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
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]
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

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: 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

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: 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]

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: 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: