrainedStrValue, id: DecodedDatabaseIdField, model_class: typing_extensions.Literal[Page] = 'Page', username: str, email_hash: str, published: bool, importable: bool, deleted: bool, latest_revision_id: DecodedDatabaseIdField, revision_ids: List[DecodedDatabaseIdField], create_time: Optional[datetime] = None, update_time: Optional[datetime] = None, tags: TagCollection, content_format: PageContentFormat = PageContentFormat.html, content: Optional[str] = '', generate_version: Optional[str] = None, generate_time: Optional[str] = None, **extra_data: Any)[source]¶

Bases: PageSummary

content_format: PageContentFormat¶

content: Optional[str]¶

generate_version: Optional[str]¶

generate_time: Optional[str]¶

class Config[source]¶

Bases: object

extra = 'allow'¶

class galaxy.schema.schema.PageSummaryList(*, __root__: List[PageSummary] = [])[source]¶: Bases: Model

galaxy.schema.tasks module¶

class galaxy.schema.tasks.SetupHistoryExportJob(*, history_id: int, job_id: int, store_directory: str, include_files: bool, include_hidden: bool, include_deleted: bool)[source]¶

Bases: BaseModel

history_id: int¶

job_id: int¶

store_directory: str¶

include_files: bool¶

include_hidden: bool¶

include_deleted: bool¶

class galaxy.schema.tasks.PrepareDatasetCollectionDownload(*, short_term_storage_request_id: UUID, history_dataset_collection_association_id: int)[source]¶

Bases: BaseModel

short_term_storage_request_id: UUID¶

history_dataset_collection_association_id: int¶

class galaxy.schema.tasks.GeneratePdfDownload(*, short_term_storage_request_id: UUID, basic_markdown: str, document_type: PdfDocumentType)[source]¶

Bases: BaseModel

short_term_storage_request_id: UUID¶

basic_markdown: str¶

document_type: PdfDocumentType¶

class galaxy.schema.tasks.RequestUser(*, user_id: int)[source]¶

Bases: BaseModel

user_id: int¶

class galaxy.schema.tasks.GenerateHistoryDownload(*, model_store_format: ModelStoreFormat = ModelStoreFormat.TAR_DOT_GZ, include_files: bool = True, include_deleted: bool = False, include_hidden: bool = False, short_term_storage_request_id: UUID, duration: Optional[Union[int, float]] = None, history_id: int, user: RequestUser, export_association_id: Optional[int] = None)[source]¶

Bases: ShortTermStoreExportPayload

history_id: int¶

user: RequestUser¶

export_association_id: Optional[int]¶

class galaxy.schema.tasks.GenerateHistoryContentDownload(*, model_store_format: ModelStoreFormat = ModelStoreFormat.TAR_DOT_GZ, include_files: bool = True, include_deleted: bool = False, include_hidden: bool = False, short_term_storage_request_id: UUID, duration: Optional[Union[int, float]] = None, content_type: HistoryContentType, content_id: int, user: RequestUser)[source]¶

Bases: ShortTermStoreExportPayload

content_type: HistoryContentType¶

content_id: int¶

user: RequestUser¶

class galaxy.schema.tasks.BcoGenerationTaskParametersMixin(*, bco_merge_history_metadata: bool = False, bco_override_environment_variables: Optional[Dict[str, str]] = None, bco_override_empirical_error: Optional[Dict[str, str]] = None, bco_override_algorithmic_error: Optional[Dict[str, str]] = None, bco_override_xref: Optional[List[XrefItem]] = None, galaxy_url: str)[source]¶

Bases: BcoGenerationParametersMixin

galaxy_url: str¶

class galaxy.schema.tasks.GenerateInvocationDownload(*, bco_merge_history_metadata: bool = False, bco_override_environment_variables: Optional[Dict[str, str]] = None, bco_override_empirical_error: Optional[Dict[str, str]] = None, bco_override_algorithmic_error: Optional[Dict[str, str]] = None, bco_override_xref: Optional[List[XrefItem]] = None, galaxy_url: str, model_store_format: ModelStoreFormat = ModelStoreFormat.TAR_DOT_GZ, include_files: bool = True, include_deleted: bool = False, include_hidden: bool = False, short_term_storage_request_id: UUID, duration: Optional[Union[int, float]] = None, invocation_id: int, user: RequestUser)[source]¶

Bases: ShortTermStoreExportPayload, BcoGenerationTaskParametersMixin

invocation_id: int¶

user: RequestUser¶

class galaxy.schema.tasks.WriteInvocationTo(*, bco_merge_history_metadata: bool = False, bco_override_environment_variables: Optional[Dict[str, str]] = None, bco_override_empirical_error: Optional[Dict[str, str]] = None, bco_override_algorithmic_error: Optional[Dict[str, str]] = None, bco_override_xref: Optional[List[XrefItem]] = None, galaxy_url: str, model_store_format: ModelStoreFormat = ModelStoreFormat.TAR_DOT_GZ, include_files: bool = True, include_deleted: bool = False, include_hidden: bool = False, target_uri: str, invocation_id: int, user: RequestUser)[source]¶

Bases: WriteStoreToPayload, BcoGenerationTaskParametersMixin

invocation_id: int¶

user: RequestUser¶

class galaxy.schema.tasks.WriteHistoryContentTo(*, model_store_format: ModelStoreFormat = ModelStoreFormat.TAR_DOT_GZ, include_files: bool = True, include_deleted: bool = False, include_hidden: bool = False, target_uri: str, content_type: HistoryContentType, content_id: int, user: RequestUser)[source]¶

Bases: WriteStoreToPayload

content_type: HistoryContentType¶

content_id: int¶

user: RequestUser¶

class galaxy.schema.tasks.WriteHistoryTo(*, model_store_format: ModelStoreFormat = ModelStoreFormat.TAR_DOT_GZ, include_files: bool = True, include_deleted: bool = False, include_hidden: bool = False, target_uri: str, history_id: int, user: RequestUser, export_association_id: Optional[int] = None)[source]¶

Bases: WriteStoreToPayload

history_id: int¶

user: RequestUser¶

export_association_id: Optional[int]¶

class galaxy.schema.tasks.ImportModelStoreTaskRequest(*, user: RequestUser, history_id: Optional[int] = None, source_uri: str, for_library: bool, model_store_format: Optional[ModelStoreFormat] = None)[source]¶

Bases: BaseModel

user: RequestUser¶

history_id: Optional[int]¶

source_uri: str¶

for_library: bool¶

model_store_format: Optional[ModelStoreFormat]¶

class galaxy.schema.tasks.MaterializeDatasetInstanceTaskRequest(*, history_id: int, user: RequestUser, source: DatasetSourceType, content: int)[source]¶

Bases: BaseModel

history_id: int¶

user: RequestUser¶

source: DatasetSourceType¶

content: int¶

class galaxy.schema.tasks.ComputeDatasetHashTaskRequest(*, dataset_id: int, extra_files_path: Optional[str] = None, hash_function: HashFunctionNameEnum, user: Optional[RequestUser] = None)[source]¶

Bases: BaseModel

dataset_id: int¶

extra_files_path: Optional[str]¶

hash_function: HashFunctionNameEnum¶

user: Optional[RequestUser]¶

class galaxy.schema.tasks.PurgeDatasetsTaskRequest(*, dataset_ids: List[int])[source]¶

Bases: BaseModel

dataset_ids: List[int]¶

galaxy.schema.types module¶

class galaxy.schema.types.OffsetNaiveDatetime[source]¶

Bases: datetime

classmethod validate(v)[source]¶