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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
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]
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

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

Bases: BaseFetchDataTarget

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

items: 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]]
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

items: 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]]
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, label: str, doc: str, browsable: bool, writable: bool, requires_roles: Optional[str] = None, requires_groups: Optional[str] = None)[source]

Bases: Model

id: str
type: str
label: str
doc: str
browsable: bool
writable: bool
requires_roles: Optional[str]
requires_groups: Optional[str]
class galaxy.schema.remote_files.BrowsableFilesSourcePlugin(*, id: str, type: str, label: str, doc: str, browsable: typing_extensions.Literal[True], writable: bool, requires_roles: Optional[str] = None, requires_groups: Optional[str] = None, uri_root: str)[source]

Bases: FilesSourcePlugin

browsable: typing_extensions.Literal[True]
uri_root: str
class galaxy.schema.remote_files.FilesSourcePluginList(*, __root__: List[Union[BrowsableFilesSourcePlugin, FilesSourcePlugin]] = [])[source]

Bases: Model

class galaxy.schema.remote_files.RemoteEntry(*, name: str, uri: str, path: str)[source]

Bases: Model

name: str
uri: str
path: str
class galaxy.schema.remote_files.RemoteDirectory(*, name: str, uri: str, path: str, class_: typing_extensions.Literal[Directory])[source]

Bases: RemoteEntry

class_: typing_extensions.Literal[Directory]
class galaxy.schema.remote_files.RemoteFile(*, name: str, uri: str, path: str, class_: typing_extensions.Literal[File], size: int, ctime: str)[source]

Bases: RemoteEntry

class_: typing_extensions.Literal[File]
size: int
ctime: str
class galaxy.schema.remote_files.ListJstreeResponse(*, __root__: List[Any] = [])[source]

Bases: Model

class galaxy.schema.remote_files.ListUriResponse(*, __root__: List[Union[galaxy.schema.remote_files.RemoteFile, galaxy.schema.remote_files.RemoteDirectory][Union[RemoteFile, RemoteDirectory]]] = [])[source]

Bases: Model

class galaxy.schema.remote_files.CreateEntryPayload(*, target: str, name: str)[source]

Bases: Model

target: str
name: str
class galaxy.schema.remote_files.CreatedEntryResponse(*, name: str, uri: str, external_link: Optional[str] = None)[source]

Bases: Model

name: str
uri: str

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

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.BaseUserModel(*, id: EncodedDatabaseIdField, username: str, email: str, deleted: bool)[source]

Bases: Model

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

Bases: BaseUserModel

User in a transaction context.

active: bool
model_class: typing_extensions.Literal[User]
last_password_change: Optional[datetime]
class galaxy.schema.schema.LimitedUserModel(*, id: EncodedDatabaseIdField, username: Optional[str] = None, email: Optional[str] = None)[source]

Bases: Model

This is used when config options (expose_user_name and expose_user_email) are in place.

id: EncodedDatabaseIdField
username: Optional[str]
email: Optional[str]
class galaxy.schema.schema.DiskUsageUserModel(*, total_disk_usage: float, nice_total_disk_usage: str)[source]

Bases: Model

total_disk_usage: float
nice_total_disk_usage: str
class galaxy.schema.schema.CreatedUserModel(*, total_disk_usage: float, nice_total_disk_usage: str, id: EncodedDatabaseIdField, username: str, email: str, deleted: bool, active: bool, model_class: typing_extensions.Literal[User] = 'User', last_password_change: Optional[datetime] = None, preferred_object_store_id: Optional[str] = None)[source]

Bases: UserModel, DiskUsageUserModel

preferred_object_store_id: Optional[str]
class galaxy.schema.schema.AnonUserModel(*, total_disk_usage: float, nice_total_disk_usage: str, quota_percent: Any = None)[source]

Bases: DiskUsageUserModel

quota_percent: Any
class galaxy.schema.schema.DetailedUserModel(*, total_disk_usage: float, nice_total_disk_usage: str, quota_percent: Any = None, id: EncodedDatabaseIdField, username: str, email: str, deleted: bool, is_admin: bool, purged: bool, preferences: Dict[Any, Any], preferred_object_store_id: Optional[str] = None, quota: str, quota_bytes: Any, tags_used: List[str])[source]

Bases: BaseUserModel, AnonUserModel

is_admin: bool
purged: bool
preferences: Dict[Any, Any]
preferred_object_store_id: Optional[str]
quota: str
quota_bytes: Any
tags_used: List[str]
class galaxy.schema.schema.UserCreationPayload(*, password: str, email: str, username: str)[source]

Bases: Model

password: str
email: str
username: str
class galaxy.schema.schema.RemoteUserCreationPayload(*, remote_user_email: str)[source]

Bases: Model

remote_user_email: str
class galaxy.schema.schema.UserDeletionPayload(*, purge: bool = False)[source]

Bases: Model

purge: bool
class galaxy.schema.schema.FavoriteObject(*, object_id: str)[source]

Bases: Model

object_id: str
class galaxy.schema.schema.FavoriteObjectsSummary(*, tools: List[str])[source]

Bases: Model

tools: List[str]
class galaxy.schema.schema.FavoriteObjectType(value)[source]

Bases: str, Enum

An enumeration.

tools = 'tools'
class galaxy.schema.schema.DeletedCustomBuild(*, message: str)[source]

Bases: Model

message: str
class galaxy.schema.schema.CustomBuildBaseModel(*, name: str)[source]

Bases: Model

name: str
class galaxy.schema.schema.CustomBuildLenType(value)[source]

Bases: str, Enum

An enumeration.

file = 'file'
fasta = 'fasta'
text = 'text'
class galaxy.schema.schema.CustomBuildCreationPayload(*, name: str, len_type: CustomBuildLenType, len_value: str)[source]

Bases: CustomBuildBaseModel

len_type: CustomBuildLenType
len_value: str
class galaxy.schema.schema.CreatedCustomBuild(*, name: str, len: EncodedDatabaseIdField, count: Optional[str] = None, fasta: Optional[EncodedDatabaseIdField] = None, linecount: Optional[EncodedDatabaseIdField] = None)[source]

Bases: CustomBuildBaseModel

len: EncodedDatabaseIdField
count: Optional[str]
fasta: Optional[EncodedDatabaseIdField]
linecount: Optional[EncodedDatabaseIdField]
class galaxy.schema.schema.CustomBuildModel(*, name: str, len: EncodedDatabaseIdField, count: Optional[str] = None, fasta: Optional[EncodedDatabaseIdField] = None, linecount: Optional[EncodedDatabaseIdField] = None, id: str)[source]

Bases: CreatedCustomBuild

id: str
class galaxy.schema.schema.CustomBuildsCollection(*, __root__: List[CustomBuildModel])[source]

Bases: Model

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.DataItemSourceType(value)[source]

Bases: str, Enum

An enumeration.

hda = 'hda'
ldda = 'ldda'
hdca = 'hdca'
dce = 'dce'
dc = 'dc'
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]

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
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, 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
deleted: bool
visible: bool
class galaxy.schema.schema.HistoryItemCommon(*, id: DecodedDatabaseIdField, name: Optional[str] = None, history_id: DecodedDatabaseIdField, hid: int, 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.HDACommon(*, id: DecodedDatabaseIdField, name: Optional[str] = None, history_id: DecodedDatabaseIdField, hid: int, 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, history_content_type: typing_extensions.Literal[dataset][typing_extensions.Literal[dataset]], **extra_data: Any)[source]

Bases: HistoryItemCommon

history_content_type: typing_extensions.Literal[dataset][typing_extensions.Literal[dataset]]
class galaxy.schema.schema.HDASummary(*, id: DecodedDatabaseIdField, name: Optional[str] = None, history_id: DecodedDatabaseIdField, hid: int, 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, history_content_type: typing_extensions.Literal[dataset][typing_extensions.Literal[dataset]], dataset_id: DecodedDatabaseIdField, state: DatasetState, extension: str, purged: bool, **extra_data: Any)[source]

Bases: HDACommon

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, 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, history_content_type: typing_extensions.Literal[dataset][typing_extensions.Literal[dataset]], accessible: bool, state: DatasetState, **extra_data: Any)[source]

Bases: HDACommon

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, 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, history_content_type: typing_extensions.Literal[dataset][typing_extensions.Literal[dataset]], 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, 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, history_content_type: typing_extensions.Literal[dataset][typing_extensions.Literal[dataset]], 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.HDCACommon(*, id: DecodedDatabaseIdField, name: Optional[str] = None, history_id: DecodedDatabaseIdField, hid: int, 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, history_content_type: typing_extensions.Literal[dataset_collection][typing_extensions.Literal[dataset_collection]], **extra_data: Any)[source]

Bases: HistoryItemCommon

history_content_type: typing_extensions.Literal[dataset_collection][typing_extensions.Literal[dataset_collection]]
class galaxy.schema.schema.HDCASummary(*, id: DecodedDatabaseIdField, name: Optional[str] = None, history_id: DecodedDatabaseIdField, hid: int, 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, history_content_type: typing_extensions.Literal[dataset_collection][typing_extensions.Literal[dataset_collection]], 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: HDCACommon

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, 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, history_content_type: typing_extensions.Literal[dataset_collection][typing_extensions.Literal[dataset_collection]], 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: EncodedDatabaseIdField, history_id: Optional[EncodedDatabaseIdField] = None, model_class: typing_extensions.Literal[Job] = 'Job', tool_id: str, state: JobState, exit_code: Optional[int] = None, create_time: datetime, update_time: datetime, galaxy_version: str)[source]

Bases: Model

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

Bases: Model

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

Bases: DatasetSourceId

uuid: UUID4
class galaxy.schema.schema.JobDetails(*, id: EncodedDatabaseIdField, history_id: Optional[EncodedDatabaseIdField] = None, model_class: typing_extensions.Literal[Job] = 'Job', tool_id: str, 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: EncodedDatabaseIdField, history_id: Optional[EncodedDatabaseIdField] = None, model_class: typing_extensions.Literal[Job] = 'Job', tool_id: str, 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

class galaxy.schema.schema.DatasetSummary(*, id: EncodedDatabaseIdField, create_time: Optional[datetime] = None, update_time: Optional[datetime] = None, state: DatasetState, deleted: bool, purged: bool, purgable: bool, file_size: int, total_size: int, uuid: UUID4)[source]

Bases: Model

id: EncodedDatabaseIdField
create_time: Optional[datetime]
update_time: Optional[datetime]
state: DatasetState
deleted: bool
purged: bool
purgable: bool
file_size: int
total_size: int
uuid: UUID4

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]