galaxy.webapps.galaxy.api package

This module does not contain API routes. It exclusively contains dependencies to be used in FastAPI routes

galaxy.webapps.galaxy.api.get_app() → StructuredApp

async galaxy.webapps.galaxy.api.get_app_with_request_session() → AsyncGenerator[StructuredApp, None]

class galaxy.webapps.galaxy.api.GalaxyTypeDepends(callable, dep_type)

Bases: Depends

Variant of fastapi Depends that can also work on WSGI Galaxy controllers.

__init__(callable, dep_type)

galaxy.webapps.galaxy.api.depends(dep_type: Type[T]) → T

galaxy.webapps.galaxy.api.get_session_manager(app: StructuredApp = Depends(get_app_with_request_session)) → GalaxySessionManager

galaxy.webapps.galaxy.api.get_session(session_manager=Depends(get_session_manager), security: IdEncodingHelper = GalaxyTypeDepends(_do_resolve), galaxysession: str = Security(APIKeyCookie)) → Optional[GalaxySession]

galaxy.webapps.galaxy.api.get_api_user(user_manager: UserManager = GalaxyTypeDepends(_do_resolve), key: str = Security(APIKeyQuery), x_api_key: str = Security(APIKeyHeader), run_as: Optional[DecodedDatabaseIdField] = Header(None)) → Optional[User]

galaxy.webapps.galaxy.api.get_user(galaxy_session=Depends(get_session), api_user=Depends(get_api_user)) → Optional[User]

class galaxy.webapps.galaxy.api.UrlBuilder(request: Request)

Bases: object

__init__(request: Request)

class galaxy.webapps.galaxy.api.GalaxyASGIRequest(request: Request)

Bases: GalaxyAbstractRequest

Wrapper around Starlette/FastAPI Request object.

Implements the GalaxyAbstractRequest interface to provide access to some properties of the request commonly used.

__init__(request: Request)

property base: str

Base URL of the request.

property url_path: str

property host: str

The host address.

property environ: MutableMapping[str, Any]

Fallback WSGI environ.

This is not a full environ, there is no body. This is only meant to make routes.url_for work.

class galaxy.webapps.galaxy.api.GalaxyASGIResponse(response: Response)

Bases: GalaxyAbstractResponse

Wrapper around Starlette/FastAPI Response object.

Implements the GalaxyAbstractResponse interface to provide access to some properties of the response object commonly used.

__init__(response: Response)

property headers

The response headers.

galaxy.webapps.galaxy.api.get_current_history_from_session(galaxy_session: Optional[GalaxySession]) → Optional[History]

galaxy.webapps.galaxy.api.get_trans(request: Request, response: Response, app: StructuredApp = Depends(get_app_with_request_session), user=Depends(get_user), galaxy_session=Depends(get_session)) → SessionRequestContext

galaxy.webapps.galaxy.api.get_admin_user(trans: SessionRequestContext = Depends(get_trans))

class galaxy.webapps.galaxy.api.BaseGalaxyAPIController(app: StructuredApp)

Bases: BaseAPIController

__init__(app: StructuredApp)

Initialize an interface for application ‘app’

class galaxy.webapps.galaxy.api.RestVerb(value)

Bases: str, Enum

An enumeration.

get = 'GET'

head = 'HEAD'

post = 'POST'

put = 'PUT'

patch = 'PATCH'

delete = 'DELETE'

options = 'OPTIONS'

class galaxy.webapps.galaxy.api.Router(*, prefix: str = '', tags: ~typing.Optional[~typing.List[~typing.Union[str, ~enum.Enum]]] = None, dependencies: ~typing.Optional[~typing.Sequence[~fastapi.params.Depends]] = None, default_response_class: ~typing.Type[~starlette.responses.Response] = <fastapi.datastructures.DefaultPlaceholder object>, responses: ~typing.Optional[~typing.Dict[~typing.Union[int, str], ~typing.Dict[str, ~typing.Any]]] = None, callbacks: ~typing.Optional[~typing.List[~starlette.routing.BaseRoute]] = None, routes: ~typing.Optional[~typing.List[~starlette.routing.BaseRoute]] = None, redirect_slashes: bool = True, default: ~typing.Optional[~typing.Callable[[~typing.MutableMapping[str, ~typing.Any], ~typing.Callable[[], ~typing.Awaitable[~typing.MutableMapping[str, ~typing.Any]]], ~typing.Callable[[~typing.MutableMapping[str, ~typing.Any]], ~typing.Awaitable[None]]], ~typing.Awaitable[None]]] = None, dependency_overrides_provider: ~typing.Optional[~typing.Any] = None, route_class: ~typing.Type[~fastapi.routing.APIRoute] = <class 'fastapi.routing.APIRoute'>, on_startup: ~typing.Optional[~typing.Sequence[~typing.Callable[[], ~typing.Any]]] = None, on_shutdown: ~typing.Optional[~typing.Sequence[~typing.Callable[[], ~typing.Any]]] = None, deprecated: ~typing.Optional[bool] = None, include_in_schema: bool = True, generate_unique_id_function: ~typing.Callable[[~fastapi.routing.APIRoute], str] = <fastapi.datastructures.DefaultPlaceholder object>)

Bases: InferringRouter

A FastAPI Inferring Router tailored to Galaxy.

wrap_with_alias(verb: RestVerb, *args, alias: Optional[str] = None, **kwd)

Wraps FastAPI methods with additional alias keyword and require_admin handling.

@router.get(“/api/thing”, alias=”/api/deprecated_thing”) will then create routes for /api/thing and /api/deprecated_thing.

static construct_aliases(path: str, alias: Optional[str])

get(*args, **kwd)

Extend FastAPI.get to accept a require_admin Galaxy flag.

patch(*args, **kwd)

Extend FastAPI.patch to accept a require_admin Galaxy flag.

put(*args, **kwd)

Extend FastAPI.put to accept a require_admin Galaxy flag.

post(*args, **kwd)

Extend FastAPI.post to accept a require_admin Galaxy flag.

delete(*args, **kwd)

Extend FastAPI.delete to accept a require_admin Galaxy flag.

options(*args, **kwd)

head(*args, **kwd)

property cbv

Short-hand for frequently used Galaxy-pattern of FastAPI class based views.

Creates a class-based view for for this router, for more information see: https://fastapi-utils.davidmontague.xyz/user-guide/class-based-views/

class galaxy.webapps.galaxy.api.APIContentTypeRoute(path: str, endpoint: ~typing.Callable[[...], ~typing.Any], *, response_model: ~typing.Any = <fastapi.datastructures.DefaultPlaceholder object>, status_code: ~typing.Optional[int] = None, tags: ~typing.Optional[~typing.List[~typing.Union[str, ~enum.Enum]]] = None, dependencies: ~typing.Optional[~typing.Sequence[~fastapi.params.Depends]] = None, summary: ~typing.Optional[str] = None, description: ~typing.Optional[str] = None, response_description: str = 'Successful Response', responses: ~typing.Optional[~typing.Dict[~typing.Union[int, str], ~typing.Dict[str, ~typing.Any]]] = None, deprecated: ~typing.Optional[bool] = None, name: ~typing.Optional[str] = None, methods: ~typing.Optional[~typing.Union[~typing.Set[str], ~typing.List[str]]] = None, operation_id: ~typing.Optional[str] = None, response_model_include: ~typing.Optional[~typing.Union[~typing.Set[~typing.Union[int, str]], ~typing.Dict[~typing.Union[int, str], ~typing.Any]]] = None, response_model_exclude: ~typing.Optional[~typing.Union[~typing.Set[~typing.Union[int, str]], ~typing.Dict[~typing.Union[int, str], ~typing.Any]]] = None, response_model_by_alias: bool = True, response_model_exclude_unset: bool = False, response_model_exclude_defaults: bool = False, response_model_exclude_none: bool = False, include_in_schema: bool = True, response_class: ~typing.Union[~typing.Type[~starlette.responses.Response], ~fastapi.datastructures.DefaultPlaceholder] = <fastapi.datastructures.DefaultPlaceholder object>, dependency_overrides_provider: ~typing.Optional[~typing.Any] = None, callbacks: ~typing.Optional[~typing.List[~starlette.routing.BaseRoute]] = None, openapi_extra: ~typing.Optional[~typing.Dict[str, ~typing.Any]] = None, generate_unique_id_function: ~typing.Union[~typing.Callable[[~fastapi.routing.APIRoute], str], ~fastapi.datastructures.DefaultPlaceholder] = <fastapi.datastructures.DefaultPlaceholder object>)

Bases: APIRoute

Determines endpoint to match using content-type.

match_content_type: str

accept_matches(scope: MutableMapping[str, Any]) → Tuple[Match, MutableMapping[str, Any]]

matches(scope: MutableMapping[str, Any]) → Tuple[Match, MutableMapping[str, Any]]

galaxy.webapps.galaxy.api.as_form(cls: Type[BaseModel])

Adds an as_form class method to decorated models. The as_form class method can be used with FastAPI endpoints.

See https://github.com/tiangolo/fastapi/issues/2387#issuecomment-731662551

async galaxy.webapps.galaxy.api.try_get_request_body_as_json(request: Request) → Optional[Any]

Returns the request body as a JSON object if the content type is JSON.

class galaxy.webapps.galaxy.api.IndexQueryTag(tag, description, alias, admin_only)

Bases: tuple

property tag

Alias for field number 0

property description

Alias for field number 1

property alias

Alias for field number 2

property admin_only

Alias for field number 3

as_markdown()

galaxy.webapps.galaxy.api.search_query_param(model_name: str, tags: list, free_text_fields: list) → Optional[str]

Submodules

galaxy.webapps.galaxy.api.annotations module

API operations on annotations.

class galaxy.webapps.galaxy.api.annotations.BaseAnnotationsController(app: StructuredApp)

Bases: BaseGalaxyAPIController, UsesStoredWorkflowMixin, UsesAnnotations

tagged_item_id: str

index(trans: ProvidesHistoryContext, **kwd)

create(trans: ProvidesHistoryContext, payload: dict, **kwd)

delete(trans: ProvidesHistoryContext, **kwd)

undelete(trans: ProvidesHistoryContext, **kwd)

class galaxy.webapps.galaxy.api.annotations.HistoryAnnotationsController(app: StructuredApp)

Bases: BaseAnnotationsController

controller_name = 'history_annotations'

tagged_item_id: str = 'history_id'

history_manager: HistoryManager = GalaxyTypeDepends(_do_resolve)

class galaxy.webapps.galaxy.api.annotations.HistoryContentAnnotationsController(app: StructuredApp)

Bases: BaseAnnotationsController

controller_name = 'history_content_annotations'

tagged_item_id: str = 'history_content_id'

hda_manager: HDAManager = GalaxyTypeDepends(_do_resolve)

class galaxy.webapps.galaxy.api.annotations.WorkflowAnnotationsController(app: StructuredApp)

Bases: BaseAnnotationsController

controller_name = 'workflow_annotations'

tagged_item_id: str = 'workflow_id'

galaxy.webapps.galaxy.api.authenticate module

API key retrieval through BaseAuth

Sample usage

curl --user zipzap@foo.com:password http://localhost:8080/api/authenticate/baseauth

Returns

{
    "api_key": "baa4d6e3a156d3033f05736255f195f9"
}

class galaxy.webapps.galaxy.api.authenticate.AuthenticationController(app: StructuredApp)

Bases: BaseGalaxyAPIController

authentication_service = GalaxyTypeDepends(_do_resolve)

options(trans: GalaxyWebTransaction, **kwd)

A no-op endpoint to return generic OPTIONS for the API. Any OPTIONS request to /api/* maps here. Right now this is solely to inform preflight CORS checks, which are API wide. Might be better placed elsewhere, but for now this is the initial entrypoint for relevant consumers.

class galaxy.webapps.galaxy.api.authenticate.FastAPIAuthenticate(*, authentication_service: AuthenticationService = GalaxyTypeDepends(_do_resolve))

Bases: object

authentication_service: AuthenticationService = GalaxyTypeDepends(_do_resolve)

get_api_key(*, request: Request) → APIKeyResponse

__init__(*args: Any, **kwargs: Any) → None

galaxy.webapps.galaxy.api.cloud module

API operations on Cloud-based storages, such as Amazon Simple Storage Service (S3).

class galaxy.webapps.galaxy.api.cloud.CloudController(app: StructuredApp, cloud_manager: CloudManager, datasets_serializer: DatasetSerializer)

Bases: BaseGalaxyAPIController

RESTfull controller for interaction with Amazon S3.

__init__(app: StructuredApp, cloud_manager: CloudManager, datasets_serializer: DatasetSerializer)

Initialize an interface for application ‘app’

index(trans, **kwargs)

GET /api/cloud/storage

Lists cloud-based buckets (e.g., S3 bucket, Azure blob) user has defined.

Returns

A list of cloud-based buckets user has defined.

get(trans, payload, **kwargs)

POST /api/cloud/storage/get

gets given objects from a given cloud-based bucket to a Galaxy history.

Parameters

• trans (galaxy.webapps.base.webapp.GalaxyWebTransaction) – Galaxy web transaction

• payload (dict) –

  A dictionary structure containing the following keys:

  • history_id: the (encoded) id of history to which the object should be received to.

  • bucket: the name of a bucket from which data should be fetched from (e.g., a bucket name on AWS S3).

  • objects: a list of the names of objects to be fetched.

  • authz_id: the encoded ID of CloudAuthz to be used for authorizing access to the resource

    provider. You may get a list of the defined authorizations via /api/cloud/authz. Also, you can use /api/cloud/authz/create to define a new authorization.

  • input_args [Optional; default value is an empty dict] a dictionary containing the following keys:

    ** dbkey: [Optional; default value: is ?]

    Sets the genome (e.g., hg19) of the objects being fetched to Galaxy.

    ** file_type: [Optional; default value is auto]

    Sets the Galaxy datatype (e.g., bam) for the objects being fetched to Galaxy. See the following link for a complete list of Galaxy data types: https://galaxyproject.org/learn/datatypes/

    ** space_to_tab: [Optional; default value is False]

    A boolean value (“true” or “false”) that sets if spaces should be converted to tab in the objects being fetched to Galaxy. Applicable only if to_posix_lines is True

    ** to_posix_lines: [Optional; default value is Yes]

    A boolean value (“true” or “false”); if “Yes”, converts universal line endings to POSIX line endings. Set to “False” if you upload a gzip, bz2 or zip archive containing a binary file.

• kwargs –

Return type

dictionary

Returns

a dictionary containing a summary view of the datasets copied from the given cloud-based storage.

send(trans, payload, **kwargs)

POST /api/cloud/storage/send

Sends given dataset(s) in a given history to a given cloud-based bucket. Each dataset is named using the label assigned to the dataset in the given history (see HistoryDatasetAssociation.name). If no dataset ID is given, this API sends all the datasets belonging to a given history to a given cloud-based bucket.

Parameters

• trans (galaxy.webapps.base.webapp.GalaxyWebTransaction) – Galaxy web transaction

• payload (dictionary) –

  A dictionary structure containing the following keys:

  • history_id the (encoded) id of history from which the object should be downloaed.

  • bucket: the name of a bucket to which data should be sent (e.g., a bucket name on AWS S3).

  • authz_id: the encoded ID of CloudAuthz to be used for authorizing access to the resource

    provider. You may get a list of the defined authorizations via /api/cloud/authz. Also, you can use /api/cloud/authz/create to define a new authorization.

  • dataset_ids: [Optional; default: None]

    A list of encoded dataset IDs belonging to the specified history that should be sent to the given bucket. If not provided, Galaxy sends all the datasets belonging the specified history.

  • overwrite_existing: [Optional; default: False]

    A boolean value. If set to “True”, and an object with same name of the dataset to be sent already exist in the bucket, Galaxy replaces the existing object with the dataset to be sent. If set to “False”, Galaxy appends datetime to the dataset name to prevent overwriting an existing object.

Return type

dictionary

Returns

Information about the (un)successfully submitted dataset send jobs, containing the following keys:

• bucket_name: The name of bucket to which the listed datasets are queued

  to be sent.

• sent_dataset_labels: A list of JSON objects with the following key-value pair: ** object: The name of object is queued to be created. ** job_id: The id of the queued send job.

• failed_dataset_labels: A list of JSON objects with the following key-value pair

  representing the datasets Galaxy failed to create (and queue) send job for:

  ** object: The name of object is queued to be created. ** error: A descriptive error message.

galaxy.webapps.galaxy.api.cloudauthz module

API operations on defining cloud authorizations.

Through means of cloud authorization a user is able to grant a Galaxy server a secure access to his/her cloud-based resources without sharing his/her long-lasting credentials.

User provides a provider-specific configuration, which Galaxy users to request temporary credentials from the provider to access the user’s resources.

class galaxy.webapps.galaxy.api.cloudauthz.CloudAuthzController(app: StructuredApp)

Bases: BaseGalaxyAPIController

RESTfull controller for defining cloud authorizations.

__init__(app: StructuredApp)

Initialize an interface for application ‘app’

index(trans, **kwargs)

GET /api/cloud/authz

Lists all the cloud authorizations user has defined.

Parameters

• trans (galaxy.webapps.base.webapp.GalaxyWebTransaction) – Galaxy web transaction

• kwargs – empty dict

Return type

list of dict

Returns

a list of cloud authorizations (each represented in key-value pair format) defined for the user.

create(trans, payload, **kwargs)

• POST /api/cloud/authz

  Request to store the payload as a cloudauthz (cloud authorization) configuration for a user.

Parameters

• trans (galaxy.webapps.base.webapp.GalaxyWebTransaction) – Galaxy web transaction

• payload (dict) –

  A dictionary structure containing the following keys: * provider: the cloud-based resource provider to which this configuration belongs to.

  • config: a dictionary containing all the configuration required to request temporary credentials

    from the provider. See the following page for details: https://galaxyproject.org/authnz/

  • authn_id: the (encoded) ID of a third-party authentication of a user. To have this ID, user must

    have logged-in to this Galaxy server using third-party identity (e.g., Google), or has associated his/her Galaxy account with a third-party OIDC-based identity. See this page: https://galaxyproject.org/authnz/config/

  • description: [Optional] a brief description for this configuration.

• kwargs – empty dict

Return type

dict

Returns

a dictionary with the following kvp: * status: HTTP response code * message: A message complementary to the response code.

delete(trans, encoded_authz_id, **kwargs)

• DELETE /api/cloud/authz/{encoded_authz_id}

  Deletes the CloudAuthz record with the given encoded_authz_id from database.

Parameters

• trans (galaxy.webapps.base.webapp.GalaxyWebTransaction) – Galaxy web transaction

• encoded_authz_id (string) – The encoded ID of the CloudAuthz record to be marked deleted.

:rtype JSON :return The cloudauthz record marked as deleted, serialized as a JSON object.

update(trans, encoded_authz_id, payload, **kwargs)

PUT /api/cloud/authz/{encoded_authz_id}

Updates the values for the cloudauthz configuration with the given encoded_authz_id.

With this API only the following attributes of a cloudauthz configuration can be updated: authn_id, provider, config, deleted.

Parameters

• trans (galaxy.webapps.base.webapp.GalaxyWebTransaction) – Galaxy web transaction

• encoded_authz_id (string) – The encoded ID of the CloudAuthz record to be updated.

• payload (dict) –

  A dictionary structure containing the attributes to modified with their new values. It can contain any number of the following attributes:

  • provider: the cloud-based resource provider

    to which this configuration belongs to.

  • authn_id: the (encoded) ID of a third-party authentication of a user.

    To have this ID, user must have logged-in to this Galaxy server using third-party identity (e.g., Google), or has associated their Galaxy account with a third-party OIDC-based identity. See this page: https://galaxyproject.org/authnz/config/

    Note: A user can associate a cloudauthz record with their own authentications only. If the given authentication with authn_id belongs to a different user, Galaxy will throw the ItemAccessibilityException exception.

  • config: a dictionary containing all the configuration required to

    request temporary credentials from the provider. See the following page for details: https://galaxyproject.org/authnz/

  • deleted: a boolean type marking the specified cloudauthz as (un)deleted.

galaxy.webapps.galaxy.api.common module

This module contains utility functions shared across the api package.

galaxy.webapps.galaxy.api.common.parse_serialization_params(view: Optional[str] = None, keys: Optional[str] = None, default_view: Optional[str] = None, **_) → SerializationParams

galaxy.webapps.galaxy.api.common.query_serialization_params(view: Optional[str] = Query(None), keys: Optional[str] = Query(None)) → SerializationParams

galaxy.webapps.galaxy.api.common.get_value_filter_query_params(q: Optional[List[str]] = Query(None), qv: Optional[List[str]] = Query(None)) → ValueFilterQueryParams

This function is meant to be used as a Dependency. See https://fastapi.tiangolo.com/tutorial/dependencies/#first-steps

galaxy.webapps.galaxy.api.common.get_filter_query_params(q: Optional[List[str]] = Query(None), qv: Optional[List[str]] = Query(None), offset: Optional[int] = Query(0), limit: Optional[int] = Query(None), order: Optional[str] = Query(None)) → FilterQueryParams

This function is meant to be used as a Dependency. See https://fastapi.tiangolo.com/tutorial/dependencies/#first-steps

galaxy.webapps.galaxy.api.common.get_update_permission_payload(payload: Dict[str, Any]) → UpdateDatasetPermissionsPayload

Converts the generic payload dictionary into a UpdateDatasetPermissionsPayload model with custom parsing. This is an attempt on supporting multiple aliases for the permissions params.

galaxy.webapps.galaxy.api.common.get_query_parameters_from_request_excluding(request: Request, exclude: Set[str]) → dict

Gets all the request query parameters excluding the given parameters names in exclude set.

This is useful when an endpoint uses arbitrary or dynamic query parameters that cannot be anticipated or documented beforehand. The exclude set can be used to avoid including those parameters that are already handled by the endpoint.

galaxy.webapps.galaxy.api.common.query_parameter_as_list(query)

Used as FastAPI dependable for query parameters that need to behave as a list of values separated by comma or as multiple instances of the same parameter.

Important

the query annotation provided must define the alias exactly as the name of the actual parameter name.

Usage example:

ValueQueryParam = Query(
    default=None,
    alias="value", # Important! this is the parameter name that will be displayed in the API docs
    title="My Value",
    description="A single value, a comma-separated list of values or a list of values.",
)

@router.get("/api/my_route")
def index(
    self,
    values: Optional[List[str]] = Depends(query_parameter_as_list(ValueQueryParam)),
):
    ...

This will render in the API docs as a single string query parameter but will make the following requests equivalent:

• api/my_route?value=val1,val2,val3

• api/my_route?value=val1&value=val2&value=val3

galaxy.webapps.galaxy.api.configuration module

API operations allowing clients to determine Galaxy instance’s capabilities and configuration settings.

class galaxy.webapps.galaxy.api.configuration.FastAPIConfiguration(*, configuration_manager: ConfigurationManager = GalaxyTypeDepends(_do_resolve))

Bases: object

configuration_manager: ConfigurationManager = GalaxyTypeDepends(_do_resolve)

whoami(*, trans: ProvidesUserContext = Depends(get_trans)) → Optional[UserModel]

Return information about the current authenticated user.

index(*, trans: ProvidesUserContext = Depends(get_trans), view: Optional[str] = Query(None), keys: Optional[str] = Query(None)) → Dict[str, Any]

Return an object containing exposable configuration settings.

A more complete list is returned if the user is an admin. Pass in view and a comma-seperated list of keys to control which configuration settings are returned.

version() → Dict[str, Any]

Return Galaxy version information: major/minor version, optional extra info.

dynamic_tool_confs() → List[Dict[str, str]]

Return dynamic tool configuration files.

decode_id(*, encoded_id: str = Path(Ellipsis)) → Dict[str, int]

Decode a given id.

tool_lineages() → List[Dict[str, Dict]]

Return tool lineages for tools that have them.

reload_toolbox()

Reload the Galaxy toolbox (but not individual tools).

__init__(*args: Any, **kwargs: Any) → None

galaxy.webapps.galaxy.api.container_resolution module

API operations allowing clients to manage container resolution.

class galaxy.webapps.galaxy.api.container_resolution.ContainerResolutionAPIController(app: StructuredApp)

Bases: BaseGalaxyAPIController

__init__(app: StructuredApp)

Initialize an interface for application ‘app’

index(trans, **kwd)

GET /api/container_resolvers

show(trans, index)

GET /api/container_resolvers/<id>

resolve(trans, index=None, **kwds)

GET /api/container_resolvers/resolve GET /api/container_resolvers/{index}/resolve

Resolve described requirement against specified container resolvers.

Parameters

• tool_id (str) – tool_id to resolve against containers

• requirements_only (boolean) – ignore tool containers, properties - just search based on tool requirements set to True to mimic default behavior of tool dependency API.

• index (int) – index of the container resolver, if unset resolvers searched in order

• container_type (str) – restrict resolution to specified container type (e.g. ‘docker’, ‘singularity’)

• resolver_type (str) – restrict resolution to specified resolver type (e.g. ‘build_mulled’, ‘explicit’)

• install (boolean) – allow installation of new containers (for build_mulled* containers) the way job resolution will operate, defaults to False

Return type

dict

Returns

a dictified description of the container dependency, with attribute dependency_type: None if no match was found.

resolve_toolbox(trans, **kwds)

GET /api/container_resolvers/toolbox GET /api/container_resolvers/{index}/toolbox

Apply resolve() to each tool in the toolbox and return the results as a list. See documentation for resolve() for a description of parameters that can be consumed and a description of the resulting items.

Parameters

tool_ids (str) – tool_ids to filter toolbox on

Return type

list

Returns

list of items returned from resolve()

resolve_toolbox_with_install(trans, payload, **kwds)

POST /api/container_resolvers/toolbox/install POST /api/container_resolvers/{index}/toolbox/install

Do the resolution of dependencies like resolve_toolbox(), but allow building and installing new containers. payload of POST body maybe contain same parameters as resolve_toolbox query parameters.

Return type

list

Returns

list of items returned from resolve()

resolve_with_install(trans, payload, **kwds)

POST /api/container_resolvers/resolve/install POST /api/container_resolvers/{index}/resolve/install

Do the resolution of dependencies like resolve(), but allow building and installing new containers during installation. payload of POST body maybe contain same parameters as resolve query parameters.

Return type

dict

Returns

a dictified description of the container dependency, with attribute dependency_type: None if no match was found.

galaxy.webapps.galaxy.api.dataset_collections module

class galaxy.webapps.galaxy.api.dataset_collections.FastAPIDatasetCollections(*, service: DatasetCollectionsService = GalaxyTypeDepends(_do_resolve))

Bases: object

service: DatasetCollectionsService = GalaxyTypeDepends(_do_resolve)

create(*, trans: ProvidesHistoryContext = Depends(get_trans), payload: CreateNewCollectionPayload = Body(Ellipsis)) → HDCADetailed

copy(*, trans: ProvidesHistoryContext = Depends(get_trans), id: DecodedDatabaseIdField = Path(Ellipsis), payload: UpdateCollectionAttributePayload = Body(Ellipsis))

attributes(*, trans: ProvidesHistoryContext = Depends(get_trans), id: DecodedDatabaseIdField = Path(Ellipsis), instance_type: typing_extensions.Literal[history, library] = Query(history)) → DatasetCollectionAttributesResult

suitable_converters(*, trans: ProvidesHistoryContext = Depends(get_trans), id: DecodedDatabaseIdField = Path(Ellipsis), instance_type: typing_extensions.Literal[history, library] = Query(history)) → SuitableConverters

show(*, trans: ProvidesHistoryContext = Depends(get_trans), id: DecodedDatabaseIdField = Path(Ellipsis), instance_type: typing_extensions.Literal[history, library] = Query(history)) → Union[HDCADetailed, HDCASummary]

contents(*, trans: ProvidesHistoryContext = Depends(get_trans), hdca_id: DecodedDatabaseIdField = Path(Ellipsis), parent_id: DecodedDatabaseIdField = Path(Ellipsis), instance_type: typing_extensions.Literal[history, library] = Query(history), limit: Optional[int] = Query(None), offset: Optional[int] = Query(None)) → DatasetCollectionContentElements

content(*, trans: ProvidesHistoryContext = Depends(get_trans), dce_id: DecodedDatabaseIdField = Path(Ellipsis)) → DCESummary

__init__(*args: Any, **kwargs: Any) → None

galaxy.webapps.galaxy.api.datasets module

API operations on the contents of a history dataset.

class galaxy.webapps.galaxy.api.datasets.FastAPIDatasets(*, service: DatasetsService = GalaxyTypeDepends(_do_resolve))

Bases: object

service: DatasetsService = GalaxyTypeDepends(_do_resolve)

index(*, trans=Depends(get_trans), history_id: Optional[DecodedDatabaseIdField] = Query(None), serialization_params: SerializationParams = Depends(query_serialization_params), filter_query_params: FilterQueryParams = Depends(get_filter_query_params)) → List[Union[HDADetailed, HDASummary, HDCADetailed, HDCASummary, CustomHistoryItem]]

show_storage(*, trans=Depends(get_trans), dataset_id: DecodedDatabaseIdField = Path(Ellipsis), hda_ldda: DatasetSourceType = Query(hda)) → DatasetStorageDetails

show_inheritance_chain(*, trans=Depends(get_trans), dataset_id: DecodedDatabaseIdField = Path(Ellipsis), hda_ldda: DatasetSourceType = Query(hda)) → DatasetInheritanceChain

get_content_as_text(*, trans=Depends(get_trans), dataset_id: DecodedDatabaseIdField = Path(Ellipsis)) → DatasetTextContentDetails

converted_ext(*, trans=Depends(get_trans), dataset_id: DecodedDatabaseIdField = Path(Ellipsis), ext: str = Path(Ellipsis), serialization_params: SerializationParams = Depends(query_serialization_params)) → Union[HDADetailed, HDASummary]

Return information about datasets made by converting this dataset to a new format.

If there is no existing converted dataset for the format in ext, one will be created.

Note: view and keys are also available to control the serialization of the dataset.

converted(*, trans=Depends(get_trans), dataset_id: DecodedDatabaseIdField = Path(Ellipsis)) → ConvertedDatasetsMap

Return a map of <converted extension> : <converted id> containing all the existing converted datasets.

update_permissions(*, trans=Depends(get_trans), dataset_id: DecodedDatabaseIdField = Path(Ellipsis), payload: Dict[str, Any] = Body(Ellipsis)) → DatasetAssociationRoles

Set permissions of the given history dataset to the given role ids.

extra_files(*, trans=Depends(get_trans), history_id: DecodedDatabaseIdField = Path(Ellipsis), history_content_id: DecodedDatabaseIdField = Path(Ellipsis))

display_history_content(*, request: Request, trans=Depends(get_trans), history_id: Optional[DecodedDatabaseIdField] = Path(Ellipsis), history_content_id: DecodedDatabaseIdField = Path(Ellipsis), preview: bool = Query(False), filename: Optional[str] = Query(None), to_ext: Optional[str] = Query(None), raw: bool = Query(False))

Streams the dataset for download or the contents preview to be displayed in a browser.

display(*, request: Request, trans=Depends(get_trans), history_content_id: DecodedDatabaseIdField = Path(Ellipsis), preview: bool = Query(False), filename: Optional[str] = Query(None), to_ext: Optional[str] = Query(None), raw: bool = Query(False))

Streams the dataset for download or the contents preview to be displayed in a browser.

get_metadata_file_history_content(*, trans=Depends(get_trans), history_id: DecodedDatabaseIdField = Path(Ellipsis), history_content_id: DecodedDatabaseIdField = Path(Ellipsis), metadata_file: str = Query(Ellipsis))

get_metadata_file_datasets(*, trans=Depends(get_trans), history_content_id: DecodedDatabaseIdField = Path(Ellipsis), metadata_file: str = Query(Ellipsis))

show(*, request: Request, trans=Depends(get_trans), dataset_id: DecodedDatabaseIdField = Path(Ellipsis), hda_ldda: DatasetSourceType = Query(hda), data_type: Optional[RequestDataType] = Query(None), serialization_params: SerializationParams = Depends(query_serialization_params))

Note: Due to the multipurpose nature of this endpoint, which can receive a wild variety of parameters and return different kinds of responses, the documentation here will be limited. To get more information please check the source code.

delete_batch(*, trans=Depends(get_trans), payload: DeleteDatasetBatchPayload = Body(Ellipsis)) → DeleteDatasetBatchResult

Deletes or purges a batch of datasets. Warning: only the ownership of the datasets (and upload state for HDAs) is checked, no other checks or restrictions are made.

compute_hash(*, trans=Depends(get_trans), dataset_id: DecodedDatabaseIdField = Path(Ellipsis), hda_ldda: DatasetSourceType = Query(hda), payload: ComputeDatasetHashPayload = Body(Ellipsis)) → AsyncTaskResultSummary

__init__(*args: Any, **kwargs: Any) → None

galaxy.webapps.galaxy.api.datatypes module

API operations allowing clients to determine datatype supported by Galaxy.

class galaxy.webapps.galaxy.api.datatypes.FastAPIDatatypes(*, datatypes_registry: Registry = GalaxyTypeDepends(_do_resolve))

Bases: object

datatypes_registry: Registry = GalaxyTypeDepends(_do_resolve)

async index(*, extension_only: Optional[bool] = Query(True), upload_only: Optional[bool] = Query(True)) → Union[List[DatatypeDetails], List[str]]

Gets the list of all available data types.

async mapping() → DatatypesMap

Gets mappings for data types.

async types_and_mapping(*, extension_only: Optional[bool] = Query(True), upload_only: Optional[bool] = Query(True)) → DatatypesCombinedMap

Combines the datatype information from (/api/datatypes) and the mapping information from (/api/datatypes/mapping) into a single response.

async sniffers() → List[str]

Gets the list of all installed data type sniffers.

async converters() → DatatypeConverterList

Gets the list of all installed converters.

async edam_formats() → Dict[str, str]

Gets a map of datatypes and their corresponding EDAM formats.

async edam_formats_detailed()

Gets a map of datatypes and their corresponding EDAM formats. EDAM formats contain the EDAM iri, label, and definition.

async edam_data() → Dict[str, str]

Gets a map of datatypes and their corresponding EDAM data.

async edam_data_detailed()

Gets a map of datatypes and their corresponding EDAM data. EDAM data contains the EDAM iri, label, and definition.

__init__(*args: Any, **kwargs: Any) → None

galaxy.webapps.galaxy.api.display_applications module

API operations on annotations.

class galaxy.webapps.galaxy.api.display_applications.DisplayApplicationsController(app: StructuredApp)

Bases: BaseGalaxyAPIController

manager = GalaxyTypeDepends(_do_resolve)

index(trans, **kwd)

GET /api/display_applications/

Returns the list of display applications.

Returns

list of available display applications

Return type

list

reload(trans, payload=None, **kwd)

POST /api/display_applications/reload

Reloads the list of display applications.

Parameters

ids (list) – list containing ids of display to be reloaded

galaxy.webapps.galaxy.api.dynamic_tools module

class galaxy.webapps.galaxy.api.dynamic_tools.DynamicToolsController(app)

Bases: BaseAPIController

RESTful controller for interactions with dynamic tools.

Dynamic tools are tools defined in the database. Use the tools controller to run these tools and view functional information.

index(trans, **kwds)

GET /api/dynamic_tools

This returns meta-information about the dynamic tool, such as tool_uuid. To use the tool or view funtional information such as inputs and outputs, use the standard tools API indexed by the ID (and optionally version) returned from this endpoint.

show(trans, id, **kwd)

GET /api/dynamic_tools/{encoded_dynamic_tool_id|tool_uuid}

create(trans, payload, **kwd)

POST /api/dynamic_tools

The payload is expected to be a tool definition to dynamically load into Galaxy’s toolbox.

Parameters

• representation (dict) – a JSON-ified tool description to load

• uuid (str) – the uuid to associate with the tool being created

delete(trans, id, **kwd)

DELETE /api/dynamic_tools/{encoded_dynamic_tool_id|tool_uuid}

Deactivate the specified dynamic tool. Deactivated tools will not be loaded into the toolbox.

galaxy.webapps.galaxy.api.extended_metadata module

API operations on annotations.

class galaxy.webapps.galaxy.api.extended_metadata.BaseExtendedMetadataController(app: StructuredApp)

Bases: BaseGalaxyAPIController, UsesExtendedMetadataMixin, UsesLibraryMixinItems, UsesStoredWorkflowMixin, Generic[T]

exmeta_item_id: str

index(trans, **kwd)

create(trans, payload, **kwd)

class galaxy.webapps.galaxy.api.extended_metadata.LibraryDatasetExtendMetadataController(app: StructuredApp)

Bases: BaseExtendedMetadataController[LibraryDatasetDatasetAssociation]

controller_name = 'library_dataset_extended_metadata'

exmeta_item_id: str = 'library_content_id'

class galaxy.webapps.galaxy.api.extended_metadata.HistoryDatasetExtendMetadataController(app: StructuredApp)

Bases: BaseExtendedMetadataController[HistoryDatasetAssociation]

controller_name = 'history_dataset_extended_metadata'

exmeta_item_id: str = 'history_content_id'

hda_manager: HDAManager = GalaxyTypeDepends(_do_resolve)

galaxy.webapps.galaxy.api.folder_contents module

API operations on the contents of a library folder.

class galaxy.webapps.galaxy.api.folder_contents.FastAPILibraryFoldersContents(*, service: LibraryFolderContentsService = GalaxyTypeDepends(_do_resolve))

Bases: object

service: LibraryFolderContentsService = GalaxyTypeDepends(_do_resolve)

index(*, trans: ProvidesUserContext = Depends(get_trans), folder_id: LibraryFolderDatabaseIdField = Path(Ellipsis), limit: int = Query(10), offset: int = Query(0), search_text: Optional[str] = Query(None), include_deleted: Optional[bool] = Query(False), order_by: typing_extensions.Literal[name, description, type, size, update_time] = Query(name), sort_desc: Optional[bool] = Query(False))

Returns a list of a folder’s contents (files and sub-folders).

Additional metadata for the folder is provided in the response as a separate object containing data for breadcrumb path building, permissions and other folder’s details.

Note: When sorting, folders always have priority (they show-up before any dataset regardless of the sorting).

Security note: - Accessing a library folder or sub-folder requires only access to the parent library. - Deleted folders can only be accessed by admins or users with MODIFY permission. - Datasets may be public, private or restricted (to a group of users). Listing deleted datasets has the same requirements as folders.

create(*, trans: ProvidesUserContext = Depends(get_trans), folder_id: LibraryFolderDatabaseIdField = Path(Ellipsis), payload: CreateLibraryFilePayload = Body(Ellipsis))

__init__(*args: Any, **kwargs: Any) → None

galaxy.webapps.galaxy.api.folders module

API operations on library folders.

class galaxy.webapps.galaxy.api.folders.FastAPILibraryFolders(*, service: LibraryFoldersService = GalaxyTypeDepends(_do_resolve))

Bases: object

service: LibraryFoldersService = GalaxyTypeDepends(_do_resolve)

show(*, trans: ProvidesUserContext = Depends(get_trans), id: LibraryFolderDatabaseIdField = Path(Ellipsis)) → LibraryFolderDetails

Returns detailed information about the library folder with the given ID.

create(*, trans: ProvidesUserContext = Depends(get_trans), id: LibraryFolderDatabaseIdField = Path(Ellipsis), payload: CreateLibraryFolderPayload = Body(Ellipsis)) → LibraryFolderDetails

Returns detailed information about the newly created library folder.

update(*, trans: ProvidesUserContext = Depends(get_trans), id: LibraryFolderDatabaseIdField = Path(Ellipsis), payload: UpdateLibraryFolderPayload = Body(Ellipsis)) → LibraryFolderDetails

Updates the information of an existing library folder.

delete(*, trans: ProvidesUserContext = Depends(get_trans), id: LibraryFolderDatabaseIdField = Path(Ellipsis), undelete: Optional[bool] = Query(None)) → LibraryFolderDetails

Marks the specified library folder as deleted (or undeleted).

get_permissions(*, trans: ProvidesUserContext = Depends(get_trans), id: LibraryFolderDatabaseIdField = Path(Ellipsis), scope: Optional[LibraryPermissionScope] = Query(None), page: Optional[int] = Query(1), page_limit: Optional[int] = Query(10), q: Optional[str] = Query(None)) → Union[LibraryFolderCurrentPermissions, LibraryAvailablePermissions]

Gets the current or available permissions of a particular library. The results can be paginated and additionally filtered by a query.

set_permissions(*, trans: ProvidesUserContext = Depends(get_trans), id: LibraryFolderDatabaseIdField = Path(Ellipsis), action: Optional[LibraryFolderPermissionAction] = Query(None), payload: LibraryFolderPermissionsPayload = Body(Ellipsis)) → LibraryFolderCurrentPermissions

Sets the permissions to manage a library folder.

__init__(*args: Any, **kwargs: Any) → None

galaxy.webapps.galaxy.api.forms module

API operations on FormDefinition objects.

class galaxy.webapps.galaxy.api.forms.FormDefinitionAPIController(app: StructuredApp)

Bases: BaseGalaxyAPIController

index(trans, **kwd)

GET /api/forms Displays a collection (list) of forms.

show(trans, id, **kwd)

GET /api/forms/{encoded_form_id} Displays information about a form.

create(trans, payload, **kwd)

POST /api/forms Creates a new form.

galaxy.webapps.galaxy.api.genomes module

galaxy.webapps.galaxy.api.genomes.get_id(base, format)

class galaxy.webapps.galaxy.api.genomes.FastAPIGenomes(*, manager: GenomesManager = GalaxyTypeDepends(_do_resolve))

Bases: object

manager: GenomesManager = GalaxyTypeDepends(_do_resolve)

index(*, trans: ProvidesUserContext = Depends(get_trans), chrom_info: bool = Query(None)) → List[List[str]]

show(*, trans: ProvidesUserContext = Depends(get_trans), id: str = Path(Ellipsis), reference: bool = Query(None), num: int = Query(None), chrom: str = Query(None), low: int = Query(None), high: int = Query(None), format: str = Query(None)) → Any

indexes(*, id: str = Path(Ellipsis), type: str = Query(fasta_indexes), format: str = Query(None)) → Any

sequences(*, trans: ProvidesUserContext = Depends(get_trans), id: str = Path(Ellipsis), reference: bool = Query(None), chrom: str = Query(None), low: int = Query(None), high: int = Query(None), format: str = Query(None)) → Any

__init__(*args: Any, **kwargs: Any) → None

galaxy.webapps.galaxy.api.group_roles module

API operations on Group objects.

galaxy.webapps.galaxy.api.group_roles.group_role_to_model(trans, group_id: int, role) → GroupRoleModel

class galaxy.webapps.galaxy.api.group_roles.FastAPIGroupRoles(*, manager: GroupRolesManager = GalaxyTypeDepends(_do_resolve))

Bases: object

manager: GroupRolesManager = GalaxyTypeDepends(_do_resolve)

index(*, trans: ProvidesAppContext = Depends(get_trans), group_id: DecodedDatabaseIdField = Path(Ellipsis)) → GroupRoleListModel

show(*, trans: ProvidesAppContext = Depends(get_trans), group_id: DecodedDatabaseIdField = Path(Ellipsis), role_id: DecodedDatabaseIdField = Path(Ellipsis)) → GroupRoleModel

update(*, trans: ProvidesAppContext = Depends(get_trans), group_id: DecodedDatabaseIdField = Path(Ellipsis), role_id: DecodedDatabaseIdField = Path(Ellipsis)) → GroupRoleModel

delete(*, trans: ProvidesAppContext = Depends(get_trans), group_id: DecodedDatabaseIdField = Path(Ellipsis), role_id: DecodedDatabaseIdField = Path(Ellipsis)) → GroupRoleModel

__init__(*args: Any, **kwargs: Any) → None

galaxy.webapps.galaxy.api.group_users module

API operations on Group objects.

galaxy.webapps.galaxy.api.group_users.group_user_to_model(trans, group_id, user)

class galaxy.webapps.galaxy.api.group_users.FastAPIGroupUsers(*, manager: GroupUsersManager = GalaxyTypeDepends(_do_resolve))

Bases: object

manager: GroupUsersManager = GalaxyTypeDepends(_do_resolve)

index(*, trans: ProvidesAppContext = Depends(get_trans), group_id: DecodedDatabaseIdField = Path(Ellipsis)) → GroupUserListModel

GET /api/groups/{encoded_group_id}/users Displays a collection (list) of groups.

show(*, trans: ProvidesAppContext = Depends(get_trans), group_id: DecodedDatabaseIdField = Path(Ellipsis), user_id: DecodedDatabaseIdField = Path(Ellipsis)) → GroupUserModel

Displays information about a group user.

update(*, trans: ProvidesAppContext = Depends(get_trans), group_id: DecodedDatabaseIdField = Path(Ellipsis), user_id: DecodedDatabaseIdField = Path(Ellipsis)) → GroupUserModel

PUT /api/groups/{encoded_group_id}/users/{encoded_user_id} Adds a user to a group

delete(*, trans: ProvidesAppContext = Depends(get_trans), group_id: DecodedDatabaseIdField = Path(Ellipsis), user_id: DecodedDatabaseIdField = Path(Ellipsis)) → GroupUserModel

DELETE /api/groups/{encoded_group_id}/users/{encoded_user_id} Removes a user from a group

__init__(*args: Any, **kwargs: Any) → None

galaxy.webapps.galaxy.api.groups module

API operations on Group objects.

class galaxy.webapps.galaxy.api.groups.GroupAPIController(app: StructuredApp)

Bases: BaseGalaxyAPIController

manager = GalaxyTypeDepends(_do_resolve)

index(trans: ProvidesAppContext, **kwd)

GET /api/groups Displays a collection (list) of groups.

create(trans: ProvidesAppContext, payload: Dict[str, Any], **kwd)

POST /api/groups Creates a new group.

show(trans: ProvidesAppContext, id: EncodedDatabaseIdField, **kwd)

GET /api/groups/{encoded_group_id} Displays information about a group.

update(trans: ProvidesAppContext, id: EncodedDatabaseIdField, payload: Dict[str, Any], **kwd)

PUT /api/groups/{encoded_group_id} Modifies a group.

galaxy.webapps.galaxy.api.histories module

API operations on a history.

See also

galaxy.model.History

class galaxy.webapps.galaxy.api.histories.DeleteHistoryPayload(*, purge: bool = False)

Bases: BaseModel

purge: bool

class galaxy.webapps.galaxy.api.histories.CreateHistoryFormData(*, 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)

Bases: CreateHistoryPayload

Uses Form data instead of JSON

async as_form(history_id=Form(None), all_datasets=Form(True), archive_source=Form(None), archive_type=Form(url), archive_file=Form(None), /)

name: Optional[str]

history_id: Optional[DecodedDatabaseIdField]

all_datasets: Optional[bool]

archive_source: Optional[str]

archive_type: Optional[HistoryImportArchiveSourceType]

archive_file: Optional[Any]

class galaxy.webapps.galaxy.api.histories.FastAPIHistories(*, service: HistoriesService = GalaxyTypeDepends(_do_resolve))

Bases: object

service: HistoriesService = GalaxyTypeDepends(_do_resolve)

index(*, trans: ProvidesHistoryContext = Depends(get_trans), filter_query_params: FilterQueryParams = Depends(get_filter_query_params), serialization_params: SerializationParams = Depends(query_serialization_params), all: Optional[bool] = Query(False), deleted: Optional[bool] = Query(False)) → List[Union[HistorySummary, HistoryDetailed, Any]]

index_deleted(*, trans: ProvidesHistoryContext = Depends(get_trans), filter_query_params: FilterQueryParams = Depends(get_filter_query_params), serialization_params: SerializationParams = Depends(query_serialization_params), all: Optional[bool] = Query(False)) → List[Union[HistorySummary, HistoryDetailed, Any]]

published(*, trans: ProvidesHistoryContext = Depends(get_trans), filter_query_params: FilterQueryParams = Depends(get_filter_query_params), serialization_params: SerializationParams = Depends(query_serialization_params)) → List[Union[HistorySummary, HistoryDetailed, Any]]

shared_with_me(*, trans: ProvidesHistoryContext = Depends(get_trans), filter_query_params: FilterQueryParams = Depends(get_filter_query_params), serialization_params: SerializationParams = Depends(query_serialization_params)) → List[Union[HistorySummary, HistoryDetailed, Any]]

show_recent(*, trans: ProvidesHistoryContext = Depends(get_trans), serialization_params: SerializationParams = Depends(query_serialization_params)) → Union[HistorySummary, HistoryDetailed, Any]

show(*, trans: ProvidesHistoryContext = Depends(get_trans), history_id: DecodedDatabaseIdField = Path(Ellipsis), serialization_params: SerializationParams = Depends(query_serialization_params)) → Union[HistorySummary, HistoryDetailed, Any]

prepare_store_download(*, trans: ProvidesHistoryContext = Depends(get_trans), history_id: DecodedDatabaseIdField = Path(Ellipsis), payload: StoreExportPayload = Body(Ellipsis)) → AsyncFile

write_store(*, trans: ProvidesHistoryContext = Depends(get_trans), history_id: DecodedDatabaseIdField = Path(Ellipsis), payload: WriteStoreToPayload = Body(Ellipsis)) → AsyncTaskResultSummary

citations(*, trans: ProvidesHistoryContext = Depends(get_trans), history_id: DecodedDatabaseIdField = Path(Ellipsis)) → List[Any]

create(*, trans: ProvidesHistoryContext = Depends(get_trans), payload: CreateHistoryPayload = Depends(_as_form), payload_as_json: Optional[Any] = Depends(try_get_request_body_as_json), serialization_params: SerializationParams = Depends(query_serialization_params)) → Union[JobImportHistoryResponse, HistorySummary, HistoryDetailed, Any]

The new history can also be copied form a existing history or imported from an archive or URL.

delete(*, trans: ProvidesHistoryContext = Depends(get_trans), history_id: DecodedDatabaseIdField = Path(Ellipsis), serialization_params: SerializationParams = Depends(query_serialization_params), purge: bool = Query(False), payload: Optional[DeleteHistoryPayload] = Body(None)) → Union[HistorySummary, HistoryDetailed, Any]

undelete(*, trans: ProvidesHistoryContext = Depends(get_trans), history_id: DecodedDatabaseIdField = Path(Ellipsis), serialization_params: SerializationParams = Depends(query_serialization_params)) → Union[HistorySummary, HistoryDetailed, Any]

update(*, trans: ProvidesHistoryContext = Depends(get_trans), history_id: DecodedDatabaseIdField = Path(Ellipsis), payload: Any = Body(Ellipsis), serialization_params: SerializationParams = Depends(query_serialization_params)) → Union[HistorySummary, HistoryDetailed, Any]

create_from_store(*, trans: ProvidesHistoryContext = Depends(get_trans), serialization_params: SerializationParams = Depends(query_serialization_params), payload: CreateHistoryFromStore = Body(Ellipsis)) → Union[HistorySummary, HistoryDetailed, Any]

create_from_store_async(*, trans: ProvidesHistoryContext = Depends(get_trans), payload: CreateHistoryFromStore = Body(Ellipsis)) → AsyncTaskResultSummary

index_exports(*, trans: ProvidesHistoryContext = Depends(get_trans), history_id: DecodedDatabaseIdField = Path(Ellipsis), limit: Optional[int] = Query(None), offset: Optional[int] = Query(0), accept: str = Header(application / json)) → Union[JobExportHistoryArchiveListResponse, ExportTaskListResponse]

By default the legacy job-based history exports (jeha) are returned.

Change the accept content type header to return the new task-based history exports.

archive_export(*, response: Response, trans=Depends(get_trans), history_id: DecodedDatabaseIdField = Path(Ellipsis), payload: Optional[ExportHistoryArchivePayload] = Body(None)) → Union[JobExportHistoryArchiveModel, JobIdResponse]

This will start a job to create a history export archive.

Calling this endpoint multiple times will return the 202 status code until the archive has been completely generated and is ready to download. When ready, it will return the 200 status code along with the download link information.

If the history will be exported to a directory_uri, instead of returning the download link information, the Job ID will be returned so it can be queried to determine when the file has been written.

Deprecation notice: Please use /api/histories/{id}/prepare_store_download or /api/histories/{id}/write_store instead.

archive_download(*, trans: ProvidesHistoryContext = Depends(get_trans), history_id: DecodedDatabaseIdField = Path(Ellipsis), jeha_id: Union[DecodedDatabaseIdField, typing_extensions.Literal[latest]] = Path(Ellipsis))

See PUT /api/histories/{id}/exports to initiate the creation of the history export - when ready, that route will return 200 status code (instead of 202) and this route can be used to download the archive.

Deprecation notice: Please use /api/histories/{id}/prepare_store_download or /api/histories/{id}/write_store instead.

get_custom_builds_metadata(*, trans: ProvidesHistoryContext = Depends(get_trans), history_id: DecodedDatabaseIdField = Path(Ellipsis)) → CustomBuildsMetadataResponse

sharing(*, trans: ProvidesUserContext = Depends(get_trans), history_id: DecodedDatabaseIdField = Path(Ellipsis)) → SharingStatus

Return the sharing status of the item.

enable_link_access(*, trans: ProvidesUserContext = Depends(get_trans), history_id: DecodedDatabaseIdField = Path(Ellipsis)) → SharingStatus

Makes this item accessible by a URL link and return the current sharing status.

disable_link_access(*, trans: ProvidesUserContext = Depends(get_trans), history_id: DecodedDatabaseIdField = Path(Ellipsis)) → SharingStatus

Makes this item inaccessible by a URL link and return the current sharing status.

publish(*, trans: ProvidesUserContext = Depends(get_trans), history_id: DecodedDatabaseIdField = Path(Ellipsis)) → SharingStatus

Makes this item publicly available by a URL link and return the current sharing status.

unpublish(*, trans: ProvidesUserContext = Depends(get_trans), history_id: DecodedDatabaseIdField = Path(Ellipsis)) → SharingStatus

Removes this item from the published list and return the current sharing status.

share_with_users(*, trans: ProvidesUserContext = Depends(get_trans), history_id: DecodedDatabaseIdField = Path(Ellipsis), payload: ShareWithPayload = Body(Ellipsis)) → ShareWithStatus

Shares this item with specific users and return the current sharing status.

set_slug(*, trans: ProvidesUserContext = Depends(get_trans), history_id: DecodedDatabaseIdField = Path(Ellipsis), payload: SetSlugPayload = Body(Ellipsis))

Sets a new slug to access this item by URL. The new slug must be unique.

__init__(*args: Any, **kwargs: Any) → None

galaxy.webapps.galaxy.api.history_contents module

API operations on the contents of a history.

galaxy.webapps.galaxy.api.history_contents.ContentTypeQueryParam(default: Optional[HistoryContentType])

galaxy.webapps.galaxy.api.history_contents.get_index_query_params(v: Optional[str] = Query(None), dataset_details: Optional[str] = Query(None)) → HistoryContentsIndexParams

This function is meant to be used as a dependency to render the OpenAPI documentation correctly

galaxy.webapps.galaxy.api.history_contents.parse_index_query_params(v: Optional[str] = None, dataset_details: Optional[str] = None, **_) → HistoryContentsIndexParams

Parses query parameters for the history contents index operation and returns a model containing the values in the correct type.

galaxy.webapps.galaxy.api.history_contents.get_legacy_index_query_params(ids: Optional[str] = Query(None), types: Optional[List[str]] = Query(None), details: Optional[str] = Query(None), deleted: Optional[bool] = Query(None), visible: Optional[bool] = Query(None)) → LegacyHistoryContentsIndexParams

This function is meant to be used as a dependency to render the OpenAPI documentation correctly

galaxy.webapps.galaxy.api.history_contents.parse_legacy_index_query_params(ids: Optional[str] = None, types: Optional[Union[List[str], str]] = None, details: Optional[str] = None, deleted: Optional[bool] = None, visible: Optional[bool] = None, **_) → LegacyHistoryContentsIndexParams

Parses (legacy) query parameters for the history contents index operation and returns a model containing the values in the correct type.

galaxy.webapps.galaxy.api.history_contents.parse_content_types(types: Union[List[str], str]) → List[HistoryContentType]

galaxy.webapps.galaxy.api.history_contents.parse_dataset_details(details: Optional[str])

Parses the different values that the dataset_details parameter can have from a string.

galaxy.webapps.galaxy.api.history_contents.get_index_jobs_summary_params(ids: Optional[str] = Query(None), types: Optional[str] = Query(None)) → HistoryContentsIndexJobsSummaryParams

This function is meant to be used as a dependency to render the OpenAPI documentation correctly

galaxy.webapps.galaxy.api.history_contents.parse_index_jobs_summary_params(ids: Optional[str] = None, types: Optional[str] = None, **_) → HistoryContentsIndexJobsSummaryParams

Parses query parameters for the history contents index_jobs_summary operation and returns a model containing the values in the correct type.

class galaxy.webapps.galaxy.api.history_contents.FastAPIHistoryContents(*, service: HistoriesContentsService = GalaxyTypeDepends(_do_resolve))

Bases: object

service: HistoriesContentsService = GalaxyTypeDepends(_do_resolve)

index_typed(*, trans: ProvidesHistoryContext = Depends(get_trans), history_id: DecodedDatabaseIdField = Path(Ellipsis), index_params: HistoryContentsIndexParams = Depends(get_index_query_params), type: HistoryContentType = Path(Ellipsis), legacy_params: LegacyHistoryContentsIndexParams = Depends(get_legacy_index_query_params), serialization_params: SerializationParams = Depends(query_serialization_params), filter_query_params: FilterQueryParams = Depends(get_filter_query_params), accept: str = Header(application / json)) → Union[HistoryContentsResult, HistoryContentsWithStatsResult]

Return a list of either HDA/HDCA data for the history with the given ID.

• The contents can be filtered and queried using the appropriate parameters.

• The amount of information returned for each item can be customized.

Note: Anonymous users are allowed to get their current history contents.

index(*, trans: ProvidesHistoryContext = Depends(get_trans), history_id: DecodedDatabaseIdField = Path(Ellipsis), index_params: HistoryContentsIndexParams = Depends(get_index_query_params), type: Optional[str] = Query(None), legacy_params: LegacyHistoryContentsIndexParams = Depends(get_legacy_index_query_params), serialization_params: SerializationParams = Depends(query_serialization_params), filter_query_params: FilterQueryParams = Depends(get_filter_query_params), accept: str = Header(application / json)) → Union[HistoryContentsResult, HistoryContentsWithStatsResult]

Return a list of HDA/HDCA data for the history with the given ID.

• The contents can be filtered and queried using the appropriate parameters.

• The amount of information returned for each item can be customized.

Note: Anonymous users are allowed to get their current history contents.

show_jobs_summary(*, trans: ProvidesHistoryContext = Depends(get_trans), history_id: DecodedDatabaseIdField = Path(Ellipsis), id: DecodedDatabaseIdField = Path(Ellipsis), type: HistoryContentType = Path(Ellipsis)) → Union[galaxy.schema.schema.JobStateSummary, galaxy.schema.schema.ImplicitCollectionJobsStateSummary, galaxy.schema.schema.WorkflowInvocationStateSummary][Union[JobStateSummary, ImplicitCollectionJobsStateSummary, WorkflowInvocationStateSummary]]

Return detailed information about an HDA or HDCAs jobs.

Warning: We allow anyone to fetch job state information about any object they can guess an encoded ID for - it isn’t considered protected data. This keeps polling IDs as part of state calculation for large histories and collections as efficient as possible.

show(*, trans: ProvidesHistoryContext = Depends(get_trans), history_id: DecodedDatabaseIdField = Path(Ellipsis), id: DecodedDatabaseIdField = Path(Ellipsis), type: HistoryContentType = Path(Ellipsis), fuzzy_count: Optional[int] = Query(None), serialization_params: SerializationParams = Depends(query_serialization_params)) → Union[HDADetailed, HDASummary, HDCADetailed, HDCASummary, CustomHistoryItem]

Return detailed information about an HDA or HDCA within a history.

Note: Anonymous users are allowed to get their current history contents.

show_legacy(*, trans: ProvidesHistoryContext = Depends(get_trans), history_id: DecodedDatabaseIdField = Path(Ellipsis), type: HistoryContentType = Query(dataset), id: DecodedDatabaseIdField = Path(Ellipsis), fuzzy_count: Optional[int] = Query(None), serialization_params: SerializationParams = Depends(query_serialization_params)) → Union[HDADetailed, HDASummary, HDCADetailed, HDCASummary, CustomHistoryItem]

Return detailed information about an HDA or HDCA within a history.

Note: Anonymous users are allowed to get their current history contents.

prepare_store_download(*, trans: ProvidesHistoryContext = Depends(get_trans), history_id: DecodedDatabaseIdField = Path(Ellipsis), id: DecodedDatabaseIdField = Path(Ellipsis), type: HistoryContentType = Path(Ellipsis), payload: StoreExportPayload = Body(Ellipsis)) → AsyncFile

write_store(*, trans: ProvidesHistoryContext = Depends(get_trans), history_id: DecodedDatabaseIdField = Path(Ellipsis), id: DecodedDatabaseIdField = Path(Ellipsis), type: HistoryContentType = Path(Ellipsis), payload: WriteStoreToPayload = Body(Ellipsis)) → AsyncTaskResultSummary

index_jobs_summary(*, trans: ProvidesHistoryContext = Depends(get_trans), history_id: DecodedDatabaseIdField = Path(Ellipsis), params: HistoryContentsIndexJobsSummaryParams = Depends(get_index_jobs_summary_params)) → List[Union[galaxy.schema.schema.JobStateSummary, galaxy.schema.schema.ImplicitCollectionJobsStateSummary, galaxy.schema.schema.WorkflowInvocationStateSummary][Union[JobStateSummary, ImplicitCollectionJobsStateSummary, WorkflowInvocationStateSummary]]]

Return job state summary info for jobs, implicit groups jobs for collections or workflow invocations.

Warning: We allow anyone to fetch job state information about any object they can guess an encoded ID for - it isn’t considered protected data. This keeps polling IDs as part of state calculation for large histories and collections as efficient as possible.

download_dataset_collection_history_content(*, trans: ProvidesHistoryContext = Depends(get_trans), history_id: Optional[DecodedDatabaseIdField] = Path(Ellipsis), id: DecodedDatabaseIdField = Path(Ellipsis))

Download the content of a history dataset collection as a zip archive while maintaining approximate collection structure.

download_dataset_collection(*, trans: ProvidesHistoryContext = Depends(get_trans), id: DecodedDatabaseIdField = Path(Ellipsis))

Download the content of a history dataset collection as a zip archive while maintaining approximate collection structure.

prepare_collection_download(*, trans: ProvidesHistoryContext = Depends(get_trans), id: DecodedDatabaseIdField = Path(Ellipsis)) → AsyncFile

The history dataset collection will be written as a zip archive to the returned short term storage object. Progress tracking this file’s creation can be tracked with the short_term_storage API.

create_typed(*, trans: ProvidesHistoryContext = Depends(get_trans), history_id: DecodedDatabaseIdField = Path(Ellipsis), type: HistoryContentType = Path(Ellipsis), serialization_params: SerializationParams = Depends(query_serialization_params), payload: CreateHistoryContentPayload = Body(Ellipsis)) → Union[HDADetailed, HDASummary, HDCADetailed, HDCASummary, CustomHistoryItem, List[Union[HDADetailed, HDASummary, HDCADetailed, HDCASummary, CustomHistoryItem]]]

Create a new HDA or HDCA in the given History.

create(*, trans: ProvidesHistoryContext = Depends(get_trans), history_id: DecodedDatabaseIdField = Path(Ellipsis), type: Optional[HistoryContentType] = Query(None), serialization_params: SerializationParams = Depends(query_serialization_params), payload: CreateHistoryContentPayload = Body(Ellipsis)) → Union[HDADetailed, HDASummary, HDCADetailed, HDCASummary, CustomHistoryItem, List[Union[HDADetailed, HDASummary, HDCADetailed, HDCASummary, CustomHistoryItem]]]

Create a new HDA or HDCA in the given History.

update_permissions(*, trans: ProvidesHistoryContext = Depends(get_trans), history_id: DecodedDatabaseIdField = Path(Ellipsis), dataset_id: DecodedDatabaseIdField = Path(Ellipsis), payload: Dict[str, Any] = Body(Ellipsis)) → DatasetAssociationRoles

Set permissions of the given history dataset to the given role ids.

update_batch(*, trans: ProvidesHistoryContext = Depends(get_trans), history_id: DecodedDatabaseIdField = Path(Ellipsis), serialization_params: SerializationParams = Depends(query_serialization_params), payload: UpdateHistoryContentsBatchPayload = Body(Ellipsis)) → HistoryContentsResult

Batch update specific properties of a set items contained in the given History.

If you provide an invalid/unknown property key the request will not fail, but no changes will be made to the items.

bulk_operation(*, trans: ProvidesHistoryContext = Depends(get_trans), history_id: DecodedDatabaseIdField = Path(Ellipsis), filter_query_params: ValueFilterQueryParams = Depends(get_value_filter_query_params), payload: HistoryContentBulkOperationPayload = Body(Ellipsis)) → HistoryContentBulkOperationResult

Executes an operation on a set of items contained in the given History.

The items to be processed can be explicitly set or determined by a dynamic query.

validate(*, trans: ProvidesHistoryContext = Depends(get_trans), history_id: DecodedDatabaseIdField = Path(Ellipsis), id: DecodedDatabaseIdField = Path(Ellipsis)) → dict

Validates the metadata associated with a dataset within a History.

update_typed(*, trans: ProvidesHistoryContext = Depends(get_trans), history_id: DecodedDatabaseIdField = Path(Ellipsis), id: DecodedDatabaseIdField = Path(Ellipsis), type: HistoryContentType = Path(Ellipsis), serialization_params: SerializationParams = Depends(query_serialization_params), payload: UpdateHistoryContentsPayload = Body(Ellipsis)) → Union[HDADetailed, HDASummary, HDCADetailed, HDCASummary, CustomHistoryItem]

Updates the values for the history content item with the given ID.

update_legacy(*, trans: ProvidesHistoryContext = Depends(get_trans), history_id: DecodedDatabaseIdField = Path(Ellipsis), id: DecodedDatabaseIdField = Path(Ellipsis), type: HistoryContentType = Query(dataset), serialization_params: SerializationParams = Depends(query_serialization_params), payload: UpdateHistoryContentsPayload = Body(Ellipsis)) → Union[HDADetailed, HDASummary, HDCADetailed, HDCASummary, CustomHistoryItem]

Updates the values for the history content item with the given ID.

delete_typed(*, response: Response, trans: ProvidesHistoryContext = Depends(get_trans), history_id: DecodedDatabaseIdField = Path(Ellipsis), id: DecodedDatabaseIdField = Path(Ellipsis), type: HistoryContentType = Path(Ellipsis), serialization_params: SerializationParams = Depends(query_serialization_params), purge: Optional[bool] = Query(False), recursive: Optional[bool] = Query(False), stop_job: Optional[bool] = Query(False), payload: DeleteHistoryContentPayload = Body(None))

Delete the history content with the given ID and path specified type.

Note: Currently does not stop any active jobs for which this dataset is an output.

delete_legacy(*, response: Response, trans: ProvidesHistoryContext = Depends(get_trans), history_id: DecodedDatabaseIdField = Path(Ellipsis), id: DecodedDatabaseIdField = Path(Ellipsis), type: HistoryContentType = Query(dataset), serialization_params: SerializationParams = Depends(query_serialization_params), purge: Optional[bool] = Query(False), recursive: Optional[bool] = Query(False), stop_job: Optional[bool] = Query(False), payload: DeleteHistoryContentPayload = Body(None))

Delete the history content with the given ID and query specified type (defaults to dataset).

Note: Currently does not stop any active jobs for which this dataset is an output.

archive_named(*, trans: ProvidesHistoryContext = Depends(get_trans), history_id: DecodedDatabaseIdField = Path(Ellipsis), filename: str = Path(Ellipsis), format: str = Path(Ellipsis), dry_run: Optional[bool] = Query(True), filter_query_params: FilterQueryParams = Depends(get_filter_query_params))

Build and return a compressed archive of the selected history contents.

Note: this is a volatile endpoint and settings and behavior may change.

archive(*, trans: ProvidesHistoryContext = Depends(get_trans), history_id: DecodedDatabaseIdField = Path(Ellipsis), filename: Optional[str] = Query(None), dry_run: Optional[bool] = Query(True), filter_query_params: FilterQueryParams = Depends(get_filter_query_params))

Build and return a compressed archive of the selected history contents.

Note: this is a volatile endpoint and settings and behavior may change.

create_from_store(*, trans: ProvidesHistoryContext = Depends(get_trans), history_id: DecodedDatabaseIdField = Path(Ellipsis), serialization_params: SerializationParams = Depends(query_serialization_params), create_payload: CreateHistoryContentFromStore = Body(Ellipsis)) → List[Union[HDADetailed, HDASummary, HDCADetailed, HDCASummary, CustomHistoryItem]]

Create history contents from model store. Input can be a tarfile created with build_objects script distributed with galaxy-data, from an exported history with files stripped out, or hand-crafted JSON dictionary.

materialize_dataset(*, trans: ProvidesHistoryContext = Depends(get_trans), history_id: DecodedDatabaseIdField = Path(Ellipsis), id: DecodedDatabaseIdField = Path(Ellipsis)) → AsyncTaskResultSummary

materialize_to_history(*, trans: ProvidesHistoryContext = Depends(get_trans), history_id: DecodedDatabaseIdField = Path(Ellipsis), materialize_api_payload: MaterializeDatasetInstanceAPIRequest = Body(Ellipsis)) → AsyncTaskResultSummary

__init__(*args: Any, **kwargs: Any) → None

galaxy.webapps.galaxy.api.item_tags module

API operations related to tagging items.

class galaxy.webapps.galaxy.api.item_tags.BaseItemTagsController(app: StructuredApp)

Bases: BaseGalaxyAPIController, UsesTagsMixin

index(trans, **kwd)

show(trans, tag_name, **kwd)

create(trans, tag_name, payload=None, **kwd)

update(trans, tag_name, payload=None, **kwd)

delete(trans, tag_name, **kwd)

class galaxy.webapps.galaxy.api.item_tags.HistoryContentTagsController(app: StructuredApp)

Bases: BaseItemTagsController

controller_name = 'history_content_tags'

tagged_item_class = 'HistoryDatasetAssociation'

tagged_item_id = 'history_content_id'

class galaxy.webapps.galaxy.api.item_tags.HistoryTagsController(app: StructuredApp)

Bases: BaseItemTagsController

controller_name = 'history_tags'

tagged_item_class = 'History'

tagged_item_id = 'history_id'

class galaxy.webapps.galaxy.api.item_tags.WorkflowTagsController(app: StructuredApp)

Bases: BaseItemTagsController

controller_name = 'workflow_tags'

tagged_item_class = 'StoredWorkflow'

tagged_item_id = 'workflow_id'

galaxy.webapps.galaxy.api.job_files module

API for asynchronous job running mechanisms can use to fetch or put files related to running and queued jobs.

class galaxy.webapps.galaxy.api.job_files.JobFilesAPIController(app: StructuredApp)

Bases: BaseGalaxyAPIController

This job files controller allows remote job running mechanisms to read and modify the current state of files for queued and running jobs. It is certainly not meant to represent part of Galaxy’s stable, user facing API.

Furthermore, even if a user key corresponds to the user running the job, it should not be accepted for authorization - this API allows access to low-level unfiltered files and such authorization would break Galaxy’s security model for tool execution.

index(trans, job_id, **kwargs)

GET /api/jobs/{job_id}/files

Get a file required to staging a job (proper datasets, extra inputs, task-split inputs, working directory files).

Parameters

• job_id (str) – encoded id string of the job

• path (str) – Path to file.

• job_key (str) – A key used to authenticate this request as acting on behalf or a job runner for the specified job.

..note:

This API method is intended only for consumption by job runners, not end users.

Return type

binary

Returns

contents of file

create(self, trans, job_id, payload, **kwargs)

• POST /api/jobs/{job_id}/files

  Populate an output file (formal dataset, task split part, working directory file (such as those related to metadata)). This should be a multipart post with a ‘file’ parameter containing the contents of the actual file to create.

Parameters

• job_id (str) – encoded id string of the job

• payload (dict) – dictionary structure containing:: ‘job_key’ = Key authenticating ‘path’ = Path to file to create.

..note:

This API method is intended only for consumption by job runners, not end users.

Return type

dict

Returns

an okay message

galaxy.webapps.galaxy.api.job_lock module

galaxy.webapps.galaxy.api.job_lock.job_lock_status(job_manager: JobManager = GalaxyTypeDepends(_do_resolve)) → JobLock

Get job lock status.

galaxy.webapps.galaxy.api.job_lock.update_job_lock(job_manager: JobManager = GalaxyTypeDepends(_do_resolve), job_lock: JobLock = Body(Ellipsis)) → JobLock

Set job lock status.

galaxy.webapps.galaxy.api.job_ports module

API for asynchronous job running mechanisms can use to fetch or put files related to running and queued jobs.

class galaxy.webapps.galaxy.api.job_ports.JobPortsAPIController(app: StructuredApp)

Bases: BaseGalaxyAPIController

This job files controller allows remote job running mechanisms to modify the current state of ports for queued and running jobs. It is certainly not meant to represent part of Galaxy’s stable, user facing API.

See the JobFiles API for information about per-job API keys.

__init__(app: StructuredApp)

Initialize an interface for application ‘app’

create(self, trans, job_id, payload, **kwargs)

• POST /api/jobs/{job_id}/ports

  Populate port information for interactive tools.

Parameters

• job_id (str) – encoded id string of the job

• payload (dict) – dictionary structure containing:: ‘job_key’ = Key authenticating ‘container_runtime’ = Path to file to create.

..note:

This API method is intended only for consumption by job runners, not end users.

Return type

dict

Returns

an okay message

galaxy.webapps.galaxy.api.jobs module

API operations on a jobs.

See also

galaxy.model.Jobs

class galaxy.webapps.galaxy.api.jobs.FastAPIJobs(*, service: JobsService = GalaxyTypeDepends(_do_resolve))

Bases: object

service: JobsService = GalaxyTypeDepends(_do_resolve)

show(*, id: DecodedDatabaseIdField, trans: ProvidesUserContext = Depends(get_trans), full: Optional[bool] = False) → Dict[str, Any]

Return dictionary containing description of job data

Parameters - id: ID of job to return - full: Return extra information ?

index(*, trans: ProvidesUserContext = Depends(get_trans), states: Optional[List[str]] = Depends(parse_elements), user_details: bool = Query(False), user_id: Optional[DecodedDatabaseIdField] = Query(None), view: JobIndexViewEnum = Query(collection), tool_ids: Optional[List[str]] = Depends(parse_elements), tool_ids_like: Optional[List[str]] = Depends(parse_elements), date_range_min: Optional[Union[datetime, date]] = Query(None), date_range_max: Optional[Union[datetime, date]] = Query(None), history_id: Optional[DecodedDatabaseIdField] = Query(None), workflow_id: Optional[DecodedDatabaseIdField] = Query(None), invocation_id: Optional[DecodedDatabaseIdField] = Query(None), order_by: JobIndexSortByEnum = Query(update_time), search: Optional[str] = Query(None), limit: int = Query(500), offset: int = Query(0)) → List[Dict[str, Any]]

__init__(*args: Any, **kwargs: Any) → None

class galaxy.webapps.galaxy.api.jobs.JobController(app: StructuredApp)

Bases: BaseGalaxyAPIController, UsesVisualizationMixin

job_manager = GalaxyTypeDepends(_do_resolve)

job_search = GalaxyTypeDepends(_do_resolve)

hda_manager = GalaxyTypeDepends(_do_resolve)

common_problems(trans: ProvidesUserContext, id, **kwd)

• GET /api/jobs/{id}/common_problems

  check inputs and job for common potential problems to aid in error reporting

inputs(trans: ProvidesUserContext, id, **kwd) → List[dict]

GET /api/jobs/{id}/inputs

returns input datasets created by job

Parameters

id (string) – Encoded job id

Return type

list of dicts

Returns

list of dictionaries containing input dataset associations

outputs(trans, id)

• GET /api/jobs/{id}/outputs

  returns output datasets created by job

Parameters

id (string) – Encoded job id

Return type

list of dicts

Returns

list of dictionaries containing output dataset associations

delete(trans, id)

• Delete /api/jobs/{id}

  cancels specified job

Parameters

• id (string) – Encoded job id

• message (string) – Stop message.

resume(trans: ProvidesUserContext, id, **kwd) → List[dict]

• PUT /api/jobs/{id}/resume

  Resumes a paused job

Parameters

id (string) – Encoded job id

Return type

list of dicts

Returns

list of dictionaries containing output dataset associations

metrics(trans: ProvidesUserContext, **kwd)

• GET /api/jobs/{job_id}/metrics

• GET /api/datasets/{dataset_id}/metrics

  Return job metrics for specified job. Job accessibility checks are slightly different than dataset checks, so both methods are available.

Parameters

• job_id (string) – Encoded job id

• dataset_id (string) – Encoded HDA or LDDA id

• hda_ldda (string) – hda if dataset_id is an HDA id (default), ldda if it is an ldda id.

Return type

list

Returns

list containing job metrics

destination_params(trans: ProvidesUserContext, **kwd)

• GET /api/jobs/{job_id}/destination_params

  Return destination parameters for specified job.

Parameters

job_id (string) – Encoded job id

Return type

list

Returns

list containing job destination parameters

parameters_display(trans: ProvidesUserContext, **kwd)

• GET /api/jobs/{job_id}/parameters_display

• GET /api/datasets/{dataset_id}/parameters_display

  Resolve parameters as a list for nested display. More client logic here than is ideal but it is hard to reason about tool parameter types on the client relative to the server. Job accessibility checks are slightly different than dataset checks, so both methods are available.

  This API endpoint is unstable and tied heavily to Galaxy’s JS client code, this endpoint will change frequently.

Parameters

• job_id (string) – Encoded job id

• dataset_id (string) – Encoded HDA or LDDA id

• hda_ldda (string) – hda if dataset_id is an HDA id (default), ldda if it is an ldda id.

Return type

list

Returns

job parameters for for display

build_for_rerun(trans: ProvidesHistoryContext, id, **kwd)

• GET /api/jobs/{id}/build_for_rerun

  returns a tool input/param template prepopulated with this job’s information, suitable for rerunning or rendering parameters of the job.

Parameters

id (string) – Encoded job id

Return type

dictionary

Returns

dictionary containing output dataset associations

create(trans: ProvidesUserContext, payload, **kwd)

See the create method in tools.py in order to submit a job.

search(trans, payload)

• POST /api/jobs/search:

  return jobs for current user

Parameters

payload (dict) – Dictionary containing description of requested job. This is in the same format as a request to POST /apt/tools would take to initiate a job

Return type

list

Returns

list of dictionaries containing summary job information of the jobs that match the requested job run

This method is designed to scan the list of previously run jobs and find records of jobs that had the exact some input parameters and datasets. This can be used to minimize the amount of repeated work, and simply recycle the old results.

error(trans, id)

• POST /api/jobs/{id}/error

  submits a bug report via the API.

Parameters

id (string) – Encoded job id

Return type

dictionary

Returns

dictionary containing information regarding where the error report was sent.

show_job_lock(trans: ProvidesUserContext, **kwd)

• GET /api/job_lock

  return boolean indicating if job lock active.

update_job_lock(trans: ProvidesUserContext, payload, **kwd)

• PUT /api/job_lock

  return boolean indicating if job lock active.

galaxy.webapps.galaxy.api.libraries module

API operations on a data library.

class galaxy.webapps.galaxy.api.libraries.FastAPILibraries(*, service: LibrariesService = GalaxyTypeDepends(_do_resolve))

Bases: object

service: LibrariesService = GalaxyTypeDepends(_do_resolve)

index(*, trans: ProvidesUserContext = Depends(get_trans), deleted: Optional[bool] = Query(None)) → LibrarySummaryList

Returns a list of summary data for all libraries.

index_deleted(*, trans: ProvidesUserContext = Depends(get_trans)) → LibrarySummaryList

Returns a list of summary data for all libraries marked as deleted.

show(*, trans: ProvidesUserContext = Depends(get_trans), id: DecodedDatabaseIdField = Path(Ellipsis)) → LibrarySummary

Returns summary information about a particular library.

create(*, trans: ProvidesUserContext = Depends(get_trans), payload: CreateLibraryPayload = Body(Ellipsis)) → LibrarySummary

Creates a new library and returns its summary information. Currently, only admin users can create libraries.

create_from_store(*, trans: ProvidesUserContext = Depends(get_trans), payload: CreateLibrariesFromStore = Body(Ellipsis)) → List[LibrarySummary]

update(*, trans: ProvidesUserContext = Depends(get_trans), id: DecodedDatabaseIdField = Path(Ellipsis), payload: UpdateLibraryPayload = Body(Ellipsis)) → LibrarySummary

Updates the information of an existing library.

delete(*, trans: ProvidesUserContext = Depends(get_trans), id: DecodedDatabaseIdField = Path(Ellipsis), undelete: Optional[bool] = Query(None), payload: Optional[DeleteLibraryPayload] = Body(None)) → LibrarySummary

Marks the specified library as deleted (or undeleted). Currently, only admin users can delete or restore libraries.

get_permissions(*, trans: ProvidesUserContext = Depends(get_trans), id: DecodedDatabaseIdField = Path(Ellipsis), scope: Optional[LibraryPermissionScope] = Query(None), is_library_access: Optional[bool] = Query(None), page: Optional[int] = Query(1), page_limit: Optional[int] = Query(10), q: Optional[str] = Query(None)) → Union[LibraryCurrentPermissions, LibraryAvailablePermissions]

Gets the current or available permissions of a particular library. The results can be paginated and additionally filtered by a query.

set_permissions(*, trans: ProvidesUserContext = Depends(get_trans), id: DecodedDatabaseIdField = Path(Ellipsis), action: Optional[LibraryPermissionAction] = Query(None), payload: Union[LibraryPermissionsPayload, LegacyLibraryPermissionsPayload] = Body(Ellipsis)) → Union[LibraryLegacySummary, LibraryCurrentPermissions]

Sets the permissions to access and manipulate a library.

__init__(*args: Any, **kwargs: Any) → None

galaxy.webapps.galaxy.api.library_contents module

API operations on the contents of a data library.

class galaxy.webapps.galaxy.api.library_contents.LibraryContentsController(app: StructuredApp, hda_manager: HDAManager)

Bases: BaseGalaxyAPIController, UsesLibraryMixinItems, UsesFormDefinitionsMixin, LibraryActions

__init__(app: StructuredApp, hda_manager: HDAManager)

Initialize an interface for application ‘app’

index(trans, library_id, **kwd)

GET /api/libraries/{library_id}/contents:

Return a list of library files and folders.

Note

This endpoint is slow for large libraries. Returns all content traversing recursively through all folders.

See also

galaxy.webapps.galaxy.api.FolderContentsController.index for a faster non-recursive solution

Parameters

library_id (str) – the encoded id of the library

Returns

list of dictionaries of the form:

• id: the encoded id of the library item

• name: the ‘library path’

  or relationship of the library item to the root

• type: ‘file’ or ‘folder’

• url: the url to get detailed information on the library item

Return type

list

Raises

MalformedId, InconsistentDatabase, RequestParameterInvalidException, InternalServerError

show(trans, id, library_id, **kwd)

GET /api/libraries/{library_id}/contents/{id}

Returns information about library file or folder.

Parameters

• id (str) – the encoded id of the library item to return

• library_id (str) – the encoded id of the library that contains this item

Returns

detailed library item information

Return type

dict

See also

galaxy.model.LibraryDataset.to_dict() and galaxy.model.LibraryFolder.dict_element_visible_keys

create(trans, library_id, payload, **kwd)

POST /api/libraries/{library_id}/contents:

Create a new library file or folder.

To copy an HDA into a library send create_type of ‘file’ and the HDA’s encoded id in from_hda_id (and optionally ldda_message).

To copy an HDCA into a library send create_type of ‘file’ and the HDCA’s encoded id in from_hdca_id (and optionally ldda_message).

Parameters

• library_id (str) – the encoded id of the library where to create the new item

• payload (dict) –

  dictionary structure containing:

  • folder_id: the encoded id of the parent folder of the new item

  • create_type: the type of item to create (‘file’, ‘folder’ or ‘collection’)

  • from_hda_id: (optional, only if create_type is ‘file’) the

    encoded id of an accessible HDA to copy into the library

  • ldda_message: (optional) the new message attribute of the LDDA created

  • extended_metadata: (optional) sub-dictionary containing any extended

    metadata to associate with the item

  • upload_option: (optional) one of ‘upload_file’ (default), ‘upload_directory’ or ‘upload_paths’

  • server_dir: (optional, only if upload_option is

    ’upload_directory’) relative path of the subdirectory of Galaxy library_import_dir (if admin) or user_library_import_dir (if non-admin) to upload. All and only the files (i.e. no subdirectories) contained in the specified directory will be uploaded.

  • filesystem_paths: (optional, only if upload_option is

    ’upload_paths’ and the user is an admin) file paths on the Galaxy server to upload to the library, one file per line

  • link_data_only: (optional, only when upload_option is

    ’upload_directory’ or ‘upload_paths’) either ‘copy_files’ (default) or ‘link_to_files’. Setting to ‘link_to_files’ symlinks instead of copying the files

  • name: (optional, only if create_type is ‘folder’) name of the

    folder to create

  • description: (optional, only if create_type is ‘folder’)

    description of the folder to create

  • tag_using_filenames: (optional)

    create tags on datasets using the file’s original name

  • tags: (optional)

    create the given list of tags on datasets

Returns

a dictionary describing the new item unless from_hdca_id is supplied, in that case a list of such dictionaries is returned.

Return type

object

update(trans, id, library_id, payload, **kwd)

PUT /api/libraries/{library_id}/contents/{id}

Create an ImplicitlyConvertedDatasetAssociation.

See also

galaxy.model.ImplicitlyConvertedDatasetAssociation

Parameters

• id (str) – the encoded id of the library item to return

• library_id (str) – the encoded id of the library that contains this item

• payload (dict) – dictionary structure containing:: ‘converted_dataset_id’:

Return type

None

Returns

None

delete(trans, library_id, id, **kwd)

DELETE /api/libraries/{library_id}/contents/{id}

Delete the LibraryDataset with the given id.

Parameters

• id (str) – the encoded id of the library dataset to delete

• kwd (dict) –

  (optional) dictionary structure containing:

  • payload: a dictionary itself containing:

    • purge: if True, purge the LD

Return type

dict

Returns

an error object if an error occurred or a dictionary containing: * id: the encoded id of the library dataset, * deleted: if the library dataset was marked as deleted, * purged: if the library dataset was purged

galaxy.webapps.galaxy.api.library_datasets module

API operations on the library datasets.

class galaxy.webapps.galaxy.api.library_datasets.LibraryDatasetsController(app: StructuredApp)

Bases: BaseGalaxyAPIController, UsesVisualizationMixin, LibraryActions

__init__(app: StructuredApp)

Initialize an interface for application ‘app’

show(trans, id, **kwd)

GET /api/libraries/datasets/{encoded_dataset_id}

Show the details of a library dataset.

Parameters

id (an encoded id string) – the encoded id of the library dataset to query

Returns

detailed library dataset information

Return type

dictionary

show_version(trans, encoded_dataset_id, encoded_ldda_id, **kwd)

GET /api/libraries/datasets/{encoded_dataset_id}/versions/{encoded_ldda_id}

Display a specific version of a library dataset (i.e. ldda).

Parameters

• encoded_dataset_id (an encoded id string) – the encoded id of the related library dataset

• encoded_ldda_id (an encoded id string) – the encoded id of the ldda to query

Returns

dict of ldda’s details

Return type

dictionary

Raises

ObjectNotFound

show_roles(trans, encoded_dataset_id, **kwd)

GET /api/libraries/datasets/{encoded_dataset_id}/permissions

Display information about current or available roles for a given dataset permission.

Parameters

• encoded_dataset_id (an encoded id string) – the encoded id of the dataset to query

• scope (string) – either ‘current’ or ‘available’

Returns

either dict of current roles for all permission types or dict of available roles to choose from (is the same for any permission type)

Return type

dictionary

Raises

InsufficientPermissionsException

update(trans, encoded_dataset_id, payload=None, **kwd)

PATCH /api/libraries/datasets/{encoded_dataset_id}

Update the given library dataset (the latest linked ldda).

Parameters

• encoded_dataset_id (an encoded id string) – the encoded id of the library dataset to update

• payload (dict) – dictionary structure containing:: :param name: new ld’s name, must be longer than 0 :type name: str :param misc_info: new ld’s misc info :type misc_info: str :param file_ext: new ld’s extension, must exist in the Galaxy registry :type file_ext: str :param genome_build: new ld’s genome build :type genome_build: str :param tags: list of dataset tags :type tags: list

Returns

detailed library dataset information

Return type

dictionary

update_permissions(trans, encoded_dataset_id, payload=None, **kwd)

POST /api/libraries/datasets/{encoded_dataset_id}/permissions

Set permissions of the given library dataset to the given role ids.

Parameters

• encoded_dataset_id (an encoded id string) – the encoded id of the dataset to update permissions of

• payload –

  dictionary structure containing:

  param action

  (required) describes what action should be performed available actions: make_private, remove_restrictions, set_permissions

  type action

  string

  param access_ids[]

  list of Role.id defining roles that should have access permission on the dataset

  type access_ids[]

  string or list

  param manage_ids[]

  list of Role.id defining roles that should have manage permission on the dataset

  type manage_ids[]

  string or list

  param modify_ids[]

  list of Role.id defining roles that should have modify permission on the library dataset item

  type modify_ids[]

  string or list

Type

dictionary

Returns

dict of current roles for all available permission types

Return type

dictionary

Raises

RequestParameterInvalidException, ObjectNotFound, InsufficientPermissionsException, InternalServerError RequestParameterMissingException

delete(trans, encoded_dataset_id, **kwd)

DELETE /api/libraries/datasets/{encoded_dataset_id}

Mark the dataset deleted or undeleted.

Parameters

• encoded_dataset_id (an encoded id string) – the encoded id of the dataset to change

• undelete (bool) – flag whether to undeleted instead of deleting

Returns

dict containing information about the dataset

Return type

dictionary

load(trans, payload=None, **kwd)

POST /api/libraries/datasets

Load dataset(s) from the given source into the library.

Parameters

payload –

dictionary structure containing: :param encoded_folder_id: the encoded id of the folder to import dataset(s) to :type encoded_folder_id: an encoded id string :param source:

source the datasets should be loaded from. Source can be:

• user directory

  root folder specified in galaxy.ini as “$user_library_import_dir” example path: path/to/galaxy/$user_library_import_dir/user@example.com/{user can browse everything here} the folder with the user login has to be created beforehand

• (admin)import directory

  root folder specified in galaxy ini as “$library_import_dir” example path: path/to/galaxy/$library_import_dir/{admin can browse everything here}

• (admin)any absolute or relative path

  option allowed with “allow_library_path_paste” in galaxy.ini

type source

str

param link_data

flag whether to link the dataset to data or copy it to Galaxy, defaults to copy while linking is set to True all symlinks will be resolved _once_

type link_data

bool

param preserve_dirs

flag whether to preserve the directory structure when importing dir if False only datasets will be imported

type preserve_dirs

bool

param file_type

file type of the loaded datasets, defaults to ‘auto’ (autodetect)

type file_type

str

param dbkey

dbkey of the loaded genome, defaults to ‘?’ (unknown)

type dbkey

str

param tag_using_filenames

flag whether to generate dataset tags from filenames

type tag_using_filenames

bool

:type dictionary

Returns

dict containing information about the created upload job

Return type

dictionary

Raises

RequestParameterMissingException, AdminRequiredException, ConfigDoesNotAllowException, RequestParameterInvalidException InsufficientPermissionsException, ObjectNotFound

download(trans, archive_format, **kwd)

GET /api/libraries/datasets/download/{archive_format} POST /api/libraries/datasets/download/{archive_format}

Download requested datasets (identified by encoded IDs) in requested archive_format.

example: GET localhost:8080/api/libraries/datasets/download/tbz?ld_ids%255B%255D=a0d84b45643a2678&ld_ids%255B%255D=fe38c84dcd46c828

Note

supported archive_format values are: ‘zip’, ‘tgz’, ‘tbz’, ‘uncompressed’

Parameters

• archive_format (string) – string representing requested archive archive_format

• ld_ids[] (an array) – an array of encoded dataset ids

• folder_ids[] (an array) – an array of encoded folder ids

Returns

either archive with the requested datasets packed inside or a single uncompressed dataset

Return type

file

Raises

MessageException, ItemDeletionException, ItemAccessibilityException, HTTPBadRequest, OSError, IOError, ObjectNotFound

galaxy.webapps.galaxy.api.licenses module

class galaxy.webapps.galaxy.api.licenses.FastAPILicenses(*, licenses_manager: LicensesManager = GalaxyTypeDepends(_do_resolve))

Bases: object

licenses_manager: LicensesManager = GalaxyTypeDepends(_do_resolve)

async index() → List[LicenseMetadataModel]

Returns an index with all the available [SPDX licenses](https://spdx.org/licenses/).

async get(*, id=Path(Ellipsis)) → LicenseMetadataModel

Returns the license metadata associated with the given [SPDX license short ID](https://spdx.github.io/spdx-spec/appendix-I-SPDX-license-list/).

__init__(*args: Any, **kwargs: Any) → None

galaxy.webapps.galaxy.api.metrics module

API operations for for querying and recording user metrics from some client (typically a user’s browser).

class galaxy.webapps.galaxy.api.metrics.FastAPIMetrics(*, manager: MetricsManager = GalaxyTypeDepends(_do_resolve))

Bases: object

manager: MetricsManager = GalaxyTypeDepends(_do_resolve)

create(*, trans: ProvidesUserContext = Depends(get_trans), payload: CreateMetricsPayload = Body(Ellipsis)) → Any

Record any metrics sent and return some status object.

__init__(*args: Any, **kwargs: Any) → None

galaxy.webapps.galaxy.api.page_revisions module

API for updating Galaxy Pages

class galaxy.webapps.galaxy.api.page_revisions.PageRevisionsController(app: StructuredApp)

Bases: BaseGalaxyAPIController

manager: PageManager = GalaxyTypeDepends(_do_resolve)

index(self, trans, page_id, **kwd)

• GET /api/pages/{page_id}/revisions

  return a list of Page revisions

Parameters

page_id – Display the revisions of Page with ID=page_id

Return type

list

Returns

dictionaries containing different revisions of the page

create(self, trans, page_id, payload **kwd)

• POST /api/pages/{page_id}/revisions

  Create a new revision for a page

Parameters

• page_id – Add revision to Page with ID=page_id

• payload – A dictionary containing:: ‘content’ = New content of new page revision

Return type

dictionary

Returns

Dictionary with ‘success’ or ‘error’ element to indicate the result of the request

galaxy.webapps.galaxy.api.pages module

API for updating Galaxy Pages

class galaxy.webapps.galaxy.api.pages.FastAPIPages(*, service: PagesService = GalaxyTypeDepends(_do_resolve))

Bases: object

service: PagesService = GalaxyTypeDepends(_do_resolve)

async index(*, trans: ProvidesUserContext = Depends(get_trans), deleted: bool = Query(False), user_id: Optional[DecodedDatabaseIdField] = Query(None), show_published: bool = Query(True), show_shared: bool = Query(False), sort_by: PageSortByEnum = Query(update_time), sort_desc: bool = Query(True), limit: int = Query(100), offset: int = Query(0)) → PageSummaryList

Get a list with summary information of all Pages available to the user.

create(*, trans: ProvidesUserContext = Depends(get_trans), payload: CreatePagePayload = Body(Ellipsis)) → PageSummary

Get a list with details of all Pages available to the user.

async delete(*, trans: ProvidesUserContext = Depends(get_trans), id: DecodedDatabaseIdField = Path(Ellipsis))

Marks the Page with the given ID as deleted.

async show_pdf(*, trans: ProvidesUserContext = Depends(get_trans), id: DecodedDatabaseIdField = Path(Ellipsis))

Return a PDF document of the last revision of the Page.

This feature may not be available in this Galaxy.

async prepare_pdf(*, trans: ProvidesUserContext = Depends(get_trans), id: DecodedDatabaseIdField = Path(Ellipsis)) → AsyncFile

Return a STS download link for this page to be downloaded as a PDF.

This feature may not be available in this Galaxy.

async show(*, trans: ProvidesUserContext = Depends(get_trans), id: DecodedDatabaseIdField = Path(Ellipsis)) → PageDetails

Return summary information about a specific Page and the content of the last revision.

sharing(*, trans: ProvidesUserContext = Depends(get_trans), id: DecodedDatabaseIdField = Path(Ellipsis)) → SharingStatus

Return the sharing status of the item.

enable_link_access(*, trans: ProvidesUserContext = Depends(get_trans), id: DecodedDatabaseIdField = Path(Ellipsis)) → SharingStatus

Makes this item accessible by a URL link and return the current sharing status.

disable_link_access(*, trans: ProvidesUserContext = Depends(get_trans), id: DecodedDatabaseIdField = Path(Ellipsis)) → SharingStatus

Makes this item inaccessible by a URL link and return the current sharing status.

publish(*, trans: ProvidesUserContext = Depends(get_trans), id: DecodedDatabaseIdField = Path(Ellipsis)) → SharingStatus

Makes this item publicly available by a URL link and return the current sharing status.

unpublish(*, trans: ProvidesUserContext = Depends(get_trans), id: DecodedDatabaseIdField = Path(Ellipsis)) → SharingStatus

Removes this item from the published list and return the current sharing status.

share_with_users(*, trans: ProvidesUserContext = Depends(get_trans), id: DecodedDatabaseIdField = Path(Ellipsis), payload: ShareWithPayload = Body(Ellipsis)) → ShareWithStatus

Shares this item with specific users and return the current sharing status.

set_slug(*, trans: ProvidesUserContext = Depends(get_trans), id: DecodedDatabaseIdField = Path(Ellipsis), payload: SetSlugPayload = Body(Ellipsis))

Sets a new slug to access this item by URL. The new slug must be unique.

__init__(*args: Any, **kwargs: Any) → None

galaxy.webapps.galaxy.api.plugins module

Plugins resource control over the API.

class galaxy.webapps.galaxy.api.plugins.PluginsController(app: StructuredApp)

Bases: BaseGalaxyAPIController

RESTful controller for interactions with plugins.

hda_manager: HDAManager = GalaxyTypeDepends(_do_resolve)

history_manager: HistoryManager = GalaxyTypeDepends(_do_resolve)

index(trans, **kwargs)

GET /api/plugins:

show(trans, id, **kwargs)

GET /api/plugins/{id}:

galaxy.webapps.galaxy.api.provenance module

API operations provenance

class galaxy.webapps.galaxy.api.provenance.BaseProvenanceController(app: StructuredApp)

Bases: BaseGalaxyAPIController

index(trans, **kwd)

show(trans, elem_name, **kwd)

create(trans, tag_name, payload=None, **kwd)

delete(trans, tag_name, **kwd)

class galaxy.webapps.galaxy.api.provenance.HDAProvenanceController(app: StructuredApp)

Bases: BaseProvenanceController

controller_name = 'history_content_provenance'

provenance_item_class = 'HistoryDatasetAssociation'

provenance_item_id = 'history_content_id'

hda_manager: HDAManager = GalaxyTypeDepends(_do_resolve)

class galaxy.webapps.galaxy.api.provenance.LDDAProvenanceController(app: StructuredApp)

Bases: BaseProvenanceController

controller_name = 'ldda_provenance'

provenance_item_class = 'LibraryDatasetDatasetAssociation'

provenance_item_id = 'library_content_id'

hda_manager: HDAManager = GalaxyTypeDepends(_do_resolve)

galaxy.webapps.galaxy.api.quotas module

API operations on Quota objects.

class galaxy.webapps.galaxy.api.quotas.FastAPIQuota(*, service: QuotasService = GalaxyTypeDepends(_do_resolve))

Bases: object

service: QuotasService = GalaxyTypeDepends(_do_resolve)

index(*, trans: ProvidesUserContext = Depends(get_trans)) → QuotaSummaryList

Displays a list with information of quotas that are currently active.

index_deleted(*, trans: ProvidesUserContext = Depends(get_trans)) → QuotaSummaryList

Displays a list with information of quotas that have been deleted.

show(*, trans: ProvidesUserContext = Depends(get_trans), id: DecodedDatabaseIdField = Path(Ellipsis)) → QuotaDetails

Displays details on a particular active quota.

show_deleted(*, trans: ProvidesUserContext = Depends(get_trans), id: DecodedDatabaseIdField = Path(Ellipsis)) → QuotaDetails

Displays details on a particular quota that has been deleted.

create(*, payload: CreateQuotaParams, trans: ProvidesUserContext = Depends(get_trans)) → CreateQuotaResult

Creates a new quota.

update(*, payload: UpdateQuotaParams, id: DecodedDatabaseIdField = Path(Ellipsis), trans: ProvidesUserContext = Depends(get_trans)) → str

Updates an existing quota.

delete(*, id: DecodedDatabaseIdField = Path(Ellipsis), trans: ProvidesUserContext = Depends(get_trans), payload: DeleteQuotaPayload = Body(None)) → str

Deletes an existing quota.

undelete(*, id: DecodedDatabaseIdField = Path(Ellipsis), trans: ProvidesUserContext = Depends(get_trans)) → str

Restores a previously deleted quota.

__init__(*args: Any, **kwargs: Any) → None

galaxy.webapps.galaxy.api.remote_files module

API operations on remote files.

class galaxy.webapps.galaxy.api.remote_files.FastAPIRemoteFiles(*, manager: RemoteFilesManager = GalaxyTypeDepends(_do_resolve))

Bases: object

manager: RemoteFilesManager = GalaxyTypeDepends(_do_resolve)

async index(*, user_ctx: ProvidesUserContext = Depends(get_trans), target: str = Query(ftpdir), format: Optional[RemoteFilesFormat] = Query(uri), recursive: Optional[bool] = Query(None), disable: Optional[RemoteFilesDisableMode] = Query(None)) → List[Dict[str, Any]]

Lists all remote files available to the user from different sources.

async plugins(*, user_ctx: ProvidesUserContext = Depends(get_trans)) → FilesSourcePluginList

Display plugin information for each of the gxfiles:// URI targets available.

__init__(*args: Any, **kwargs: Any) → None

galaxy.webapps.galaxy.api.roles module

API operations on Role objects.

galaxy.webapps.galaxy.api.roles.role_to_model(role)

class galaxy.webapps.galaxy.api.roles.FastAPIRoles(*, role_manager: RoleManager = GalaxyTypeDepends(_do_resolve))

Bases: object

role_manager: RoleManager = GalaxyTypeDepends(_do_resolve)

index(*, trans: ProvidesUserContext = Depends(get_trans)) → RoleListModel

show(*, id: DecodedDatabaseIdField, trans: ProvidesUserContext = Depends(get_trans)) → RoleModel

create(*, trans: ProvidesUserContext = Depends(get_trans), role_definition_model: RoleDefinitionModel = Body(Ellipsis)) → RoleModel

__init__(*args: Any, **kwargs: Any) → None

galaxy.webapps.galaxy.api.sanitize_allow module

API operations allowing clients to retrieve and modify the HTML sanitization allow list.

class galaxy.webapps.galaxy.api.sanitize_allow.SanitizeAllowController(app)

Bases: BaseAPIController

index(trans, **kwd)

GET /api/sanitize_allow Return an object showing the current state of the toolbox and allow list.

create(trans, tool_id, **kwd)

PUT /api/sanitize_allow Add a new tool_id to the allowlist.

delete(trans, tool_id, **kwd)

DELETE /api/sanitize_allow Remove tool_id from allowlist.

galaxy.webapps.galaxy.api.search module

API for searching Galaxy Datasets

class galaxy.webapps.galaxy.api.search.SearchController(app: StructuredApp)

Bases: BaseGalaxyAPIController, SharableItemSecurityMixin

create(trans: ProvidesUserContext, payload: dict, **kwd)

POST /api/search Do a search of the various elements of Galaxy.

galaxy.webapps.galaxy.api.short_term_storage module

API operations around galaxy.web.short_term_storage infrastructure.

class galaxy.webapps.galaxy.api.short_term_storage.FastAPIShortTermStorage(*, short_term_storage_monitor: ShortTermStorageMonitor = GalaxyTypeDepends(_do_resolve))

Bases: object

short_term_storage_monitor: ShortTermStorageMonitor = GalaxyTypeDepends(_do_resolve)

is_ready(*, storage_request_id: UUID) → bool

serve(*, storage_request_id: UUID)

__init__(*args: Any, **kwargs: Any) → None

galaxy.webapps.galaxy.api.tags module

API Controller providing Galaxy Tags

class galaxy.webapps.galaxy.api.tags.FastAPITags(*, manager: TagsManager = GalaxyTypeDepends(_do_resolve))

Bases: object

manager: TagsManager = GalaxyTypeDepends(_do_resolve)

update(*, trans: ProvidesUserContext = Depends(get_trans), payload: ItemTagsPayload = Body(Ellipsis))

Replaces the tags associated with an item with the new ones specified in the payload.

• The previous tags will be __deleted__.

• If no tags are provided in the request body, the currently associated tags will also be __deleted__.

__init__(*args: Any, **kwargs: Any) → None

galaxy.webapps.galaxy.api.tasks module

API Controller providing experimental access to Celery Task State.

class galaxy.webapps.galaxy.api.tasks.FastAPITasks(*, manager: AsyncTasksManager = GalaxyTypeDepends(_do_resolve))

Bases: object

manager: AsyncTasksManager = GalaxyTypeDepends(_do_resolve)

state(*, task_id: UUID) → str

__init__(*args: Any, **kwargs: Any) → None

galaxy.webapps.galaxy.api.tool_data module

class galaxy.webapps.galaxy.api.tool_data.ImportToolDataBundle(*, source: Union[ImportToolDataBundleDatasetSource, ImportToolDataBundleUriSource])

Bases: BaseModel

source: Union[ImportToolDataBundleDatasetSource, ImportToolDataBundleUriSource]

class galaxy.webapps.galaxy.api.tool_data.FastAPIToolData(*, tool_data_manager: ToolDataManager = GalaxyTypeDepends(_do_resolve))

Bases: object

tool_data_manager: ToolDataManager = GalaxyTypeDepends(_do_resolve)

async index() → ToolDataEntryList

Get the list of all available data tables.

async create(*, import_bundle_model: ImportToolDataBundle = Body(Ellipsis)) → AsyncTaskResultSummary

async show(*, table_name: str = Path(Ellipsis)) → ToolDataDetails

Get details of a given tool data table.

async reload(*, table_name: str = Path(Ellipsis)) → ToolDataDetails

Reloads a data table and return its details.

async show_field(*, table_name: str = Path(Ellipsis), field_name: str = Path(Ellipsis)) → ToolDataField

Reloads a data table and return its details.

async download_field_file(*, table_name: str = Path(Ellipsis), field_name: str = Path(Ellipsis), file_name: str = Path(Ellipsis))

Download a file associated with the data table field.

async delete(*, payload: ToolDataItem, table_name: str = Path(Ellipsis)) → ToolDataDetails

Removes an item from a data table and reloads it to return its updated details.

__init__(*args: Any, **kwargs: Any) → None

galaxy.webapps.galaxy.api.tool_dependencies module

API operations allowing clients to manage tool dependencies.

class galaxy.webapps.galaxy.api.tool_dependencies.ToolDependenciesAPIController(app: StructuredApp)

Bases: BaseGalaxyAPIController

__init__(app: StructuredApp)

Initialize an interface for application ‘app’

index(trans: ProvidesAppContext, **kwd)

GET /api/dependency_resolvers

show(trans: ProvidesAppContext, id: str)

GET /api/dependency_resolvers/<id>

update(trans)

PUT /api/dependency_resolvers

Reload tool dependency resolution configuration.

resolver_dependency(trans: ProvidesAppContext, id: str, **kwds)

GET /api/dependency_resolvers/{index}/dependency

Resolve described requirement against specified dependency resolver.

Parameters

• index (int) – index of the dependency resolver

• kwds (dict) – dictionary structure containing extra parameters

• name (str) – name of the requirement to find a dependency for (required)

• version (str) – version of the requirement to find a dependency for (required)

• exact (bool) – require an exact match to specify requirement (do not discard version information to resolve dependency).

Return type

dict

Returns

a dictified description of the dependency, with attribute dependency_type: None if no match was found.

install_dependency(trans: ProvidesAppContext, id: Optional[str] = None, **kwds)

POST /api/dependency_resolvers/{index}/dependency POST /api/dependency_resolvers/dependency

Install described requirement against specified dependency resolver.

Parameters

• index (int) – index of the dependency resolver

• kwds (dict) – dictionary structure containing extra parameters

• name (str) – name of the requirement to find a dependency for (required)

• version (str) – version of the requirement to find a dependency for (required)

• exact (bool) – require an exact match to specify requirement (do not discard version information to resolve dependency).

• tool_id (str) – tool_id to install requirements for

Return type

dict

Returns

a dictified description of the dependency, with attribute dependency_type: None if no match was found.

manager_dependency(trans: ProvidesAppContext, **kwds)

GET /api/dependency_resolvers/dependency

Resolve described requirement against all dependency resolvers, returning the match with highest priority.

Parameters

• index (int) – index of the dependency resolver

• kwds (dict) – dictionary structure containing extra parameters

• name (str) – name of the requirement to find a dependency for (required)

• version (str) – version of the requirement to find a dependency for (required)

• exact (bool) – require an exact match to specify requirement (do not discard version information to resolve dependency).

Return type

dict

Returns

a dictified description of the dependency, with type: None if no match was found.

resolver_requirements(trans: ProvidesAppContext, id, **kwds)

GET /api/dependency_resolvers/{index}/requirements

Find all “simple” requirements that could be resolved “exactly” by this dependency resolver. The dependency resolver must implement ListDependencyResolver.

Parameters

index (int) – index of the dependency resolver

Return type

dict

Returns

a dictified description of the requirement that could be resolved.

manager_requirements(trans: ProvidesAppContext, **kwds)

GET /api/dependency_resolvers/requirements

Find all “simple” requirements that could be resolved “exactly” by all dependency resolvers that support this operation.

Parameters

index (int) – index of the dependency resolver

Return type

dict

Returns

a dictified description of the requirement that could be resolved (keyed on ‘requirement’) and the index of the corresponding resolver (keyed on ‘index’).

clean(trans: ProvidesAppContext, id=None, **kwds)

POST /api/dependency_resolvers/{index}/clean

Cleans up intermediate files created by resolvers during the dependency installation.

Parameters

index (int) – index of the dependency resolver

Return type

dict

Returns

a dictified description of the requirement that could be resolved (keyed on ‘requirement’) and the index of the corresponding resolver (keyed on ‘index’).

summarize_toolbox(trans: ProvidesAppContext, **kwds)

GET /api/dependency_resolvers/toolbox

Summarize requirements across toolbox (for Tool Management grid). This is an experiemental API particularly tied to the GUI - expect breaking changes until this notice is removed.

Container resolution via this API is especially experimental and the container resolution API should be used to summarize this information instead in most cases.

Parameters

• index (int) – index of the dependency resolver

• tool_ids (str) – tool_id to install dependency for

• resolver_type (str) – restrict to uninstall to specified resolver type

• include_containers (bool) – include container resolvers in resolution

• container_type (str) – restrict to uninstall to specified container type

• index_by (str) – By default consider only context of requirements, group tools by requirements. Set this to ‘tools’ to summarize across all tools though. Tools may provide additional context for container resolution for instance.

Return type

list

Returns

dictified descriptions of the dependencies, with attribute dependency_type: None if no match was found.

toolbox_install(trans: ProvidesAppContext, payload, index=None, **kwds)

POST /api/dependency_resolvers/{index}/toolbox/install POST /api/dependency_resolvers/toolbox/install

Install described requirement against specified dependency resolver(s). This is an experiemental API particularly tied to the GUI - expect breaking changes until this notice is removed.

Parameters

• index (int) – index of the dependency resolver

• tool_ids (str) – tool_id to install dependency for

• resolver_type (str) – restrict to uninstall to specified resolver type

• include_containers (bool) – include container resolvers in resolution

• container_type (str) – restrict to uninstall to specified container type

toolbox_uninstall(trans: ProvidesAppContext, payload, index=None, **kwds)

POST /api/dependency_resolvers/{index}/toolbox/uninstall POST /api/dependency_resolvers/toolbox/uninstall

Uninstall described requirement against specified dependency resolver(s). This is an experiemental API particularly tied to the GUI - expect breaking changes until this notice is removed.

Parameters

• index (int) – index of the dependency resolver

• tool_ids (str) – tool_id to install dependency for

• include_containers (bool) – include container resolvers in resolution

• container_type (str) – restrict to uninstall to specified container type

• resolver_type (str) – restrict to uninstall to specified resolver type

unused_dependency_paths(trans: ProvidesAppContext, **kwds)

GET /api/dependency_resolvers/unused_paths

delete_unused_dependency_paths(trans: ProvidesAppContext, payload, **kwds)

PUT /api/dependency_resolvers/unused_paths

galaxy.webapps.galaxy.api.tool_entry_points module

API for asynchronous job running mechanisms can use to fetch or put files related to running and queued jobs.

class galaxy.webapps.galaxy.api.tool_entry_points.ToolEntryPointsAPIController(app: StructuredApp)

Bases: BaseGalaxyAPIController

__init__(app: StructuredApp)

Initialize an interface for application ‘app’

index(trans: ProvidesUserContext, running=False, job_id=None, **kwd)

• GET /api/entry_points

  Returns tool entry point information. Currently passing a job_id parameter is required, as this becomes more general that won’t be needed.

Parameters

• job_id (string) – Encoded job id

• running (boolean) – filter to only include running job entry points.

Return type

list

Returns

list of entry point dictionaries.

access_entry_point(trans: ProvidesUserContext, id, **kwd)

• GET /api/entry_points/{id}/access

  Return the URL target described by the entry point.

Parameters

id (string) – Encoded entry point id

Return type

dictionary

Returns

dictionary containing target for interactivetool entry point

stop_entry_point(trans: ProvidesUserContext, id, **kwds)

DELETE /api/entry_points/{id}

galaxy.webapps.galaxy.api.tool_shed_repositories module

galaxy.webapps.galaxy.api.tool_shed_repositories.get_message_for_no_shed_tool_config()

class galaxy.webapps.galaxy.api.tool_shed_repositories.ToolShedRepositoriesController(app: StructuredApp)

Bases: BaseGalaxyAPIController

RESTful controller for interactions with tool shed repositories.

service: ToolShedRepositoriesService = GalaxyTypeDepends(_do_resolve)

install_repository_revision(trans: ProvidesUserContext, payload, **kwd)

POST /api/tool_shed_repositories/install_repository_revision Install a specified repository revision from a specified tool shed into Galaxy.

Parameters

key – the current Galaxy admin user’s API key

The following parameters are included in the payload. :param tool_shed_url (required): the base URL of the Tool Shed from which to install the Repository :param name (required): the name of the Repository :param owner (required): the owner of the Repository :param changeset_revision (required): the changeset_revision of the RepositoryMetadata object associated with the Repository :param new_tool_panel_section_label (optional):

label of a new section to be added to the Galaxy tool panel in which to load tools contained in the Repository. Either this parameter must be an empty string or the tool_panel_section_id parameter must be an empty string or both must be an empty string (both cannot be used simultaneously).

Parameters

• (optional) (shed_tool_conf) – id of the Galaxy tool panel section in which to load tools contained in the Repository. If this parameter is an empty string and the above new_tool_panel_section_label parameter is an empty string, tools will be loaded outside of any sections in the tool panel. Either this parameter must be an empty string or the tool_panel_section_id parameter must be an empty string of both must be an empty string (both cannot be used s