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galaxy.schema package¶

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

Bases: 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: ConstrainedIntValue = 0, limit: 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: ConstrainedIntValue = 0, limit: ConstrainedIntValue = None, q: Optional[Union[List[str], str]] = None, qv: Optional[Union[List[str], str]] = None, order: 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: str = None, keys: List[str] = None, default_view: 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'¶

Submodules¶

galaxy.schema.fetch_data module¶

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

Bases: BaseModel

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: EncodedDatabaseIdField)[source]¶

Bases: FetchBaseModel

type: typing_extensions.Literal[library_folder]¶

library_folder_id: EncodedDatabaseIdField¶

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

Bases: FetchBaseModel

items_from: Optional[str]¶

src: Src¶

fuzzy_root: Optional[bool]¶

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

class Config[source]¶

Bases: object

extra = 'forbid'¶

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

Bases: BaseDataElement

src: typing_extensions.Literal[files]¶

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

Bases: BaseDataElement

src: typing_extensions.Literal[server_dir]¶

server_dir: str¶

link_data_only: Optional[bool]¶

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

Bases: BaseModel

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: str = None, tags: List[str] = None, name: str = None, src: typing_extensions.Literal[ftp_import], ftp_path: str, elements_from: 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: str = None, dbkey: str = '?', info: str = None, ext: str = 'auto', space_to_tab: bool = False, to_posix_lines: bool = False, deferred: bool = False, tags: List[str] = None, created_from_basename: str = None, extra_files: ExtraFiles = None, auto_decompress: bool = False, elements_from: ElementsFromType = None, collection_type: str = None, MD5: str = None, src: typing_extensions.Literal[path], path: str, link_data_only: bool = None)[source]¶

Bases: BaseDataElement

src: typing_extensions.Literal[path]¶

path: str¶

items_from: Optional[ElementsFromType]¶

link_data_only: Optional[bool]¶

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

Bases: BaseDataElement

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

Bases: BaseFetchDataTarget

destination: Union[HdaDestination, LibraryFolderDestination, LibraryDestination]¶

Bases: BaseDataTarget

class galaxy.schema.fetch_data.DataElementsFromTarget(*, src: ItemsFromSrc, path: str = None, ftp_path: str = None, server_dir: str = None, url: 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: str = None, tags: List[str] = None, name: str = None, elements: List[Union[Union[galaxy.schema.fetch_data.FileDataElement, galaxy.schema.fetch_data.PastedDataElement, galaxy.schema.fetch_data.UrlDataElement, galaxy.schema.fetch_data.PathDataElement, galaxy.schema.fetch_data.ServerDirElement, galaxy.schema.fetch_data.FtpImportElement, galaxy.schema.fetch_data.CompositeDataElement][Union[FileDataElement, PastedDataElement, UrlDataElement, PathDataElement, ServerDirElement, FtpImportElement, CompositeDataElement]], NestedElement]])[source]¶

Bases: BaseCollectionTarget

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

filename: str¶

local_filename: str¶

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

Bases: FetchBaseModel

history_id: EncodedDatabaseIdField¶

class Config[source]¶

Bases: object

extra = 'allow'¶

classmethod targets_string_to_json(v)[source]¶

class galaxy.schema.fetch_data.FetchDataPayload(*, history_id: EncodedDatabaseIdField, 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: EncodedDatabaseIdField, 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]¶

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

Bases: int, BaseDatabaseIdField

classmethod validate(v)[source]¶

security: IdEncodingHelper¶

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

Bases: str, BaseDatabaseIdField

classmethod validate(v)[source]¶

security: IdEncodingHelper¶

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

galaxy.schema.remote_files module¶

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

Bases: str, Enum

An enumeration.

ftpdir = 'ftpdir'¶

userdir = 'userdir'¶

importdir = 'importdir'¶

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

Bases: str, Enum

An enumeration.

flat = 'flat'¶

jstree = 'jstree'¶

uri = 'uri'¶

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

Bases: str, Enum

An enumeration.

folders = 'folders'¶

files = 'files'¶

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

Bases: BaseModel

id: str¶

type: str¶

uri_root: str¶

label: str¶

doc: str¶

writable: bool¶

requires_roles: Optional[str]¶

requires_groups: Optional[str]¶

class Config[source]¶

Bases: object

extra = 'allow'¶

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

galaxy.schema.schema module¶

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

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

Bases: BaseModel

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

class Config[source]¶

Bases: object

use_enum_values = True¶

allow_population_by_field_name = True¶

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

Bases: Model

User in a transaction context.

id: EncodedDatabaseIdField¶

username: str¶

email: str¶

active: bool¶

deleted: bool¶

last_password_change: Optional[datetime]¶

model_class: str¶

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

Bases: BaseModel

User group model

model_class: str¶

id: EncodedDatabaseIdField¶

name: str¶

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

Bases: str, Enum

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

Job = 'Job'¶

ImplicitCollectionJobs = 'ImplicitCollectionJobs'¶

WorkflowInvocation = 'WorkflowInvocation'¶

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

Bases: str, Enum

Available types of History contents.

dataset = 'dataset'¶

dataset_collection = 'dataset_collection'¶

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

Bases: str, Enum

Available types of History archive sources.

url = 'url'¶

file = 'file'¶

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

Bases: str, Enum

Available types of dataset collection elements.

hda = 'hda'¶

dataset_collection = 'dataset_collection'¶

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

Bases: str, Enum

An enumeration.

hda = 'hda'¶

ldda = 'ldda'¶

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

Bases: str, Enum

An enumeration.

hda = 'hda'¶

ldda = 'ldda'¶

hdca = 'hdca'¶

new_collection = 'new_collection'¶

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

Bases: str, Enum

An enumeration.

hda = 'hda'¶

hdca = 'hdca'¶

library = 'library'¶

library_folder = 'library_folder'¶

new_collection = 'new_collection'¶

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

Bases: str, Enum

An enumeration.

history = 'history'¶

library = 'library'¶

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[EncodedDatabaseIdField] = [], access: List[EncodedDatabaseIdField] = [])[source]¶

Bases: Model

Role-based permissions for accessing and managing a dataset.

manage: List[EncodedDatabaseIdField]¶

access: List[EncodedDatabaseIdField]¶

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

Bases: Model

Represents some text with an Hyperlink.

target: str¶

href: AnyUrl¶

text: str¶

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

Bases: Model

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

label: str¶

links: List[Hyperlink]¶

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

Bases: Model

class Config[source]¶

Bases: object

extra = 'allow'¶

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

Bases: Model

Basic information provided by items contained in a History.

id: EncodedDatabaseIdField¶

name: Optional[str]¶

history_id: EncodedDatabaseIdField¶

hid: int¶

history_content_type: HistoryContentType¶

deleted: bool¶

visible: bool¶

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

Bases: HistoryItemBase

Common information provided by items contained in a History.

class Config[source]¶

Bases: object

extra = 'allow'¶

type_id: Optional[str]¶

type: str¶

create_time: Optional[datetime]¶

update_time: Optional[datetime]¶

url: str¶

tags: TagCollection¶

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

Bases: HistoryItemCommon

History Dataset Association summary information.

dataset_id: EncodedDatabaseIdField¶

state: states¶

extension: str¶

purged: bool¶

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

Bases: HistoryItemBase

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

accessible: bool¶

state: states¶

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

Bases: HDASummary

History Dataset Association detailed information.

model_class: str¶

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: validated_states¶

validated_state_message: Optional[str]¶

annotation: Optional[str]¶

download_url: str¶

type: str¶

api_type: str¶

created_from_basename: Optional[str]¶

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

Bases: HDADetailed

History Dataset Association extended information.

tool_version: str¶

parent_id: Optional[EncodedDatabaseIdField]¶

designation: Optional[str]¶

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

Bases: Model

Dataset Collection summary information.

model_class: str¶

id: EncodedDatabaseIdField¶

create_time: datetime¶

update_time: datetime¶

collection_type: str¶

populated_state: populated_states¶

populated_state_message: Optional[str]¶

element_count: Optional[int]¶

class galaxy.schema.schema.HDAObject(*, id: EncodedDatabaseIdField, model_class: str = 'HistoryDatasetAssociation', state: states, hda_ldda: DatasetSourceType = DatasetSourceType.hda, history_id: EncodedDatabaseIdField, **extra_data: Any)[source]¶

Bases: Model

History Dataset Association Object

id: EncodedDatabaseIdField¶

model_class: str¶

state: states¶

hda_ldda: DatasetSourceType¶

history_id: EncodedDatabaseIdField¶

class Config[source]¶

Bases: object

extra = 'allow'¶

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

Bases: Model

Dataset Collection Object

id: EncodedDatabaseIdField¶

model_class: str¶

collection_type: str¶

populated: Optional[bool]¶

element_count: Optional[int]¶

contents_url: Optional[str]¶

elements: List[DCESummary]¶

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

Bases: Model

Dataset Collection Element summary information.

id: EncodedDatabaseIdField¶

model_class: str¶

element_index: int¶

element_identifier: str¶

element_type: DCEType¶

object: Union[HDAObject, HDADetailed, DCObject]¶

class galaxy.schema.schema.DCDetailed(*, model_class: str = 'DatasetCollection', id: EncodedDatabaseIdField, create_time: datetime, update_time: datetime, collection_type: str = None, populated_state: populated_states, populated_state_message: str = None, element_count: 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, 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¶

deleted_new: int¶

resubmitted: int¶

queued: int¶

ok: int¶

failed: int¶

deleted: int¶

upload: int¶

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

Bases: HistoryItemCommon

History Dataset Collection Association summary information.

model_class: str¶

type: str¶

collection_type: str¶

populated_state: populated_states¶

populated_state_message: Optional[str]¶

element_count: Optional[int]¶

job_source_id: Optional[EncodedDatabaseIdField]¶

job_source_type: Optional[JobSourceType]¶

job_state_summary: Optional[HDCJobStateSummary]¶

contents_url: str¶

collection_id: EncodedDatabaseIdField¶

class galaxy.schema.schema.HDCADetailed(*, id: EncodedDatabaseIdField, name: str = None, history_id: EncodedDatabaseIdField, hid: int, history_content_type: HistoryContentType, deleted: bool, visible: bool, type_id: str = None, type: str = 'collection', create_time: datetime = None, update_time: datetime = None, url: str, tags: TagCollection, model_class: str = 'HistoryDatasetCollectionAssociation', collection_type: str = None, populated_state: populated_states, populated_state_message: str = None, element_count: int = None, job_source_id: EncodedDatabaseIdField = None, job_source_type: JobSourceType = None, job_state_summary: HDCJobStateSummary = None, contents_url: str, collection_id: EncodedDatabaseIdField, 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: BaseModel

Provides basic configuration for all the History models.

class Config[source]¶

Bases: object

use_enum_values = True¶

extra = 'allow'¶

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

Bases: Model

Identifies a dataset or collection contained in a History.

history_content_type: HistoryContentType¶

id: EncodedDatabaseIdField¶

class galaxy.schema.schema.UpdateContentItem(*, history_content_type: HistoryContentType, id: EncodedDatabaseIdField, **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'¶

history_content_type: HistoryContentType¶

id: EncodedDatabaseIdField¶

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: 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: HistoryContentItem, error: str)[source]¶

Bases: Model

item: HistoryContentItem¶

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(**extra_data: Any)[source]¶

Bases: HistoryBase

Contains arbitrary property values that will be updated for a particular history item.

class Config[source]¶

Bases: object

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

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

Bases: HistoryBase

History summary information.

model_class: str¶

id: EncodedDatabaseIdField¶

name: str¶

deleted: bool¶

purged: bool¶

url: str¶

published: bool¶

annotation: Optional[str]¶

tags: TagCollection¶

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

Bases: HistorySummary

History detailed information.

contents_url: str¶

size: int¶

user_id: EncodedDatabaseIdField¶

create_time: datetime¶

update_time: datetime¶

importable: bool¶

slug: Optional[str]¶

username_and_slug: Optional[str]¶

genome_build: Optional[str]¶

state: states¶

state_ids: Dict[states, List[EncodedDatabaseIdField]]¶

state_details: Dict[states, int]¶

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

Bases: HistoryDetailed

History detailed information used in the new Beta History.

annotation: Optional[str]¶

empty: bool¶

nice_size: str¶

purged: bool¶

tags: TagCollection¶

hid_counter: int¶

contents_active: HistoryActiveContentCounts¶

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

Bases: 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.WorkflowSortByEnum(value)[source]¶

Bases: str, Enum

An enumeration.

create_time = 'create_time'¶

update_time = 'update_time'¶

name = 'name'¶

none = 'None'¶

class galaxy.schema.schema.WorkflowIndexQueryPayload(*, show_deleted: bool = False, show_hidden: bool = False, show_published: bool = None, show_shared: bool = None, sort_by: WorkflowSortByEnum = None, sort_desc: bool = None, limit: ConstrainedIntValue = None, offset: int = 0, search: 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[WorkflowSortByEnum]¶

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: List[str] = None, user_details: bool = False, user_id: DecodedDatabaseIdField = None, tool_ids: List[str] = None, tool_ids_like: List[str] = None, date_range_min: Optional[Union[OffsetNaiveDatetime, date]] = None, date_range_max: Optional[Union[OffsetNaiveDatetime, date]] = None, history_id: DecodedDatabaseIdField = None, workflow_id: DecodedDatabaseIdField = None, invocation_id: DecodedDatabaseIdField = None, order_by: JobIndexSortByEnum = JobIndexSortByEnum.update_time, search: 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: DecodedDatabaseIdField = None, history_id: DecodedDatabaseIdField = None, job_id: DecodedDatabaseIdField = None, user_id: DecodedDatabaseIdField = None, sort_by: InvocationSortByEnum = None, sort_desc: bool = False, include_terminal: bool = True, limit: ConstrainedIntValue = 100, offset: 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.PageSortByEnum(value)[source]¶

Bases: str, Enum

An enumeration.

create_time = 'create_time'¶

update_time = 'update_time'¶

class galaxy.schema.schema.PageIndexQueryPayload(*, deleted: bool = False, user_id: DecodedDatabaseIdField = None, sort_by: PageSortByEnum = PageSortByEnum.update_time, sort_desc: bool = True, show_published: bool = True, show_shared: bool = False, limit: int = 500, offset: int = 0)[source]¶

Bases: Model

deleted: bool¶

user_id: Optional[DecodedDatabaseIdField]¶

sort_by: PageSortByEnum¶

sort_desc: bool¶

show_published: bool¶

show_shared: bool¶

limit: int¶

offset: int¶

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

Bases: Model

name: Optional[str]¶

history_id: Optional[EncodedDatabaseIdField]¶

all_datasets: Optional[bool]¶

archive_source: Optional[str]¶

archive_type: Optional[HistoryImportArchiveSourceType]¶

archive_file: Optional[Any]¶

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

Bases: Model

name: Optional[str]¶

src: ColletionSourceType¶

id: Optional[EncodedDatabaseIdField]¶

collection_type: Optional[str]¶

element_identifiers: Optional[List[CollectionElementIdentifier]]¶

tags: Optional[List[str]]¶

class galaxy.schema.schema.CreateNewCollectionPayload(*, collection_type: str = None, element_identifiers: List[CollectionElementIdentifier] = None, name: str = None, hide_source_items: bool = False, copy_elements: bool = False, instance_type: DatasetCollectionInstanceType = DatasetCollectionInstanceType.history, history_id: EncodedDatabaseIdField = None, folder_id: EncodedDatabaseIdField = 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[DatasetCollectionInstanceType]¶

history_id: Optional[EncodedDatabaseIdField]¶

folder_id: Optional[EncodedDatabaseIdField]¶

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'¶

classmethod is_compressed(value: ModelStoreFormat)[source]¶

classmethod is_bag(value: ModelStoreFormat)[source]¶

class galaxy.schema.schema.StoreContentSource(*, store_content_uri: str = None, store_dict: Dict[str, Any] = None, model_store_format: 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: str = None, store_dict: Dict[str, Any] = None, model_store_format: 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.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.JobExportHistoryArchiveModel(*, id: EncodedDatabaseIdField, job_id: EncodedDatabaseIdField, ready: bool, preparing: bool, up_to_date: bool, download_url: str, external_download_latest_url: AnyUrl, external_download_permanent_url: AnyUrl)[source]¶

Bases: Model

id: EncodedDatabaseIdField¶

job_id: EncodedDatabaseIdField¶

ready: bool¶

preparing: bool¶

up_to_date: bool¶

download_url: str¶

external_download_latest_url: AnyUrl¶

external_download_permanent_url: AnyUrl¶

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

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

Bases: BaseModel

Generic Label/Value pair model.

label: str¶

value: str¶

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

Bases: BaseModel

installed_builds: List[LabelValuePair]¶

fasta_hdas: List[LabelValuePair]¶

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

Bases: BaseModel

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

job_id: EncodedDatabaseIdField¶

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

Bases: Model

id: EncodedDatabaseIdField¶

model_class: str¶

tool_id: str¶

history_id: Optional[EncodedDatabaseIdField]¶

state: states¶

exit_code: Optional[int]¶

create_time: datetime¶

update_time: datetime¶

galaxy_version: str¶

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

Bases: JobBaseModel

message: str¶

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

Bases: Model

id: EncodedDatabaseIdField¶

model: str¶

populated_state: populated_states¶

states: Dict[states, int]¶

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

Bases: JobStateSummary

model: str¶

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

Bases: JobStateSummary

model: str¶

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

Bases: Model

id: EncodedDatabaseIdField¶

src: DatasetSourceType¶

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

Bases: DatasetSourceId

uuid: UUID4¶

class galaxy.schema.schema.JobDetails(*, id: EncodedDatabaseIdField, model_class: str = 'Job', tool_id: str, history_id: EncodedDatabaseIdField = None, state: states, exit_code: int = None, create_time: datetime, update_time: datetime, galaxy_version: str, external_id: str = None, command_line: str = None, user_email: 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, model_class: str = 'Job', tool_id: str, history_id: EncodedDatabaseIdField = None, state: states, exit_code: int = None, create_time: datetime, update_time: datetime, galaxy_version: str, external_id: str = None, command_line: str = None, user_email: 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: 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: EncodedDatabaseIdField, model_class: str = '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: EncodedDatabaseIdField¶

model_class: str¶

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: BaseModel

label: str¶

value: str¶

uuid: UUID4¶

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

Bases: BaseModel

label: Optional[str]¶

output_name: str¶

uuid: Optional[UUID4]¶

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

Bases: BaseModel

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: str, input_steps: Dict[str, InputStep])[source]¶

Bases: BaseModel

id: int¶

type: WorkflowModuleType¶

annotation: Optional[str]¶

input_steps: Dict[str, InputStep]¶

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

Bases: ToolBasedWorkflowStep

type: WorkflowModuleType¶

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

Bases: ToolBasedWorkflowStep

type: WorkflowModuleType¶

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

Bases: ToolBasedWorkflowStep

type: WorkflowModuleType¶

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

Bases: WorkflowStepBase

type: WorkflowModuleType¶

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

Bases: ToolBasedWorkflowStep

type: WorkflowModuleType¶

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

Bases: WorkflowStepBase

type: WorkflowModuleType¶

workflow_id: EncodedDatabaseIdField¶

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

Bases: BaseModel

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: str = None, alternateName: str = None, email: str = None, faxNumber: str = None, identifier: str = None, image: ~pydantic.networks.AnyHttpUrl = None, telephone: str = None, url: ~pydantic.networks.AnyHttpUrl = None)[source]¶

Bases: Creator

class_: str¶

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

Bases: 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: EncodedDatabaseIdField, model_class: str = '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: str, license: str = None, version: int, inputs: Dict[int, WorkflowInput] = {}, creator: 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: BaseModel

name: str¶

description: str¶

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

Bases: BaseModel

name: str¶

type: str¶

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

Bases: BaseModel

id: int¶

output_name: str¶

input_subworkflow_step_id: Optional[int]¶

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

Bases: BaseModel

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

bottom: int¶

top: int¶

left: int¶

right: int¶

x: int¶

y: int¶

height: int¶

width: int¶

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

Bases: BaseModel

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: str, tool_id: str = None, uuid: UUID4, label: str = None, inputs: List[Input], outputs: List[Output], input_connections: Dict[str, InputConnection] = {}, position: WorkflowStepLayoutPosition, workflow_outputs: List[WorkflowOutput] = [], content_id: str = None, tool_version: str = None, tool_state: Json, errors: 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: BaseModel

name: str¶

owner: str¶

changeset_revision: str¶

tool_shed: str¶

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

Bases: BaseModel

action_type: str¶

output_name: str¶

action_arguments: Dict[str, Any]¶

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

Bases: BaseModel

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: BaseModel

id: EncodedDatabaseIdField¶

name: str¶

type: str¶

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

Bases: BasicRoleModel

description: Optional[str]¶

url: str¶

model_class: str¶

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

Bases: BaseModel

name: str¶

description: str¶

user_ids: Optional[List[EncodedDatabaseIdField]]¶

group_ids: Optional[List[EncodedDatabaseIdField]]¶

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

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

Bases: BaseModel

id: EncodedDatabaseIdField¶

name: str¶

url: str¶

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

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

Bases: BaseModel

id: EncodedDatabaseIdField¶

email: str¶

url: str¶

class galaxy.schema.schema.GroupUserListModel(*, __root__: List[GroupUserModel])[source]¶: Bases: BaseModel

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

Bases: str, Enum

An enumeration.

current = 'current'¶

available = 'available'¶

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

Bases: BaseModel

model_class: str¶

id: EncodedDatabaseIdField¶

name: str¶

description: Optional[str]¶

synopsis: Optional[str]¶

root_folder_id: EncodedDatabaseIdField¶

create_time: datetime¶

deleted: bool¶

class galaxy.schema.schema.LibrarySummary(*, model_class: str = 'Library', id: EncodedDatabaseIdField, name: str, description: str = '', synopsis: str = None, root_folder_id: EncodedDatabaseIdField, 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: BaseModel

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

Bases: BaseModel

name: str¶

description: Optional[str]¶

synopsis: Optional[str]¶

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

Bases: BaseModel

name: Optional[str]¶

description: Optional[str]¶

synopsis: Optional[str]¶

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

Bases: BaseModel

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: BaseModel

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[EncodedDatabaseIdField], EncodedDatabaseIdField]] = [], LIBRARY_MODIFY_in: Optional[Union[List[EncodedDatabaseIdField], EncodedDatabaseIdField]] = [], LIBRARY_ADD_in: Optional[Union[List[EncodedDatabaseIdField], EncodedDatabaseIdField]] = [], LIBRARY_MANAGE_in: Optional[Union[List[EncodedDatabaseIdField], EncodedDatabaseIdField]] = [])[source]¶

Bases: BaseModel

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

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

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

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

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[EncodedDatabaseIdField], EncodedDatabaseIdField]] = [], manage_ids: Optional[Union[List[EncodedDatabaseIdField], EncodedDatabaseIdField]] = [], modify_ids: Optional[Union[List[EncodedDatabaseIdField], EncodedDatabaseIdField]] = [])[source]¶

Bases: Model

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

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

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

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

Bases: LibraryPermissionsPayloadBase

action: Optional[LibraryPermissionAction]¶

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

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[EncodedDatabaseIdField], EncodedDatabaseIdField]] = [], manage_ids: Optional[Union[List[EncodedDatabaseIdField], EncodedDatabaseIdField]] = [], modify_ids: Optional[Union[List[EncodedDatabaseIdField], EncodedDatabaseIdField]] = [], action: LibraryFolderPermissionAction = None)[source]¶

Bases: LibraryPermissionsPayloadBase

action: Optional[LibraryFolderPermissionAction]¶

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

Bases: BaseModel

model_class: str¶

id: EncodedDatabaseIdField¶

name: str¶

description: Optional[str]¶

item_count: int¶

parent_library_id: EncodedDatabaseIdField¶

parent_id: Optional[EncodedDatabaseIdField]¶

genome_build: Optional[str]¶

update_time: datetime¶

deleted: bool¶

library_path: List[str]¶

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

Bases: BaseModel

name: str¶

description: Optional[str]¶

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

Bases: BaseModel

name: Optional[str]¶

description: Optional[str]¶

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

Bases: BaseModel

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: BaseModel

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.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: DatasetPermissionAction = DatasetPermissionAction.set_permissions, access_ids: Optional[Union[List[EncodedDatabaseIdField], EncodedDatabaseIdField]] = [], manage_ids: Optional[Union[List[EncodedDatabaseIdField], EncodedDatabaseIdField]] = [], modify_ids: Optional[Union[List[EncodedDatabaseIdField], EncodedDatabaseIdField]] = [])[source]¶

Bases: Model

action: Optional[DatasetPermissionAction]¶

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

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

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

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: BaseModel

purge: bool¶

recursive: bool¶

stop_job: bool¶

class galaxy.schema.schema.DeleteHistoryContentResult(*, id: EncodedDatabaseIdField, deleted: bool, purged: 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: EncodedDatabaseIdField¶

deleted: bool¶

purged: Optional[bool]¶

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

Bases: BaseModel

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: BaseModel

total_matches: int¶

class galaxy.schema.schema.ContentsNearStats(*, matches: int, matches_up: int, matches_down: int, total_matches: int, total_matches_up: int, total_matches_down: int, max_hid: int = None, min_hid: int = None, history_size: int, history_empty: bool)[source]¶

Bases: BaseModel

Stats used by the contents_near endpoint.

matches: int¶

matches_up: int¶

matches_down: int¶

total_matches: int¶

total_matches_up: int¶

total_matches_down: int¶

max_hid: Optional[int]¶

min_hid: Optional[int]¶

history_size: int¶

history_empty: bool¶

to_headers() → Dict[str, str][source]¶

Converts all field values to json strings.

The headers values need to be json strings or updating the response headers will raise encoding errors.

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: BaseModel

Includes stats with items counting

stats: HistoryContentStats¶

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

class galaxy.schema.schema.ContentsNearResult(*, contents: HistoryContentsResult, stats: ContentsNearStats)[source]¶

Bases: BaseModel

contents: HistoryContentsResult¶

stats: ContentsNearStats¶

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: BaseModel

can_share: bool¶

class Config[source]¶

Bases: object

extra = 'allow'¶

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

Bases: BaseModel

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

share_option: Optional[SharingOptions]¶

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

Bases: BaseModel

new_slug: str¶

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

Bases: BaseModel

id: EncodedDatabaseIdField¶

email: str¶

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

Bases: BaseModel

id: EncodedDatabaseIdField¶

title: str¶

importable: bool¶

published: bool¶

users_shared_with: List[UserEmail]¶

username_and_slug: Optional[str]¶

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

Bases: SharingStatus

errors: List[str]¶

extra: Optional[ShareWithExtra]¶

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

Bases: BaseModel

id: EncodedDatabaseIdField¶

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: BaseModel

title: str¶

slug: str¶

class galaxy.schema.schema.MaterializeDatasetInstanceAPIRequest(*, source: DatasetSourceType = None, content: EncodedDatabaseIdField = None)[source]¶

Bases: Model

source: DatasetSourceType¶

content: EncodedDatabaseIdField¶

class galaxy.schema.schema.MaterializeDatasetInstanceRequest(*, source: DatasetSourceType = None, content: EncodedDatabaseIdField = None, history_id: EncodedDatabaseIdField)[source]¶

Bases: MaterializeDatasetInstanceAPIRequest

history_id: EncodedDatabaseIdField¶

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

Bases: PageSummaryBase

content_format: PageContentFormat¶

content: Optional[str]¶

annotation: Optional[str]¶

invocation_id: Optional[EncodedDatabaseIdField]¶

class Config[source]¶

Bases: object

use_enum_values = True¶

extra = 'allow'¶

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

Bases: BaseModel

id: str¶

ignored: bool¶

name: Optional[str]¶

queue: Optional[str]¶

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

Bases: BaseModel

storage_request_id: str¶

task: AsyncTaskResultSummary¶

class galaxy.schema.schema.PageSummary(*, title: str, slug: ConstrainedStrValue, id: EncodedDatabaseIdField, model_class: str, username: str, published: bool, importable: bool, deleted: bool, latest_revision_id: EncodedDatabaseIdField, revision_ids: List[EncodedDatabaseIdField])[source]¶

Bases: PageSummaryBase

id: EncodedDatabaseIdField¶

model_class: str¶

username: str¶

published: bool¶

importable: bool¶

deleted: bool¶

latest_revision_id: EncodedDatabaseIdField¶

revision_ids: List[EncodedDatabaseIdField]¶

class galaxy.schema.schema.PageDetails(*, title: str, slug: ConstrainedStrValue, id: EncodedDatabaseIdField, model_class: str, username: str, published: bool, importable: bool, deleted: bool, latest_revision_id: EncodedDatabaseIdField, revision_ids: List[EncodedDatabaseIdField], content_format: PageContentFormat = PageContentFormat.html, content: str = '', generate_version: str = None, generate_time: 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: BaseModel

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: str, history_dataset_collection_association_id: int)[source]¶

Bases: BaseModel

short_term_storage_request_id: str¶

history_dataset_collection_association_id: int¶

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

Bases: BaseModel

short_term_storage_request_id: str¶

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, history_id: int, short_term_storage_request_id: str, user: RequestUser)[source]¶

Bases: StoreExportPayload

history_id: int¶

short_term_storage_request_id: str¶

user: RequestUser¶

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, content_type: HistoryContentType, content_id: int, short_term_storage_request_id: str, user: RequestUser)[source]¶

Bases: StoreExportPayload

content_type: HistoryContentType¶

content_id: int¶

short_term_storage_request_id: str¶

user: RequestUser¶

class galaxy.schema.tasks.GenerateInvocationDownload(*, model_store_format: ModelStoreFormat = ModelStoreFormat.TAR_DOT_GZ, include_files: bool = True, include_deleted: bool = False, include_hidden: bool = False, invocation_id: int, short_term_storage_request_id: str, user: RequestUser)[source]¶

Bases: StoreExportPayload

invocation_id: int¶

short_term_storage_request_id: str¶

user: RequestUser¶

class galaxy.schema.tasks.WriteInvocationTo(*, 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

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)[source]¶

Bases: WriteStoreToPayload

history_id: int¶

user: RequestUser¶

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

Bases: BaseModel

history_id: int¶

user: RequestUser¶

source: DatasetSourceType¶

content: int¶

galaxy.schema.types module¶

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

Bases: datetime

classmethod validate(v)[source]¶