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)[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