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galaxy.schema package¶
- class galaxy.schema.BootstrapAdminUser(*, email: Optional[str] = None, preferences: Dict[str, str] = {}, id: int = 0, bootstrap_admin_user: bool = True)[source]¶
Bases:
BaseModel
- 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.
- class galaxy.schema.PaginationQueryParams(*, offset: Optional[ConstrainedIntValue] = 0, limit: Optional[ConstrainedIntValue] = None)[source]¶
Bases:
BaseModel
Used to paginate a the request results by limiting and offsetting.
- class galaxy.schema.FilterQueryParams(*, offset: Optional[ConstrainedIntValue] = 0, limit: Optional[ConstrainedIntValue] = None, q: Optional[Union[List[str], str]] = None, qv: Optional[Union[List[str], str]] = None, order: Optional[str] = None)[source]¶
Bases:
ValueFilterQueryParams
,PaginationQueryParams
Contains full filtering options to query elements, paginate and order them.
- class galaxy.schema.SerializationParams(*, view: Optional[str] = None, keys: Optional[List[str]] = None, default_view: Optional[str] = None)[source]¶
Bases:
BaseModel
Contains common parameters for customizing model serialization.
- class galaxy.schema.PdfDocumentType(value)[source]¶
-
An enumeration.
- invocation_report = 'invocation_report'¶
- page = 'page'¶
Submodules¶
galaxy.schema.fetch_data module¶
- class galaxy.schema.fetch_data.ElementsFromType(value)[source]¶
-
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
- class galaxy.schema.fetch_data.ItemsFromSrc(value)[source]¶
-
An enumeration.
- url = 'url'¶
- files = 'files'¶
- path = 'path'¶
- ftp_import = 'ftp_import'¶
- server_dir = 'server_dir'¶
- class galaxy.schema.fetch_data.Src(value)[source]¶
-
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]¶
-
An enumeration.
- library = 'library'¶
- library_folder = 'library_folder'¶
- hdcas = 'hdcas'¶
- hdas = 'hdas'¶
- class galaxy.schema.fetch_data.HdaDestination(*, type: typing_extensions.Literal[hdas])[source]¶
Bases:
FetchBaseModel
- type: typing_extensions.Literal[hdas]¶
- class galaxy.schema.fetch_data.HdcaDestination(*, type: typing_extensions.Literal[hdca])[source]¶
Bases:
FetchBaseModel
- type: typing_extensions.Literal[hdca]¶
- class galaxy.schema.fetch_data.LibraryFolderDestination(*, type: typing_extensions.Literal[library_folder], library_folder_id: DecodedDatabaseIdField)[source]¶
Bases:
FetchBaseModel
- type: typing_extensions.Literal[library_folder]¶
- library_folder_id: DecodedDatabaseIdField¶
- class galaxy.schema.fetch_data.BaseCollectionTarget(*, auto_decompress: bool = False, destination: HdcaDestination, collection_type: Optional[str] = None, tags: Optional[List[str]] = None, name: Optional[str] = None)[source]¶
Bases:
BaseFetchDataTarget
- destination: HdcaDestination¶
- class galaxy.schema.fetch_data.LibraryDestination(*, type: typing_extensions.Literal[library], name: str, description: Optional[str] = None, synopsis: Optional[str] = None)[source]¶
Bases:
FetchBaseModel
- type: typing_extensions.Literal[library]¶
- class galaxy.schema.fetch_data.ExtraFiles(*, items_from: Optional[str] = None, src: Src, fuzzy_root: Optional[bool] = True)[source]¶
Bases:
FetchBaseModel
- class galaxy.schema.fetch_data.BaseDataElement(*, name: Optional[str] = None, dbkey: str = '?', info: Optional[str] = None, ext: str = 'auto', space_to_tab: bool = False, to_posix_lines: bool = False, deferred: bool = False, tags: Optional[List[str]] = None, created_from_basename: Optional[str] = None, extra_files: Optional[ExtraFiles] = None, auto_decompress: bool = False, elements_from: Optional[ElementsFromType] = None, collection_type: Optional[str] = None, MD5: Optional[str] = None, description: Optional[str] = None)[source]¶
Bases:
FetchBaseModel
- extra_files: Optional[ExtraFiles]¶
- items_from: Optional[ElementsFromType]¶
- class galaxy.schema.fetch_data.FileDataElement(*, name: Optional[str] = None, dbkey: str = '?', info: Optional[str] = None, ext: str = 'auto', space_to_tab: bool = False, to_posix_lines: bool = False, deferred: bool = False, tags: Optional[List[str]] = None, created_from_basename: Optional[str] = None, extra_files: Optional[ExtraFiles] = None, auto_decompress: bool = False, elements_from: Optional[ElementsFromType] = None, collection_type: Optional[str] = None, MD5: Optional[str] = None, description: Optional[str] = None, src: typing_extensions.Literal[files])[source]¶
Bases:
BaseDataElement
- src: typing_extensions.Literal[files]¶
- class galaxy.schema.fetch_data.PastedDataElement(*, name: Optional[str] = None, dbkey: str = '?', info: Optional[str] = None, ext: str = 'auto', space_to_tab: bool = False, to_posix_lines: bool = False, deferred: bool = False, tags: Optional[List[str]] = None, created_from_basename: Optional[str] = None, extra_files: Optional[ExtraFiles] = None, auto_decompress: bool = False, elements_from: Optional[ElementsFromType] = None, collection_type: Optional[str] = None, MD5: Optional[str] = None, description: Optional[str] = None, src: typing_extensions.Literal[pasted], paste_content: str)[source]¶
Bases:
BaseDataElement
- src: typing_extensions.Literal[pasted]¶
- class galaxy.schema.fetch_data.UrlDataElement(*, name: Optional[str] = None, dbkey: str = '?', info: Optional[str] = None, ext: str = 'auto', space_to_tab: bool = False, to_posix_lines: bool = False, deferred: bool = False, tags: Optional[List[str]] = None, created_from_basename: Optional[str] = None, extra_files: Optional[ExtraFiles] = None, auto_decompress: bool = False, elements_from: Optional[ElementsFromType] = None, collection_type: Optional[str] = None, MD5: Optional[str] = None, description: Optional[str] = None, src: typing_extensions.Literal[url], url: str)[source]¶
Bases:
BaseDataElement
- src: typing_extensions.Literal[url]¶
- class galaxy.schema.fetch_data.ServerDirElement(*, name: Optional[str] = None, dbkey: str = '?', info: Optional[str] = None, ext: str = 'auto', space_to_tab: bool = False, to_posix_lines: bool = False, deferred: bool = False, tags: Optional[List[str]] = None, created_from_basename: Optional[str] = None, extra_files: Optional[ExtraFiles] = None, auto_decompress: bool = False, elements_from: Optional[ElementsFromType] = None, collection_type: Optional[str] = None, MD5: Optional[str] = None, description: Optional[str] = None, src: typing_extensions.Literal[server_dir], server_dir: str, link_data_only: Optional[bool] = None)[source]¶
Bases:
BaseDataElement
- src: typing_extensions.Literal[server_dir]¶
- class galaxy.schema.fetch_data.FtpImportElement(*, name: Optional[str] = None, dbkey: str = '?', info: Optional[str] = None, ext: str = 'auto', space_to_tab: bool = False, to_posix_lines: bool = False, deferred: bool = False, tags: Optional[List[str]] = None, created_from_basename: Optional[str] = None, extra_files: Optional[ExtraFiles] = None, auto_decompress: bool = False, elements_from: Optional[ElementsFromType] = None, collection_type: Optional[str] = None, MD5: Optional[str] = None, description: Optional[str] = None, src: typing_extensions.Literal[ftp_import], ftp_path: str)[source]¶
Bases:
BaseDataElement
- src: typing_extensions.Literal[ftp_import]¶
- items_from: Optional[ElementsFromType]¶
- class galaxy.schema.fetch_data.ItemsFromModel(*, src: ItemsFromSrc, path: Optional[str] = None, ftp_path: Optional[str] = None, server_dir: Optional[str] = None, url: Optional[str] = None)[source]¶
Bases:
Model
- src: ItemsFromSrc¶
- class galaxy.schema.fetch_data.FtpImportTarget(*, auto_decompress: bool = False, destination: HdcaDestination, collection_type: Optional[str] = None, tags: Optional[List[str]] = None, name: Optional[str] = None, src: typing_extensions.Literal[ftp_import], ftp_path: str, elements_from: Optional[ElementsFromType] = None)[source]¶
Bases:
BaseCollectionTarget
- src: typing_extensions.Literal[ftp_import]¶
- items_from: Optional[ElementsFromType]¶
- class galaxy.schema.fetch_data.PathDataElement(*, name: Optional[str] = None, dbkey: str = '?', info: Optional[str] = None, ext: str = 'auto', space_to_tab: bool = False, to_posix_lines: bool = False, deferred: bool = False, tags: Optional[List[str]] = None, created_from_basename: Optional[str] = None, extra_files: Optional[ExtraFiles] = None, auto_decompress: bool = False, elements_from: Optional[ElementsFromType] = None, collection_type: Optional[str] = None, MD5: Optional[str] = None, description: Optional[str] = None, src: typing_extensions.Literal[path], path: str, link_data_only: Optional[bool] = None)[source]¶
Bases:
BaseDataElement
- src: typing_extensions.Literal[path]¶
- items_from: Optional[ElementsFromType]¶
- class galaxy.schema.fetch_data.CompositeDataElement(*, name: Optional[str] = None, dbkey: str = '?', info: Optional[str] = None, ext: str = 'auto', space_to_tab: bool = False, to_posix_lines: bool = False, deferred: bool = False, tags: Optional[List[str]] = None, created_from_basename: Optional[str] = None, extra_files: Optional[ExtraFiles] = None, auto_decompress: bool = False, elements_from: Optional[ElementsFromType] = None, collection_type: Optional[str] = None, MD5: Optional[str] = None, description: Optional[str] = None, src: typing_extensions.Literal[composite], composite: CompositeItems)[source]¶
Bases:
BaseDataElement
- src: typing_extensions.Literal[composite]¶
- composite: CompositeItems¶
- class galaxy.schema.fetch_data.CompositeItems(*, elements: List[Union[FileDataElement, PastedDataElement, UrlDataElement, PathDataElement, ServerDirElement, FtpImportElement]])[source]¶
Bases:
FetchBaseModel
- class galaxy.schema.fetch_data.NestedElement(*, name: Optional[str] = None, dbkey: str = '?', info: Optional[str] = None, ext: str = 'auto', space_to_tab: bool = False, to_posix_lines: bool = False, deferred: bool = False, tags: Optional[List[str]] = None, created_from_basename: Optional[str] = None, extra_files: Optional[ExtraFiles] = None, auto_decompress: bool = False, elements_from: Optional[ElementsFromType] = None, collection_type: Optional[str] = None, MD5: Optional[str] = None, description: Optional[str] = None, elements: List[Union[AnyElement, NestedElement]])[source]¶
Bases:
BaseDataElement
- items: List[Union[Union[galaxy.schema.fetch_data.FileDataElement, galaxy.schema.fetch_data.PastedDataElement, galaxy.schema.fetch_data.UrlDataElement, galaxy.schema.fetch_data.PathDataElement, galaxy.schema.fetch_data.ServerDirElement, galaxy.schema.fetch_data.FtpImportElement, galaxy.schema.fetch_data.CompositeDataElement][Union[FileDataElement, PastedDataElement, UrlDataElement, PathDataElement, ServerDirElement, FtpImportElement, CompositeDataElement]], NestedElement]]¶
- class galaxy.schema.fetch_data.BaseDataTarget(*, auto_decompress: bool = False, destination: Union[HdaDestination, LibraryFolderDestination, LibraryDestination])[source]¶
Bases:
BaseFetchDataTarget
- destination: Union[HdaDestination, LibraryFolderDestination, LibraryDestination]¶
- class galaxy.schema.fetch_data.DataElementsTarget(*, auto_decompress: bool = False, destination: Union[HdaDestination, LibraryFolderDestination, LibraryDestination], elements: List[Union[Union[galaxy.schema.fetch_data.FileDataElement, galaxy.schema.fetch_data.PastedDataElement, galaxy.schema.fetch_data.UrlDataElement, galaxy.schema.fetch_data.PathDataElement, galaxy.schema.fetch_data.ServerDirElement, galaxy.schema.fetch_data.FtpImportElement, galaxy.schema.fetch_data.CompositeDataElement][Union[FileDataElement, PastedDataElement, UrlDataElement, PathDataElement, ServerDirElement, FtpImportElement, CompositeDataElement]], NestedElement]])[source]¶
Bases:
BaseDataTarget
- items: List[Union[Union[galaxy.schema.fetch_data.FileDataElement, galaxy.schema.fetch_data.PastedDataElement, galaxy.schema.fetch_data.UrlDataElement, galaxy.schema.fetch_data.PathDataElement, galaxy.schema.fetch_data.ServerDirElement, galaxy.schema.fetch_data.FtpImportElement, galaxy.schema.fetch_data.CompositeDataElement][Union[FileDataElement, PastedDataElement, UrlDataElement, PathDataElement, ServerDirElement, FtpImportElement, CompositeDataElement]], NestedElement]]¶
- class galaxy.schema.fetch_data.DataElementsFromTarget(*, src: ItemsFromSrc, path: Optional[str] = None, ftp_path: Optional[str] = None, server_dir: Optional[str] = None, url: Optional[str] = None, auto_decompress: bool = False, destination: Union[HdaDestination, LibraryFolderDestination, LibraryDestination], elements_from: ElementsFromType)[source]¶
Bases:
BaseDataTarget
,ItemsFromModel
- items_from: ElementsFromType¶
- class galaxy.schema.fetch_data.HdcaDataItemsTarget(*, auto_decompress: bool = False, destination: HdcaDestination, collection_type: Optional[str] = None, tags: Optional[List[str]] = None, name: Optional[str] = None, elements: List[Union[Union[galaxy.schema.fetch_data.FileDataElement, galaxy.schema.fetch_data.PastedDataElement, galaxy.schema.fetch_data.UrlDataElement, galaxy.schema.fetch_data.PathDataElement, galaxy.schema.fetch_data.ServerDirElement, galaxy.schema.fetch_data.FtpImportElement, galaxy.schema.fetch_data.CompositeDataElement][Union[FileDataElement, PastedDataElement, UrlDataElement, PathDataElement, ServerDirElement, FtpImportElement, CompositeDataElement]], NestedElement]])[source]¶
Bases:
BaseCollectionTarget
- items: List[Union[Union[galaxy.schema.fetch_data.FileDataElement, galaxy.schema.fetch_data.PastedDataElement, galaxy.schema.fetch_data.UrlDataElement, galaxy.schema.fetch_data.PathDataElement, galaxy.schema.fetch_data.ServerDirElement, galaxy.schema.fetch_data.FtpImportElement, galaxy.schema.fetch_data.CompositeDataElement][Union[FileDataElement, PastedDataElement, UrlDataElement, PathDataElement, ServerDirElement, FtpImportElement, CompositeDataElement]], NestedElement]]¶
- class galaxy.schema.fetch_data.HdcaDataItemsFromTarget(*, src: ItemsFromSrc, path: Optional[str] = None, ftp_path: Optional[str] = None, server_dir: Optional[str] = None, url: Optional[str] = None, auto_decompress: bool = False, destination: HdcaDestination, collection_type: Optional[str] = None, tags: Optional[List[str]] = None, name: Optional[str] = None, elements_from: ElementsFromType)[source]¶
Bases:
BaseCollectionTarget
,ItemsFromModel
- items_from: ElementsFromType¶
- class galaxy.schema.fetch_data.FilesPayload(*, filename: str, local_filename: str)[source]¶
Bases:
Model
- class galaxy.schema.fetch_data.BaseDataPayload(*, history_id: DecodedDatabaseIdField, **extra_data: Any)[source]¶
Bases:
FetchBaseModel
- history_id: DecodedDatabaseIdField¶
- class galaxy.schema.fetch_data.FetchDataPayload(*, history_id: DecodedDatabaseIdField, targets: List[Union[DataElementsTarget, HdcaDataItemsTarget, DataElementsFromTarget, HdcaDataItemsFromTarget, FtpImportTarget]], **extra_data: Any)[source]¶
Bases:
BaseDataPayload
- class galaxy.schema.fetch_data.FetchDataFormPayload(*, history_id: DecodedDatabaseIdField, targets: Union[JsonWrapperValue, List[Union[DataElementsTarget, HdcaDataItemsTarget, DataElementsFromTarget, HdcaDataItemsFromTarget, FtpImportTarget]]], **extra_data: Any)[source]¶
Bases:
BaseDataPayload
- targets: Union[JsonWrapperValue, List[Union[DataElementsTarget, HdcaDataItemsTarget, DataElementsFromTarget, HdcaDataItemsFromTarget, FtpImportTarget]]]¶
galaxy.schema.fields module¶
- class galaxy.schema.fields.BaseDatabaseIdField[source]¶
Bases:
object
Database ID validation.
- security: IdEncodingHelper¶
- class galaxy.schema.fields.DecodedDatabaseIdField[source]¶
Bases:
int
,BaseDatabaseIdField
- security: IdEncodingHelper¶
- class galaxy.schema.fields.EncodedDatabaseIdField[source]¶
Bases:
str
,BaseDatabaseIdField
- security: IdEncodingHelper¶
- class galaxy.schema.fields.LibraryFolderDatabaseIdField[source]¶
Bases:
int
,BaseDatabaseIdField
- security: IdEncodingHelper¶
- class galaxy.schema.fields.EncodedLibraryFolderDatabaseIdField[source]¶
Bases:
str
,BaseDatabaseIdField
- security: IdEncodingHelper¶
galaxy.schema.remote_files module¶
- class galaxy.schema.remote_files.RemoteFilesTarget(value)[source]¶
-
An enumeration.
- ftpdir = 'ftpdir'¶
- userdir = 'userdir'¶
- importdir = 'importdir'¶
- class galaxy.schema.remote_files.RemoteFilesFormat(value)[source]¶
-
An enumeration.
- flat = 'flat'¶
- jstree = 'jstree'¶
- uri = 'uri'¶
- class galaxy.schema.remote_files.RemoteFilesDisableMode(value)[source]¶
-
An enumeration.
- folders = 'folders'¶
- files = 'files'¶
- class galaxy.schema.remote_files.FilesSourcePlugin(*, id: str, type: str, uri_root: Optional[str] = None, label: str, doc: str, writable: bool, requires_roles: Optional[str] = None, requires_groups: Optional[str] = None, **extra_data: Any)[source]¶
Bases:
Model
- class galaxy.schema.remote_files.FilesSourcePluginList(*, __root__: List[FilesSourcePlugin] = [])[source]¶
Bases:
Model
galaxy.schema.schema module¶
This module contains general pydantic models and common schema field annotations for them.
- class galaxy.schema.schema.DatasetState(value)[source]¶
-
An enumeration.
- NEW = 'new'¶
- UPLOAD = 'upload'¶
- QUEUED = 'queued'¶
- RUNNING = 'running'¶
- OK = 'ok'¶
- EMPTY = 'empty'¶
- ERROR = 'error'¶
- PAUSED = 'paused'¶
- SETTING_METADATA = 'setting_metadata'¶
- FAILED_METADATA = 'failed_metadata'¶
- DEFERRED = 'deferred'¶
- DISCARDED = 'discarded'¶
- class galaxy.schema.schema.JobState(value)[source]¶
-
An enumeration.
- NEW = 'new'¶
- RESUBMITTED = 'resubmitted'¶
- UPLOAD = 'upload'¶
- WAITING = 'waiting'¶
- QUEUED = 'queued'¶
- RUNNING = 'running'¶
- OK = 'ok'¶
- ERROR = 'error'¶
- FAILED = 'failed'¶
- PAUSED = 'paused'¶
- DELETING = 'deleting'¶
- DELETED = 'deleted'¶
- STOPPING = 'stop'¶
- STOPPED = 'stopped'¶
- SKIPPED = 'skipped'¶
- class galaxy.schema.schema.DatasetCollectionPopulatedState(value)[source]¶
-
An enumeration.
- NEW = 'new'¶
- OK = 'ok'¶
- FAILED = 'failed'¶
- class galaxy.schema.schema.Model[source]¶
Bases:
BaseModel
Base model definition with common configuration used by all derived models.
- class Config[source]¶
Bases:
object
- use_enum_values = True¶
- allow_population_by_field_name = True¶
- json_encoders = {<class 'galaxy.schema.fields.DecodedDatabaseIdField'>: <function Model.Config.<lambda>>, <class 'galaxy.schema.fields.LibraryFolderDatabaseIdField'>: <function Model.Config.<lambda>>}¶
- class galaxy.schema.schema.UserModel(*, id: DecodedDatabaseIdField, username: str, email: str, active: bool, deleted: bool, last_password_change: Optional[datetime] = None, model_class: typing_extensions.Literal[User] = 'User')[source]¶
Bases:
Model
User in a transaction context.
- class galaxy.schema.schema.GroupModel(*, model_class: typing_extensions.Literal[Group] = 'Group', id: DecodedDatabaseIdField, name: str)[source]¶
Bases:
Model
User group model
- class galaxy.schema.schema.JobSourceType(value)[source]¶
-
Available types of job sources (model classes) that produce dataset collections.
- Job = 'Job'¶
- ImplicitCollectionJobs = 'ImplicitCollectionJobs'¶
- WorkflowInvocation = 'WorkflowInvocation'¶
- class galaxy.schema.schema.HistoryContentType(value)[source]¶
-
Available types of History contents.
- dataset = 'dataset'¶
- dataset_collection = 'dataset_collection'¶
- class galaxy.schema.schema.HistoryImportArchiveSourceType(value)[source]¶
-
Available types of History archive sources.
- url = 'url'¶
- file = 'file'¶
- class galaxy.schema.schema.DCEType(value)[source]¶
-
Available types of dataset collection elements.
- hda = 'hda'¶
- dataset_collection = 'dataset_collection'¶
- class galaxy.schema.schema.DatasetSourceType(value)[source]¶
-
An enumeration.
- hda = 'hda'¶
- ldda = 'ldda'¶
- class galaxy.schema.schema.ColletionSourceType(value)[source]¶
-
An enumeration.
- hda = 'hda'¶
- ldda = 'ldda'¶
- hdca = 'hdca'¶
- new_collection = 'new_collection'¶
- class galaxy.schema.schema.HistoryContentSource(value)[source]¶
-
An enumeration.
- hda = 'hda'¶
- hdca = 'hdca'¶
- library = 'library'¶
- library_folder = 'library_folder'¶
- new_collection = 'new_collection'¶
- class galaxy.schema.schema.TagItem[source]¶
Bases:
ConstrainedStr
- regex = re.compile('^([^\\s.:])+(.[^\\s.:]+)*(:[^\\s.:]+)?$')¶
- class galaxy.schema.schema.TagCollection(*, __root__: List[TagItem])[source]¶
Bases:
Model
Represents the collection of tags associated with an item.
- class galaxy.schema.schema.MetadataFile(*, file_type: str, download_url: str)[source]¶
Bases:
Model
Metadata file associated with a dataset.
- class galaxy.schema.schema.DatasetPermissions(*, manage: List[DecodedDatabaseIdField] = [], access: List[DecodedDatabaseIdField] = [])[source]¶
Bases:
Model
Role-based permissions for accessing and managing a dataset.
- manage: List[DecodedDatabaseIdField]¶
- access: List[DecodedDatabaseIdField]¶
- class galaxy.schema.schema.Hyperlink(*, target: str, href: AnyUrl, text: str)[source]¶
Bases:
Model
Represents some text with an Hyperlink.
- href: AnyUrl¶
- class galaxy.schema.schema.DisplayApp(*, label: str, links: List[Hyperlink])[source]¶
Bases:
Model
Basic linked information about an application that can display certain datatypes.
- class galaxy.schema.schema.HistoryItemBase(*, id: DecodedDatabaseIdField, name: Optional[str] = None, history_id: DecodedDatabaseIdField, hid: int, history_content_type: HistoryContentType, deleted: bool, visible: bool)[source]¶
Bases:
Model
Basic information provided by items contained in a History.
- history_id: DecodedDatabaseIdField¶
- history_content_type: HistoryContentType¶
- class galaxy.schema.schema.HistoryItemCommon(*, id: DecodedDatabaseIdField, name: Optional[str] = None, history_id: DecodedDatabaseIdField, hid: int, history_content_type: HistoryContentType, deleted: bool, visible: bool, type_id: Optional[str] = None, type: str, create_time: Optional[datetime] = None, update_time: Optional[datetime] = None, url: str, tags: TagCollection, **extra_data: Any)[source]¶
Bases:
HistoryItemBase
Common information provided by items contained in a History.
- tags: TagCollection¶
- class galaxy.schema.schema.HDASummary(*, id: DecodedDatabaseIdField, name: Optional[str] = None, history_id: DecodedDatabaseIdField, hid: int, history_content_type: HistoryContentType, deleted: bool, visible: bool, type_id: Optional[str] = None, type: str, create_time: Optional[datetime] = None, update_time: Optional[datetime] = None, url: str, tags: TagCollection, dataset_id: DecodedDatabaseIdField, state: DatasetState, extension: str, purged: bool, **extra_data: Any)[source]¶
Bases:
HistoryItemCommon
History Dataset Association summary information.
- dataset_id: DecodedDatabaseIdField¶
- state: DatasetState¶
- class galaxy.schema.schema.HDAInaccessible(*, id: DecodedDatabaseIdField, name: Optional[str] = None, history_id: DecodedDatabaseIdField, hid: int, history_content_type: HistoryContentType, deleted: bool, visible: bool, accessible: bool, state: DatasetState)[source]¶
Bases:
HistoryItemBase
History Dataset Association information when the user can not access it.
- state: DatasetState¶
- class galaxy.schema.schema.DatasetValidatedState(value)[source]¶
-
An enumeration.
- UNKNOWN = 'unknown'¶
- INVALID = 'invalid'¶
- OK = 'ok'¶
- class galaxy.schema.schema.HDADetailed(*, id: DecodedDatabaseIdField, name: Optional[str] = None, history_id: DecodedDatabaseIdField, hid: int, history_content_type: HistoryContentType, deleted: bool, visible: bool, type_id: Optional[str] = None, type: typing_extensions.Literal[file][typing_extensions.Literal[file]] = 'file', create_time: Optional[datetime] = None, update_time: Optional[datetime] = None, url: str, tags: TagCollection, dataset_id: DecodedDatabaseIdField, state: DatasetState, extension: str, purged: bool, model_class: typing_extensions.Literal[HistoryDatasetAssociation][typing_extensions.Literal[HistoryDatasetAssociation]], hda_ldda: DatasetSourceType = DatasetSourceType.hda, accessible: bool, genome_build: Optional[str] = '?', misc_info: Optional[str] = None, misc_blurb: Optional[str] = None, file_ext: str, file_size: int, resubmitted: bool, metadata: Optional[Any] = None, metadata_dbkey: Optional[str] = '?', metadata_data_lines: int = 0, meta_files: List[MetadataFile], data_type: str, peek: Optional[str] = None, creating_job: str, rerunnable: bool, uuid: UUID4, permissions: DatasetPermissions, file_name: Optional[str] = None, display_apps: List[DisplayApp], display_types: List[DisplayApp], visualizations: List[Visualization], validated_state: DatasetValidatedState, validated_state_message: Optional[str], annotation: Optional[str], download_url: str, api_type: typing_extensions.Literal[file][typing_extensions.Literal[file]] = 'file', created_from_basename: Optional[str] = None, **extra_data: Any)[source]¶
Bases:
HDASummary
History Dataset Association detailed information.
- model_class: typing_extensions.Literal[HistoryDatasetAssociation][typing_extensions.Literal[HistoryDatasetAssociation]]¶
- hda_ldda: DatasetSourceType¶
- meta_files: List[MetadataFile]¶
- uuid: UUID4¶
- permissions: DatasetPermissions¶
- display_apps: List[DisplayApp]¶
- display_types: List[DisplayApp]¶
- visualizations: List[Visualization]¶
- validated_state: DatasetValidatedState¶
- type: typing_extensions.Literal[file][typing_extensions.Literal[file]]¶
- api_type: typing_extensions.Literal[file][typing_extensions.Literal[file]]¶
- class galaxy.schema.schema.HDAExtended(*, id: DecodedDatabaseIdField, name: Optional[str] = None, history_id: DecodedDatabaseIdField, hid: int, history_content_type: HistoryContentType, deleted: bool, visible: bool, type_id: Optional[str] = None, type: typing_extensions.Literal[file][typing_extensions.Literal[file]] = 'file', create_time: Optional[datetime] = None, update_time: Optional[datetime] = None, url: str, tags: TagCollection, dataset_id: DecodedDatabaseIdField, state: DatasetState, extension: str, purged: bool, model_class: typing_extensions.Literal[HistoryDatasetAssociation][typing_extensions.Literal[HistoryDatasetAssociation]], hda_ldda: DatasetSourceType = DatasetSourceType.hda, accessible: bool, genome_build: Optional[str] = '?', misc_info: Optional[str] = None, misc_blurb: Optional[str] = None, file_ext: str, file_size: int, resubmitted: bool, metadata: Optional[Any] = None, metadata_dbkey: Optional[str] = '?', metadata_data_lines: int = 0, meta_files: List[MetadataFile], data_type: str, peek: Optional[str] = None, creating_job: str, rerunnable: bool, uuid: UUID4, permissions: DatasetPermissions, file_name: Optional[str] = None, display_apps: List[DisplayApp], display_types: List[DisplayApp], visualizations: List[Visualization], validated_state: DatasetValidatedState, validated_state_message: Optional[str], annotation: Optional[str], download_url: str, api_type: typing_extensions.Literal[file][typing_extensions.Literal[file]] = 'file', created_from_basename: Optional[str] = None, tool_version: str, parent_id: Optional[DecodedDatabaseIdField] = None, designation: Optional[str] = None, **extra_data: Any)[source]¶
Bases:
HDADetailed
History Dataset Association extended information.
- parent_id: Optional[DecodedDatabaseIdField]¶
- class galaxy.schema.schema.DCSummary(*, model_class: typing_extensions.Literal[DatasetCollection] = 'DatasetCollection', id: DecodedDatabaseIdField, create_time: datetime, update_time: datetime, collection_type: str, populated_state: DatasetCollectionPopulatedState, populated_state_message: Optional[str] = None, element_count: Optional[int] = None)[source]¶
Bases:
Model
Dataset Collection summary information.
- model_class: typing_extensions.Literal[DatasetCollection]¶
- populated_state: DatasetCollectionPopulatedState¶
- class galaxy.schema.schema.HDAObject(*, id: DecodedDatabaseIdField, model_class: typing_extensions.Literal[HistoryDatasetAssociation] = 'HistoryDatasetAssociation', state: DatasetState, hda_ldda: DatasetSourceType = DatasetSourceType.hda, history_id: DecodedDatabaseIdField, tags: List[str], **extra_data: Any)[source]¶
Bases:
Model
History Dataset Association Object
- model_class: typing_extensions.Literal[HistoryDatasetAssociation]¶
- state: DatasetState¶
- hda_ldda: DatasetSourceType¶
- history_id: DecodedDatabaseIdField¶
- class galaxy.schema.schema.DCObject(*, id: DecodedDatabaseIdField, model_class: typing_extensions.Literal[DatasetCollection] = 'DatasetCollection', collection_type: str, populated: Optional[bool] = None, element_count: Optional[int] = None, contents_url: Optional[str] = None, elements: List[DCESummary] = [])[source]¶
Bases:
Model
Dataset Collection Object
- model_class: typing_extensions.Literal[DatasetCollection]¶
- elements: List[DCESummary]¶
- class galaxy.schema.schema.DCESummary(*, id: DecodedDatabaseIdField, model_class: typing_extensions.Literal[DatasetCollectionElement] = 'DatasetCollectionElement', element_index: int, element_identifier: str, element_type: DCEType, object: Union[HDAObject, HDADetailed, DCObject])[source]¶
Bases:
Model
Dataset Collection Element summary information.
- model_class: typing_extensions.Literal[DatasetCollectionElement]¶
- object: Union[HDAObject, HDADetailed, DCObject]¶
- class galaxy.schema.schema.DCDetailed(*, model_class: typing_extensions.Literal[DatasetCollection] = 'DatasetCollection', id: DecodedDatabaseIdField, create_time: datetime, update_time: datetime, collection_type: str, populated_state: DatasetCollectionPopulatedState, populated_state_message: Optional[str] = None, element_count: Optional[int] = None, populated: bool, elements: List[DCESummary] = [])[source]¶
Bases:
DCSummary
Dataset Collection detailed information.
- elements: List[DCESummary]¶
- class galaxy.schema.schema.HDCJobStateSummary(*, all_jobs: int = 0, new: int = 0, waiting: int = 0, running: int = 0, error: int = 0, paused: int = 0, skipped: int = 0, deleted_new: int = 0, resubmitted: int = 0, queued: int = 0, ok: int = 0, failed: int = 0, deleted: int = 0, upload: int = 0)[source]¶
Bases:
Model
Overview of the job states working inside a dataset collection.
- class galaxy.schema.schema.HDCASummary(*, id: DecodedDatabaseIdField, name: Optional[str] = None, history_id: DecodedDatabaseIdField, hid: int, history_content_type: HistoryContentType, deleted: bool, visible: bool, type_id: Optional[str] = None, type: typing_extensions.Literal[collection][typing_extensions.Literal[collection]] = 'collection', create_time: Optional[datetime] = None, update_time: Optional[datetime] = None, url: str, tags: TagCollection, model_class: typing_extensions.Literal[HistoryDatasetCollectionAssociation] = 'HistoryDatasetCollectionAssociation', collection_type: str, populated_state: DatasetCollectionPopulatedState, populated_state_message: Optional[str] = None, element_count: Optional[int] = None, job_source_id: Optional[DecodedDatabaseIdField] = None, job_source_type: Optional[JobSourceType] = None, job_state_summary: Optional[HDCJobStateSummary] = None, contents_url: str, collection_id: DecodedDatabaseIdField, **extra_data: Any)[source]¶
Bases:
HistoryItemCommon
History Dataset Collection Association summary information.
- model_class: typing_extensions.Literal[HistoryDatasetCollectionAssociation]¶
- type: typing_extensions.Literal[collection][typing_extensions.Literal[collection]]¶
- populated_state: DatasetCollectionPopulatedState¶
- job_source_id: Optional[DecodedDatabaseIdField]¶
- job_source_type: Optional[JobSourceType]¶
- job_state_summary: Optional[HDCJobStateSummary]¶
- collection_id: DecodedDatabaseIdField¶
- class galaxy.schema.schema.HDCADetailed(*, id: DecodedDatabaseIdField, name: Optional[str] = None, history_id: DecodedDatabaseIdField, hid: int, history_content_type: HistoryContentType, deleted: bool, visible: bool, type_id: Optional[str] = None, type: typing_extensions.Literal[collection][typing_extensions.Literal[collection]] = 'collection', create_time: Optional[datetime] = None, update_time: Optional[datetime] = None, url: str, tags: TagCollection, model_class: typing_extensions.Literal[HistoryDatasetCollectionAssociation] = 'HistoryDatasetCollectionAssociation', collection_type: str, populated_state: DatasetCollectionPopulatedState, populated_state_message: Optional[str] = None, element_count: Optional[int] = None, job_source_id: Optional[DecodedDatabaseIdField] = None, job_source_type: Optional[JobSourceType] = None, job_state_summary: Optional[HDCJobStateSummary] = None, contents_url: str, collection_id: DecodedDatabaseIdField, populated: bool, elements: List[DCESummary] = [], elements_datatypes: Set[str], **extra_data: Any)[source]¶
Bases:
HDCASummary
History Dataset Collection Association detailed information.
- elements: List[DCESummary]¶
- class galaxy.schema.schema.HistoryBase(**extra_data: Any)[source]¶
Bases:
Model
Provides basic configuration for all the History models.
- class galaxy.schema.schema.HistoryContentItemBase(*, history_content_type: HistoryContentType)[source]¶
Bases:
Model
Identifies a dataset or collection contained in a History.
- history_content_type: HistoryContentType¶
- class galaxy.schema.schema.HistoryContentItem(*, history_content_type: HistoryContentType, id: DecodedDatabaseIdField)[source]¶
Bases:
HistoryContentItemBase
- class galaxy.schema.schema.EncodedHistoryContentItem(*, history_content_type: HistoryContentType, id: EncodedDatabaseIdField)[source]¶
Bases:
HistoryContentItemBase
- class galaxy.schema.schema.UpdateContentItem(*, history_content_type: HistoryContentType, id: DecodedDatabaseIdField, **extra_data: Any)[source]¶
Bases:
HistoryContentItem
Used for updating a particular history item. All fields are optional.
- history_content_type: HistoryContentType¶
- class galaxy.schema.schema.UpdateHistoryContentsBatchPayload(*, items: List[UpdateContentItem], **extra_data: Any)[source]¶
Bases:
HistoryBase
Contains property values that will be updated for all the history items provided.
- items: List[UpdateContentItem]¶
- class galaxy.schema.schema.HistoryContentItemOperation(value)[source]¶
-
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.ChangeDatatypeOperationParams(*, type: typing_extensions.Literal[change_datatype], datatype: str)[source]¶
Bases:
BulkOperationParams
- type: typing_extensions.Literal[change_datatype]¶
- class galaxy.schema.schema.ChangeDbkeyOperationParams(*, type: typing_extensions.Literal[change_dbkey], dbkey: str)[source]¶
Bases:
BulkOperationParams
- type: typing_extensions.Literal[change_dbkey]¶
- class galaxy.schema.schema.TagOperationParams(*, type: Union[typing_extensions.Literal[add_tags], typing_extensions.Literal[remove_tags]], tags: List[str])[source]¶
Bases:
BulkOperationParams
- class galaxy.schema.schema.HistoryContentBulkOperationPayload(*, operation: HistoryContentItemOperation, items: Optional[List[HistoryContentItem]] = None, params: Optional[Union[ChangeDatatypeOperationParams, ChangeDbkeyOperationParams, TagOperationParams]] = None)[source]¶
Bases:
Model
- operation: HistoryContentItemOperation¶
- items: Optional[List[HistoryContentItem]]¶
- class galaxy.schema.schema.BulkOperationItemError(*, item: EncodedHistoryContentItem, error: str)[source]¶
Bases:
Model
- class galaxy.schema.schema.HistoryContentBulkOperationResult(*, success_count: int, errors: List[BulkOperationItemError])[source]¶
Bases:
Model
- errors: List[BulkOperationItemError]¶
- class galaxy.schema.schema.UpdateHistoryContentsPayload(*, name: Optional[str] = None, deleted: Optional[bool] = None, visible: Optional[bool] = None, annotation: Optional[str] = None, tags: Optional[TagCollection] = None, **extra_data: Any)[source]¶
Bases:
HistoryBase
Can contain arbitrary/dynamic fields that will be updated for a particular history item.
- tags: Optional[TagCollection]¶
- class galaxy.schema.schema.HistorySummary(*, model_class: typing_extensions.Literal[History] = 'History', id: DecodedDatabaseIdField, name: str, deleted: bool, purged: bool, archived: bool, url: str, published: bool, count: int, annotation: Optional[str], tags: TagCollection, update_time: datetime, preferred_object_store_id: Optional[str] = None, **extra_data: Any)[source]¶
Bases:
HistoryBase
History summary information.
- 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.
- class galaxy.schema.schema.HistoryDetailed(*, model_class: typing_extensions.Literal[History] = 'History', id: DecodedDatabaseIdField, name: str, deleted: bool, purged: bool, archived: bool, url: str, published: bool, count: int, annotation: Optional[str], tags: TagCollection, update_time: datetime, preferred_object_store_id: Optional[str] = None, contents_url: str, size: int, user_id: DecodedDatabaseIdField, create_time: datetime, importable: bool, slug: Optional[str] = None, username_and_slug: Optional[str] = None, genome_build: Optional[str] = '?', state: DatasetState, state_ids: Dict[DatasetState, List[DecodedDatabaseIdField]], state_details: Dict[DatasetState, int], **extra_data: Any)[source]¶
Bases:
HistorySummary
History detailed information.
- user_id: DecodedDatabaseIdField¶
- state: DatasetState¶
- state_ids: Dict[DatasetState, List[DecodedDatabaseIdField]]¶
- state_details: Dict[DatasetState, int]¶
- class galaxy.schema.schema.ExportHistoryArchivePayload(*, gzip: Optional[bool] = True, include_hidden: Optional[bool] = False, include_deleted: Optional[bool] = False, file_name: Optional[str] = None, directory_uri: Optional[str] = None, force: Optional[bool] = None)[source]¶
Bases:
Model
- class galaxy.schema.schema.WorkflowIndexQueryPayload(*, show_deleted: bool = False, show_hidden: bool = False, show_published: Optional[bool] = None, show_shared: Optional[bool] = None, sort_by: Optional[typing_extensions.Literal[create_time, update_time, name]] = None, sort_desc: Optional[bool] = None, limit: Optional[ConstrainedIntValue] = None, offset: Optional[int] = 0, search: Optional[str] = None, skip_step_counts: bool = False)[source]¶
Bases:
Model
- class galaxy.schema.schema.JobIndexSortByEnum(value)[source]¶
-
An enumeration.
- create_time = 'create_time'¶
- update_time = 'update_time'¶
- class galaxy.schema.schema.JobIndexQueryPayload(*, states: Optional[List[str]] = None, user_details: bool = False, user_id: Optional[DecodedDatabaseIdField] = None, tool_ids: Optional[List[str]] = None, tool_ids_like: Optional[List[str]] = None, date_range_min: Optional[Union[OffsetNaiveDatetime, date]] = None, date_range_max: Optional[Union[OffsetNaiveDatetime, date]] = None, history_id: Optional[DecodedDatabaseIdField] = None, workflow_id: Optional[DecodedDatabaseIdField] = None, invocation_id: Optional[DecodedDatabaseIdField] = None, order_by: JobIndexSortByEnum = JobIndexSortByEnum.update_time, search: Optional[str] = None, limit: int = 500, offset: int = 0)[source]¶
Bases:
Model
- user_id: Optional[DecodedDatabaseIdField]¶
- 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¶
- class galaxy.schema.schema.InvocationSortByEnum(value)[source]¶
-
An enumeration.
- create_time = 'create_time'¶
- update_time = 'update_time'¶
- none = 'None'¶
- class galaxy.schema.schema.InvocationIndexQueryPayload(*, workflow_id: Optional[DecodedDatabaseIdField] = None, history_id: Optional[DecodedDatabaseIdField] = None, job_id: Optional[DecodedDatabaseIdField] = None, user_id: Optional[DecodedDatabaseIdField] = None, sort_by: Optional[InvocationSortByEnum] = None, sort_desc: bool = False, include_terminal: bool = True, limit: Optional[ConstrainedIntValue] = 100, offset: Optional[int] = 0)[source]¶
Bases:
Model
- workflow_id: Optional[DecodedDatabaseIdField]¶
- history_id: Optional[DecodedDatabaseIdField]¶
- job_id: Optional[DecodedDatabaseIdField]¶
- user_id: Optional[DecodedDatabaseIdField]¶
- sort_by: Optional[InvocationSortByEnum]¶
- class galaxy.schema.schema.PageIndexQueryPayload(*, deleted: bool = False, show_published: Optional[bool] = None, show_shared: Optional[bool] = None, user_id: Optional[DecodedDatabaseIdField] = None, sort_by: typing_extensions.Literal[update_time, title, username] = 'update_time', sort_desc: Optional[bool] = False, search: Optional[str] = None, limit: Optional[ConstrainedIntValue] = 100, offset: Optional[int] = 0)[source]¶
Bases:
Model
- user_id: Optional[DecodedDatabaseIdField]¶
- sort_by: typing_extensions.Literal[update_time, title, username]¶
- class galaxy.schema.schema.CreateHistoryPayload(*, name: Optional[str] = None, history_id: Optional[DecodedDatabaseIdField] = None, all_datasets: Optional[bool] = True, archive_source: Optional[str] = None, archive_type: Optional[HistoryImportArchiveSourceType] = HistoryImportArchiveSourceType.url, archive_file: Optional[Any] = None)[source]¶
Bases:
Model
- history_id: Optional[DecodedDatabaseIdField]¶
- archive_type: Optional[HistoryImportArchiveSourceType]¶
- class galaxy.schema.schema.CollectionElementIdentifier(*, name: Optional[str] = None, src: ColletionSourceType, id: Optional[DecodedDatabaseIdField] = None, collection_type: Optional[str] = None, element_identifiers: Optional[List[CollectionElementIdentifier]] = None, tags: Optional[List[str]] = None)[source]¶
Bases:
Model
- src: ColletionSourceType¶
- element_identifiers: Optional[List[CollectionElementIdentifier]]¶
- class galaxy.schema.schema.CreateNewCollectionPayload(*, collection_type: Optional[str] = None, element_identifiers: Optional[List[CollectionElementIdentifier]] = None, name: Optional[str] = None, hide_source_items: Optional[bool] = False, copy_elements: Optional[bool] = True, instance_type: Optional[typing_extensions.Literal[history, library]] = 'history', history_id: Optional[DecodedDatabaseIdField] = None, folder_id: Optional[LibraryFolderDatabaseIdField] = None)[source]¶
Bases:
Model
- element_identifiers: Optional[List[CollectionElementIdentifier]]¶
- history_id: Optional[DecodedDatabaseIdField]¶
- folder_id: Optional[LibraryFolderDatabaseIdField]¶
- class galaxy.schema.schema.ModelStoreFormat(value)[source]¶
-
Available types of model stores for export.
- TGZ = 'tgz'¶
- TAR = 'tar'¶
- TAR_DOT_GZ = 'tar.gz'¶
- BAG_DOT_ZIP = 'bag.zip'¶
- BAG_DOT_TAR = 'bag.tar'¶
- BAG_DOT_TGZ = 'bag.tgz'¶
- ROCRATE_ZIP = 'rocrate.zip'¶
- BCO_JSON = 'bco.json'¶
- classmethod is_compressed(value: ModelStoreFormat)[source]¶
- classmethod is_bag(value: ModelStoreFormat)[source]¶
- class galaxy.schema.schema.StoreContentSource(*, store_content_uri: Optional[str] = None, store_dict: Optional[Dict[str, Any]] = None, model_store_format: Optional[ModelStoreFormat] = None)[source]¶
Bases:
Model
- model_store_format: Optional[ModelStoreFormat]¶
- class galaxy.schema.schema.CreateHistoryFromStore(*, store_content_uri: Optional[str] = None, store_dict: Optional[Dict[str, Any]] = None, model_store_format: Optional[ModelStoreFormat] = None)[source]¶
Bases:
StoreContentSource
- 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¶
- class galaxy.schema.schema.ShortTermStoreExportPayload(*, model_store_format: ModelStoreFormat = ModelStoreFormat.TAR_DOT_GZ, include_files: bool = True, include_deleted: bool = False, include_hidden: bool = False, short_term_storage_request_id: UUID, duration: Optional[Union[int, float]] = None)[source]¶
Bases:
StoreExportPayload
- class galaxy.schema.schema.BcoGenerationParametersMixin(*, bco_merge_history_metadata: bool = False, bco_override_environment_variables: Optional[Dict[str, str]] = None, bco_override_empirical_error: Optional[Dict[str, str]] = None, bco_override_algorithmic_error: Optional[Dict[str, str]] = None, bco_override_xref: Optional[List[XrefItem]] = None)[source]¶
Bases:
BaseModel
- 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
- class galaxy.schema.schema.ObjectExportResponseBase(*, id: EncodedDatabaseIdField, ready: bool, preparing: bool, up_to_date: bool)[source]¶
Bases:
Model
- class galaxy.schema.schema.JobExportHistoryArchiveModel(*, id: EncodedDatabaseIdField, ready: bool, preparing: bool, up_to_date: bool, job_id: EncodedDatabaseIdField, download_url: str, external_download_latest_url: AnyUrl, external_download_permanent_url: AnyUrl)[source]¶
Bases:
ObjectExportResponseBase
- job_id: EncodedDatabaseIdField¶
- external_download_latest_url: AnyUrl¶
- external_download_permanent_url: AnyUrl¶
- class galaxy.schema.schema.ExportObjectType(value)[source]¶
-
Types of objects that can be exported.
- HISTORY = 'history'¶
- INVOCATION = 'invocation'¶
- class galaxy.schema.schema.ExportObjectRequestMetadata(*, object_id: EncodedDatabaseIdField, object_type: ExportObjectType, user_id: Optional[EncodedDatabaseIdField] = None, payload: Union[WriteStoreToPayload, ShortTermStoreExportPayload])[source]¶
Bases:
Model
- object_id: EncodedDatabaseIdField¶
- object_type: ExportObjectType¶
- user_id: Optional[EncodedDatabaseIdField]¶
- payload: Union[WriteStoreToPayload, ShortTermStoreExportPayload]¶
- class galaxy.schema.schema.ExportObjectResultMetadata(*, success: bool, error: Optional[str] = None)[source]¶
Bases:
Model
- class galaxy.schema.schema.ExportObjectMetadata(*, request_data: ExportObjectRequestMetadata, result_data: Optional[ExportObjectResultMetadata] = None)[source]¶
Bases:
Model
- request_data: ExportObjectRequestMetadata¶
- result_data: Optional[ExportObjectResultMetadata]¶
- class galaxy.schema.schema.ObjectExportTaskResponse(*, id: EncodedDatabaseIdField, ready: bool, preparing: bool, up_to_date: bool, task_uuid: UUID4, create_time: datetime, export_metadata: Optional[ExportObjectMetadata] = None)[source]¶
Bases:
ObjectExportResponseBase
- task_uuid: UUID4¶
- export_metadata: Optional[ExportObjectMetadata]¶
- class galaxy.schema.schema.JobExportHistoryArchiveListResponse(*, __root__: List[JobExportHistoryArchiveModel])[source]¶
Bases:
Model
- class galaxy.schema.schema.ExportTaskListResponse(*, __root__: List[ObjectExportTaskResponse])[source]¶
Bases:
Model
- class galaxy.schema.schema.ArchiveHistoryRequestPayload(*, archive_export_id: Optional[DecodedDatabaseIdField] = None, purge_history: bool = False)[source]¶
Bases:
Model
- archive_export_id: Optional[DecodedDatabaseIdField]¶
- class galaxy.schema.schema.ExportRecordData(*, model_store_format: ModelStoreFormat = ModelStoreFormat.TAR_DOT_GZ, include_files: bool = True, include_deleted: bool = False, include_hidden: bool = False, target_uri: str)[source]¶
Bases:
WriteStoreToPayload
Data of an export record associated with a history that was archived.
- model_store_format: ModelStoreFormat¶
- class galaxy.schema.schema.ExportAssociationData(*, export_record_data: Optional[ExportRecordData] = None)[source]¶
Bases:
Model
- export_record_data: Optional[ExportRecordData]¶
- class galaxy.schema.schema.ArchivedHistorySummary(*, export_record_data: Optional[ExportRecordData] = None, model_class: typing_extensions.Literal[History] = 'History', id: DecodedDatabaseIdField, name: str, deleted: bool, purged: bool, archived: bool, url: str, published: bool, count: int, annotation: Optional[str], tags: TagCollection, update_time: datetime, preferred_object_store_id: Optional[str] = None, **extra_data: Any)[source]¶
Bases:
HistorySummary
,ExportAssociationData
- tags: TagCollection¶
- class galaxy.schema.schema.ArchivedHistoryDetailed(*, export_record_data: Optional[ExportRecordData] = None, model_class: typing_extensions.Literal[History] = 'History', id: DecodedDatabaseIdField, name: str, deleted: bool, purged: bool, archived: bool, url: str, published: bool, count: int, annotation: Optional[str], tags: TagCollection, update_time: datetime, preferred_object_store_id: Optional[str] = None, contents_url: str, size: int, user_id: DecodedDatabaseIdField, create_time: datetime, importable: bool, slug: Optional[str] = None, username_and_slug: Optional[str] = None, genome_build: Optional[str] = '?', state: DatasetState, state_ids: Dict[DatasetState, List[DecodedDatabaseIdField]], state_details: Dict[DatasetState, int], **extra_data: Any)[source]¶
Bases:
HistoryDetailed
,ExportAssociationData
- user_id: DecodedDatabaseIdField¶
- state: DatasetState¶
- state_ids: Dict[DatasetState, List[DecodedDatabaseIdField]]¶
- state_details: Dict[DatasetState, int]¶
- tags: TagCollection¶
- class galaxy.schema.schema.LabelValuePair(*, label: str, value: str)[source]¶
Bases:
Model
Generic Label/Value pair model.
- class galaxy.schema.schema.CustomBuildsMetadataResponse(*, installed_builds: List[LabelValuePair], fasta_hdas: List[LabelValuePair])[source]¶
Bases:
Model
- installed_builds: List[LabelValuePair]¶
- fasta_hdas: List[LabelValuePair]¶
- class galaxy.schema.schema.JobIdResponse(*, job_id: EncodedDatabaseIdField)[source]¶
Bases:
Model
Contains the ID of the job associated with a particular request.
- job_id: EncodedDatabaseIdField¶
- class galaxy.schema.schema.JobBaseModel(*, id: DecodedDatabaseIdField, model_class: typing_extensions.Literal[Job] = 'Job', tool_id: str, history_id: Optional[DecodedDatabaseIdField] = None, state: JobState, exit_code: Optional[int] = None, create_time: datetime, update_time: