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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[source]¶

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

class galaxy.webapps.galaxy.api.GalaxyTypeDepends(callable, dep_type)[source]¶

Bases: Depends

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

__init__(callable, dep_type)[source]¶

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

galaxy.webapps.galaxy.api.get_session_manager(app: StructuredApp = Depends(get_app_with_request_session)) → GalaxySessionManager[source]¶

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

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

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

class galaxy.webapps.galaxy.api.UrlBuilder(request: Request)[source]¶

Bases: object

__init__(request: Request)[source]¶

class galaxy.webapps.galaxy.api.GalaxyASGIRequest(request: Request)[source]¶

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)[source]¶

property base: str¶: Base URL of the request.

property host: str¶: The host address.

class galaxy.webapps.galaxy.api.GalaxyASGIResponse(response: Response)[source]¶

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)[source]¶

property headers¶: The response headers.

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

galaxy.webapps.galaxy.api.get_trans(request: Request, response: Response, app: StructuredApp = Depends(get_app_with_request_session), user: Optional[User] = Depends(get_user), galaxy_session: Optional[GalaxySession] = Depends(get_session)) → SessionRequestContext[source]¶

galaxy.webapps.galaxy.api.get_admin_user(trans: SessionRequestContext = Depends(get_trans))[source]¶

class galaxy.webapps.galaxy.api.BaseGalaxyAPIController(app: StructuredApp)[source]¶

Bases: BaseAPIController

__init__(app: StructuredApp)[source]¶: Initialize an interface for application ‘app’

class galaxy.webapps.galaxy.api.RestVerb(value)[source]¶

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>)[source]¶

Bases: InferringRouter

A FastAPI Inferring Router tailored to Galaxy.

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

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])[source]¶

get(*args, **kwd)[source]¶: Extend FastAPI.get to accept a require_admin Galaxy flag.

patch(*args, **kwd)[source]¶: Extend FastAPI.patch to accept a require_admin Galaxy flag.

put(*args, **kwd)[source]¶: Extend FastAPI.put to accept a require_admin Galaxy flag.

post(*args, **kwd)[source]¶: Extend FastAPI.post to accept a require_admin Galaxy flag.

delete(*args, **kwd)[source]¶: Extend FastAPI.delete to accept a require_admin Galaxy flag.

options(*args, **kwd)[source]¶

head(*args, **kwd)[source]¶

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.Optional[~typing.Type[~typing.Any]] = None, 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>)[source]¶

Bases: APIRoute

Determines endpoint to match using content-type.

match_content_type: str¶

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

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

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

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][source]¶: 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)[source]¶

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()[source]¶

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

Submodules¶

galaxy.webapps.galaxy.api.annotations module¶

API operations on annotations.

class galaxy.webapps.galaxy.api.annotations.BaseAnnotationsController(app: StructuredApp)[source]¶

Bases: BaseGalaxyAPIController, UsesStoredWorkflowMixin, UsesAnnotations

tagged_item_id: str¶

index(trans: ProvidesHistoryContext, **kwd)[source]¶

create(trans: ProvidesHistoryContext, payload: dict, **kwd)[source]¶

delete(trans: ProvidesHistoryContext, **kwd)[source]¶

undelete(trans: ProvidesHistoryContext, **kwd)[source]¶

class galaxy.webapps.galaxy.api.annotations.HistoryAnnotationsController(app: StructuredApp)[source]¶

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)[source]¶

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)[source]¶

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)[source]¶

Bases: BaseGalaxyAPIController

authentication_service = GalaxyTypeDepends(_do_resolve)¶

options(trans: GalaxyWebTransaction, **kwd)[source]¶: 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.

get_api_key(trans: GalaxyWebTransaction, **kwd) → APIKeyResponse[source]¶

GET /api/authenticate/baseauth: returns an API key for authenticated user based on BaseAuth headers

Returns: api_key in json format
Return type: dict
Raises: ObjectNotFound, HTTPBadRequest

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)[source]¶

Bases: BaseGalaxyAPIController

RESTfull controller for interaction with Amazon S3.

__init__(app: StructuredApp, cloud_manager: CloudManager, datasets_serializer: DatasetSerializer)[source]¶: Initialize an interface for application ‘app’

index(trans, **kwargs)[source]¶

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)[source]¶

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)[source]¶

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)[source]¶

Bases: BaseGalaxyAPIController

RESTfull controller for defining cloud authorizations.

__init__(app: StructuredApp)[source]¶: Initialize an interface for application ‘app’

index(trans, **kwargs)[source]¶

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)[source]¶

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)[source]¶

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)[source]¶

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[source]¶

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

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

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)[source]¶

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))[source]¶

Bases: object

configuration_manager: ConfigurationManager = GalaxyTypeDepends(_do_resolve)¶

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

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][source]¶: Return Galaxy version information: major/minor version, optional extra info.

dynamic_tool_confs() → List[Dict[str, str]][source]¶: Return dynamic tool configuration files.

decode_id(*, encoded_id: EncodedDatabaseIdField = Path(Ellipsis)) → Dict[str, int][source]¶: Decode a given id.

tool_lineages() → List[Dict[str, Dict]][source]¶: Return tool lineages for tools that have them.

reload_toolbox()[source]¶: 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)[source]¶

Bases: BaseGalaxyAPIController

__init__(app: StructuredApp)[source]¶: Initialize an interface for application ‘app’

index(trans, **kwd)[source]¶: GET /api/container_resolvers

show(trans, index)[source]¶: GET /api/container_resolvers/<id>

resolve(trans, index=None, **kwds)[source]¶

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)[source]¶

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)[source]¶

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)[source]¶

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))[source]¶

Bases: object

service: DatasetCollectionsService = GalaxyTypeDepends(_do_resolve)¶

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

copy(*, trans: ProvidesHistoryContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis), payload: UpdateCollectionAttributePayload = Body(Ellipsis))[source]¶

attributes(*, trans: ProvidesHistoryContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis), instance_type: DatasetCollectionInstanceType = Query(history)) → DatasetCollectionAttributesResult[source]¶

suitable_converters(*, trans: ProvidesHistoryContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis), instance_type: DatasetCollectionInstanceType = Query(history)) → SuitableConverters[source]¶

show(*, trans: ProvidesHistoryContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis), instance_type: DatasetCollectionInstanceType = Query(history)) → Union[HDCADetailed, HDCASummary][source]¶

contents(*, trans: ProvidesHistoryContext = Depends(get_trans), hdca_id: EncodedDatabaseIdField = Path(Ellipsis), parent_id: EncodedDatabaseIdField = Path(Ellipsis), instance_type: DatasetCollectionInstanceType = Query(history), limit: Optional[int] = Query(None), offset: Optional[int] = Query(None)) → DatasetCollectionContentElements[source]¶

__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))[source]¶

Bases: object

service: DatasetsService = GalaxyTypeDepends(_do_resolve)¶

index(*, trans=Depends(get_trans), history_id: Optional[EncodedDatabaseIdField] = 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]][source]¶

show_storage(*, trans=Depends(get_trans), dataset_id: EncodedDatabaseIdField = Path(Ellipsis), hda_ldda: DatasetSourceType = Query(hda)) → DatasetStorageDetails[source]¶

show_inheritance_chain(*, trans=Depends(get_trans), dataset_id: EncodedDatabaseIdField = Path(Ellipsis), hda_ldda: DatasetSourceType = Query(hda)) → DatasetInheritanceChain[source]¶

get_content_as_text(*, trans=Depends(get_trans), dataset_id: EncodedDatabaseIdField = Path(Ellipsis)) → DatasetTextContentDetails[source]¶

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

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: EncodedDatabaseIdField = Path(Ellipsis)) → ConvertedDatasetsMap[source]¶: Return a map of <converted extension> : <converted id> containing all the existing converted datasets.

update_permissions(*, trans=Depends(get_trans), dataset_id: EncodedDatabaseIdField = Path(Ellipsis), payload: Dict[str, Any] = Body(Ellipsis)) → DatasetAssociationRoles[source]¶: Set permissions of the given history dataset to the given role ids.

extra_files(*, trans=Depends(get_trans), history_id: EncodedDatabaseIdField = Path(Ellipsis), history_content_id: EncodedDatabaseIdField = Path(Ellipsis))[source]¶

display(*, request: Request, trans=Depends(get_trans), history_id: Optional[EncodedDatabaseIdField] = Query(None), history_content_id: EncodedDatabaseIdField = Path(Ellipsis), preview: bool = Query(False), filename: Optional[str] = Query(None), to_ext: Optional[str] = Query(None), raw: bool = Query(False))[source]¶: Streams the dataset for download or the contents preview to be displayed in a browser.

get_metadata_file(*, trans=Depends(get_trans), history_id: Optional[EncodedDatabaseIdField] = Query(None), history_content_id: EncodedDatabaseIdField = Path(Ellipsis), metadata_file: str = Query(Ellipsis))[source]¶

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

__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))[source]¶

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]][source]¶: Gets the list of all available data types.

async mapping() → DatatypesMap[source]¶: Gets mappings for data types.

async types_and_mapping(*, extension_only: Optional[bool] = Query(True), upload_only: Optional[bool] = Query(True)) → DatatypesCombinedMap[source]¶: Combines the datatype information from (/api/datatypes) and the mapping information from (/api/datatypes/mapping) into a single response.

async sniffers() → List[str][source]¶: Gets the list of all installed data type sniffers.

async converters() → DatatypeConverterList[source]¶: Gets the list of all installed converters.

async edam_formats() → Dict[str, str][source]¶: Gets a map of datatypes and their corresponding EDAM formats.

async edam_data() → Dict[str, str][source]¶: Gets a map of datatypes and their corresponding EDAM data.

__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)[source]¶

Bases: BaseGalaxyAPIController

manager = GalaxyTypeDepends(_do_resolve)¶

index(trans, **kwd)[source]¶

GET /api/display_applications/

Returns the list of display applications.

Returns: list of available display applications
Return type: list

reload(trans, payload=None, **kwd)[source]¶

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)[source]¶

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)[source]¶

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)[source]¶: GET /api/dynamic_tools/{encoded_dynamic_tool_id|tool_uuid}

create(trans, payload, **kwd)[source]¶

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)[source]¶

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)[source]¶

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

exmeta_item_id: str¶

index(trans, **kwd)[source]¶

create(trans, payload, **kwd)[source]¶

class galaxy.webapps.galaxy.api.extended_metadata.LibraryDatasetExtendMetadataController(app: StructuredApp)[source]¶

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)[source]¶

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.FolderContentsController(app: StructuredApp)[source]¶

Bases: BaseGalaxyAPIController

Class controls retrieval, creation and updating of folder contents.

service: LibraryFolderContentsService = GalaxyTypeDepends(_do_resolve)¶

index(trans, folder_id, limit=None, offset=None, search_text=None, **kwd)[source]¶

GET /api/folders/{encoded_folder_id}/contents?limit={limit}&offset={offset}

Displays a collection (list) of a folder’s contents (files and folders). Encoded folder ID is prepended with ‘F’ if it is a folder as opposed to a data set which does not have it. Full path is provided in response as a separate object providing data for breadcrumb path building.

..example:

limit and offset can be combined. Skip the first two and return five:: ‘?limit=3&offset=5’

Parameters

folder_id (encoded string) – encoded ID of the folder which contents should be library_dataset_dict
offset – offset for returned library folder datasets
limit – limit for returned library folder datasets contents should be library_dataset_dict
kwd (dict) – keyword dictionary with other params

Returns

dictionary containing all items and metadata

Type

dict

Raises

MalformedId, InconsistentDatabase, ObjectNotFound, InternalServerError

create(trans, encoded_folder_id, payload, **kwd)[source]¶

POST /api/folders/{encoded_id}/contents

Create a new library file from an HDA.

Parameters

encoded_folder_id (an encoded id string) – the encoded id of the folder to import dataset(s) to
payload (dict) – dictionary structure containing: :param from_hda_id: (optional) the id of an accessible HDA to copy into the library :type from_hda_id: encoded id :param from_hdca_id: (optional) the id of an accessible HDCA to copy into the library :type from_hdca_id: encoded id :param ldda_message: (optional) the new message attribute of the LDDA created :type ldda_message: str :param extended_metadata: (optional) dub-dictionary containing any extended metadata to associate with the item :type extended_metadata: dict

Returns

a dictionary describing the new item if from_hda_id is supplied or a list of such dictionaries describing the new items if from_hdca_id is supplied.

Return type

object

Raises

ObjectAttributeInvalidException, InsufficientPermissionsException, ItemAccessibilityException, InternalServerError

galaxy.webapps.galaxy.api.folders module¶

API operations on library folders.

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

Bases: object

service: LibraryFoldersService = GalaxyTypeDepends(_do_resolve)¶

show(*, trans: ProvidesUserContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis)) → LibraryFolderDetails[source]¶: Returns detailed information about the library folder with the given ID.

create(*, trans: ProvidesUserContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis), payload: CreateLibraryFolderPayload = Body(Ellipsis)) → LibraryFolderDetails[source]¶: Returns detailed information about the newly created library folder.

update(*, trans: ProvidesUserContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis), payload: UpdateLibraryFolderPayload = Body(Ellipsis)) → LibraryFolderDetails[source]¶: Updates the information of an existing library folder.

delete(*, trans: ProvidesUserContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis), undelete: Optional[bool] = Query(None)) → LibraryFolderDetails[source]¶: Marks the specified library folder as deleted (or undeleted).

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

Bases: BaseGalaxyAPIController

index(trans, **kwd)[source]¶: GET /api/forms Displays a collection (list) of forms.

show(trans, id, **kwd)[source]¶: GET /api/forms/{encoded_form_id} Displays information about a form.

create(trans, payload, **kwd)[source]¶: POST /api/forms Creates a new form.

galaxy.webapps.galaxy.api.genomes module¶

galaxy.webapps.galaxy.api.genomes.get_id(base, format)[source]¶

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

Bases: object

manager: GenomesManager = GalaxyTypeDepends(_do_resolve)¶

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

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[source]¶

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

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[source]¶

__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, encoded_group_id, role)[source]¶

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

Bases: object

manager: GroupRolesManager = GalaxyTypeDepends(_do_resolve)¶

index(*, trans: ProvidesAppContext = Depends(get_trans), group_id: EncodedDatabaseIdField = Path(Ellipsis)) → GroupRoleListModel[source]¶

show(*, trans: ProvidesAppContext = Depends(get_trans), group_id: EncodedDatabaseIdField = Path(Ellipsis), id: EncodedDatabaseIdField = Path(Ellipsis)) → GroupRoleModel[source]¶

update(*, trans: ProvidesAppContext = Depends(get_trans), group_id: EncodedDatabaseIdField = Path(Ellipsis), role_id: EncodedDatabaseIdField = Path(Ellipsis)) → GroupRoleModel[source]¶

delete(*, trans: ProvidesAppContext = Depends(get_trans), group_id: EncodedDatabaseIdField = Path(Ellipsis), role_id: EncodedDatabaseIdField = Path(Ellipsis)) → GroupRoleModel[source]¶

__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, encoded_group_id, user)[source]¶

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

Bases: object

manager: GroupUsersManager = GalaxyTypeDepends(_do_resolve)¶

index(*, trans: ProvidesAppContext = Depends(get_trans), group_id: EncodedDatabaseIdField = Path(Ellipsis)) → GroupUserListModel[source]¶: GET /api/groups/{encoded_group_id}/users Displays a collection (list) of groups.

show(*, trans: ProvidesAppContext = Depends(get_trans), group_id: EncodedDatabaseIdField = Path(Ellipsis), id: EncodedDatabaseIdField = Path(Ellipsis)) → GroupUserModel[source]¶: GET /api/groups/{encoded_group_id}/users/{encoded_user_id} Displays information about a group user.

update(*, trans: ProvidesAppContext = Depends(get_trans), group_id: EncodedDatabaseIdField = Path(Ellipsis), user_id: EncodedDatabaseIdField = Path(Ellipsis)) → GroupUserModel[source]¶: PUT /api/groups/{encoded_group_id}/users/{encoded_user_id} Adds a user to a group

delete(*, trans: ProvidesAppContext = Depends(get_trans), group_id: EncodedDatabaseIdField = Path(Ellipsis), user_id: EncodedDatabaseIdField = Path(Ellipsis)) → GroupUserModel[source]¶: 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)[source]¶

Bases: BaseGalaxyAPIController

manager = GalaxyTypeDepends(_do_resolve)¶

index(trans: ProvidesAppContext, **kwd)[source]¶: GET /api/groups Displays a collection (list) of groups.

create(trans: ProvidesAppContext, payload: Dict[str, Any], **kwd)[source]¶: POST /api/groups Creates a new group.

show(trans: ProvidesAppContext, id: EncodedDatabaseIdField, **kwd)[source]¶: GET /api/groups/{encoded_group_id} Displays information about a group.

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

Bases: BaseModel

purge: bool¶

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

Bases: 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[EncodedDatabaseIdField]¶

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))[source]¶

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[HistoryBeta, HistoryDetailed, HistorySummary, Any]][source]¶

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[HistoryBeta, HistoryDetailed, HistorySummary, Any]][source]¶

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

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[HistoryBeta, HistoryDetailed, HistorySummary, Any]][source]¶

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

show(*, trans: ProvidesHistoryContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis), serialization_params: SerializationParams = Depends(query_serialization_params)) → Union[HistoryBeta, HistoryDetailed, HistorySummary, Any][source]¶

prepare_store_download(*, trans: ProvidesHistoryContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis), payload: StoreExportPayload = Body(Ellipsis)) → AsyncFile[source]¶

write_store(*, trans: ProvidesHistoryContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis), payload: WriteStoreToPayload = Body(Ellipsis)) → AsyncTaskResultSummary[source]¶

citations(*, trans: ProvidesHistoryContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis)) → List[Any][source]¶

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, HistoryBeta, HistoryDetailed, HistorySummary, Any][source]¶: The new history can also be copied form a existing history or imported from an archive or URL.

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

undelete(*, trans: ProvidesHistoryContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis), serialization_params: SerializationParams = Depends(query_serialization_params)) → Union[HistoryBeta, HistoryDetailed, HistorySummary, Any][source]¶

update(*, trans: ProvidesHistoryContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis), payload: Any = Body(Ellipsis), serialization_params: SerializationParams = Depends(query_serialization_params)) → Union[HistoryBeta, HistoryDetailed, HistorySummary, Any][source]¶

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

create_from_store_async(*, trans: ProvidesHistoryContext = Depends(get_trans), payload: CreateHistoryFromStore = Body(Ellipsis)) → Union[HistoryBeta, HistoryDetailed, HistorySummary, Any][source]¶

index_exports(*, trans: ProvidesHistoryContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis)) → JobExportHistoryArchiveCollection[source]¶

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

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.

archive_download(*, trans: ProvidesHistoryContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis), jeha_id: Union[EncodedDatabaseIdField, typing_extensions.Literal[latest]] = Path(Ellipsis))[source]¶: 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.

get_custom_builds_metadata(*, trans: ProvidesHistoryContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis)) → CustomBuildsMetadataResponse[source]¶

sharing(*, trans: ProvidesUserContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis)) → SharingStatus[source]¶: Return the sharing status of the item.

enable_link_access(*, trans: ProvidesUserContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis)) → SharingStatus[source]¶: Makes this item accessible by a URL link and return the current sharing status.

disable_link_access(*, trans: ProvidesUserContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis)) → SharingStatus[source]¶: Makes this item inaccessible by a URL link and return the current sharing status.

publish(*, trans: ProvidesUserContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis)) → SharingStatus[source]¶: Makes this item publicly available by a URL link and return the current sharing status.

unpublish(*, trans: ProvidesUserContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis)) → SharingStatus[source]¶: Removes this item from the published list and return the current sharing status.

share_with_users(*, trans: ProvidesUserContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis), payload: ShareWithPayload = Body(Ellipsis)) → ShareWithStatus[source]¶: Shares this item with specific users and return the current sharing status.

set_slug(*, trans: ProvidesUserContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis), payload: SetSlugPayload = Body(Ellipsis))[source]¶: 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.get_index_query_params(v: Optional[str] = Query(None), dataset_details: Optional[str] = Query(None)) → HistoryContentsIndexParams[source]¶: 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[source]¶: 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), type: Optional[str] = Query(None), details: Optional[str] = Query(None), deleted: Optional[bool] = Query(None), visible: Optional[bool] = Query(None)) → LegacyHistoryContentsIndexParams[source]¶: 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[source]¶: 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_dataset_details(details: Optional[str])[source]¶: 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[source]¶: 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[source]¶: Parses query parameters for the history contents index_jobs_summary operation and returns a model containing the values in the correct type.

galaxy.webapps.galaxy.api.history_contents.parse_content_filter_params(params: Dict[str, Any], exclude: Optional[Set[str]] = None) → List[List[Any]][source]¶

Alternative way of parsing query parameter for filtering history contents.

Parses parameters like: ?[field]-[operator]=[value]: Example: ?update_time-gt=2015-01-29

Currently used by the contents_near endpoint. The exclude set can contain names of parameters that will be ignored and not added to the filters.

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

Bases: object

service: HistoriesContentsService = GalaxyTypeDepends(_do_resolve)¶

index(*, trans: ProvidesHistoryContext = Depends(get_trans), history_id: EncodedDatabaseIdField = Path(Ellipsis), index_params: HistoryContentsIndexParams = Depends(get_index_query_params), 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][source]¶

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: EncodedDatabaseIdField = Path(Ellipsis), id: EncodedDatabaseIdField = Path(Ellipsis), type: HistoryContentType = Query(dataset)) → Union[JobStateSummary, ImplicitCollectionJobsStateSummary, WorkflowInvocationStateSummary][source]¶

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: EncodedDatabaseIdField = Path(Ellipsis), id: EncodedDatabaseIdField = Path(Ellipsis), type: HistoryContentType = Query(dataset), fuzzy_count: Optional[int] = Query(None), serialization_params: SerializationParams = Depends(query_serialization_params)) → Union[HDADetailed, HDASummary, HDCADetailed, HDCASummary, CustomHistoryItem][source]¶

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: EncodedDatabaseIdField = Path(Ellipsis), id: EncodedDatabaseIdField = Path(Ellipsis), type: HistoryContentType = Query(dataset), payload: StoreExportPayload = Body(Ellipsis)) → AsyncFile[source]¶

write_store(*, trans: ProvidesHistoryContext = Depends(get_trans), history_id: EncodedDatabaseIdField = Path(Ellipsis), id: EncodedDatabaseIdField = Path(Ellipsis), type: HistoryContentType = Query(dataset), payload: WriteStoreToPayload = Body(Ellipsis)) → AsyncTaskResultSummary[source]¶

index_jobs_summary(*, trans: ProvidesHistoryContext = Depends(get_trans), history_id: EncodedDatabaseIdField = Path(Ellipsis), params: HistoryContentsIndexJobsSummaryParams = Depends(get_index_jobs_summary_params)) → List[Union[JobStateSummary, ImplicitCollectionJobsStateSummary, WorkflowInvocationStateSummary]][source]¶

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(*, trans: ProvidesHistoryContext = Depends(get_trans), history_id: Optional[EncodedDatabaseIdField] = Query(None), id: EncodedDatabaseIdField = Path(Ellipsis))[source]¶: 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), history_id: EncodedDatabaseIdField = Path(Ellipsis), id: EncodedDatabaseIdField = Path(Ellipsis)) → AsyncFile[source]¶: 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(*, trans: ProvidesHistoryContext = Depends(get_trans), history_id: EncodedDatabaseIdField = 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]]][source]¶: Create a new HDA or HDCA in the given History.

update_permissions(*, trans: ProvidesHistoryContext = Depends(get_trans), history_id: EncodedDatabaseIdField = Path(Ellipsis), dataset_id: EncodedDatabaseIdField = Path(Ellipsis), payload: Dict[str, Any] = Body(Ellipsis)) → DatasetAssociationRoles[source]¶: Set permissions of the given history dataset to the given role ids.

update_batch(*, trans: ProvidesHistoryContext = Depends(get_trans), history_id: EncodedDatabaseIdField = Path(Ellipsis), serialization_params: SerializationParams = Depends(query_serialization_params), payload: UpdateHistoryContentsBatchPayload = Body(Ellipsis)) → HistoryContentsResult[source]¶

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: EncodedDatabaseIdField = Path(Ellipsis), filter_query_params: ValueFilterQueryParams = Depends(get_value_filter_query_params), payload: HistoryContentBulkOperationPayload = Body(Ellipsis)) → HistoryContentBulkOperationResult[source]¶

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: EncodedDatabaseIdField = Path(Ellipsis), id: EncodedDatabaseIdField = Path(Ellipsis)) → dict[source]¶: Validates the metadata associated with a dataset within a History.

update(*, trans: ProvidesHistoryContext = Depends(get_trans), history_id: EncodedDatabaseIdField = Path(Ellipsis), id: EncodedDatabaseIdField = Path(Ellipsis), type: HistoryContentType = Query(dataset), serialization_params: SerializationParams = Depends(query_serialization_params), payload: UpdateHistoryContentsPayload = Body(Ellipsis)) → Union[HDADetailed, HDASummary, HDCADetailed, HDCASummary, CustomHistoryItem][source]¶: Updates the values for the history content item with the given ID.

delete(*, response: Response, trans: ProvidesHistoryContext = Depends(get_trans), history_id: EncodedDatabaseIdField = Path(Ellipsis), id: EncodedDatabaseIdField = 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))[source]¶

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

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

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

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: EncodedDatabaseIdField = Path(Ellipsis), serialization_params: SerializationParams = Depends(query_serialization_params), create_payload: CreateHistoryContentFromStore = Body(Ellipsis)) → List[Union[HDADetailed, HDASummary, HDCADetailed, HDCASummary, CustomHistoryItem]][source]¶: 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.

contents_near(*, request: Request, response: Response, trans: ProvidesHistoryContext = Depends(get_trans), history_id: EncodedDatabaseIdField = Path(Ellipsis), hid: int = Path(Ellipsis), direction: DirectionOptions = Path(Ellipsis), limit: int = Path(Ellipsis), since: Optional[datetime] = Query(None), serialization_params: SerializationParams = Depends(query_serialization_params)) → HistoryContentsResult[source]¶

Warning

For internal use to support the scroller functionality.

This endpoint provides random access to a large history without having to know exactly how many pages are in the final query. Pick a target HID and filters, and the endpoint will get a maximum of limit history items “around” the hid.

Additional counts are provided in the HTTP headers.

The direction determines what items are selected:

item counts:
- total matches-up: hid < {hid}
- total matches-down: hid > {hid}
- total matches: total matches-up + total matches-down + 1 (+1 for hid == {hid})
- displayed matches-up: hid <= {hid} (hid == {hid} is included)
- displayed matches-down: hid > {hid}
- displayed matches: displayed matches-up + displayed matches-down
{limit} history items:
- if direction == “before”: hid <= {hid}
- if direction == “after”: hid > {hid}
- if direction == “near”: “near” {hid}, so that n. items before <= limit // 2, n. items after <= limit // 2 + 1.

Note

This endpoint uses slightly different filter params syntax. Instead of using q/qv parameters, it uses the following syntax for query parameters:

?[field]-[operator]=[value]

Example:

?update_time-gt=2015-01-29

materialize_dataset(*, trans: ProvidesHistoryContext = Depends(get_trans), history_id: EncodedDatabaseIdField = Path(Ellipsis), id: EncodedDatabaseIdField = Path(Ellipsis)) → AsyncTaskResultSummary[source]¶

materialize_to_history(*, trans: ProvidesHistoryContext = Depends(get_trans), history_id: EncodedDatabaseIdField = Path(Ellipsis), materialize_api_payload: MaterializeDatasetInstanceAPIRequest = Body(Ellipsis)) → AsyncTaskResultSummary[source]¶

__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)[source]¶

Bases: BaseGalaxyAPIController, UsesTagsMixin

index(trans, **kwd)[source]¶

show(trans, tag_name, **kwd)[source]¶

create(trans, tag_name, payload=None, **kwd)[source]¶

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

delete(trans, tag_name, **kwd)[source]¶

class galaxy.webapps.galaxy.api.item_tags.HistoryContentTagsController(app: StructuredApp)[source]¶

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)[source]¶

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)[source]¶

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)[source]¶

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)[source]¶

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)[source]¶

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[source]¶: 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[source]¶: 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)[source]¶

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)[source]¶: Initialize an interface for application ‘app’

create(self, trans, job_id, payload, **kwargs)[source]¶

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))[source]¶

Bases: object

service: JobsService = GalaxyTypeDepends(_do_resolve)¶

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

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[EncodedDatabaseIdField] = 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[EncodedDatabaseIdField] = Query(None), workflow_id: Optional[EncodedDatabaseIdField] = Query(None), invocation_id: Optional[EncodedDatabaseIdField] = 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]][source]¶

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

class galaxy.webapps.galaxy.api.jobs.JobController(app: StructuredApp)[source]¶

Bases: BaseGalaxyAPIController, UsesVisualizationMixin

job_manager = GalaxyTypeDepends(_do_resolve)¶

job_search = GalaxyTypeDepends(_do_resolve)¶

hda_manager = GalaxyTypeDepends(_do_resolve)¶

common_problems(trans: ProvidesUserContext, id, **kwd)[source]¶

GET /api/jobs/{id}/common_problems
check inputs and job for common potential problems to aid in error reporting

inputs(trans: ProvidesUserContext, id, **kwd)[source]¶

GET /api/jobs/{id}/inputs

returns input datasets created by job

Parameters: id (string) – Encoded job id
Return type: dictionary
Returns: dictionary containing input dataset associations

outputs(trans, id)[source]¶

GET /api/jobs/{id}/outputs
returns output datasets created by job

Parameters: id (string) – Encoded job id
Return type: dictionary
Returns: dictionary containing output dataset associations

delete(trans, id)[source]¶

Delete /api/jobs/{id}
cancels specified job

Parameters

id (string) – Encoded job id
message (string) – Stop message.

resume(trans: ProvidesUserContext, id, **kwd)[source]¶

PUT /api/jobs/{id}/resume
Resumes a paused job

Parameters: id (string) – Encoded job id
Return type: dictionary
Returns: dictionary containing output dataset associations

metrics(trans: ProvidesUserContext, **kwd)[source]¶

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)[source]¶

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)[source]¶

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)[source]¶

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)[source]¶: See the create method in tools.py in order to submit a job.

search(trans, payload)[source]¶

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)[source]¶

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)[source]¶

GET /api/job_lock
return boolean indicating if job lock active.

update_job_lock(trans: ProvidesUserContext, payload, **kwd)[source]¶

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))[source]¶

Bases: object

service: LibrariesService = GalaxyTypeDepends(_do_resolve)¶

index(*, trans: ProvidesUserContext = Depends(get_trans), deleted: Optional[bool] = Query(None)) → LibrarySummaryList[source]¶: Returns a list of summary data for all libraries.

index_deleted(*, trans: ProvidesUserContext = Depends(get_trans)) → LibrarySummaryList[source]¶: Returns a list of summary data for all libraries marked as deleted.

show(*, trans: ProvidesUserContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis)) → LibrarySummary[source]¶: Returns summary information about a particular library.

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

update(*, trans: ProvidesUserContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis), payload: UpdateLibraryPayload = Body(Ellipsis)) → LibrarySummary[source]¶: Updates the information of an existing library.

delete(*, trans: ProvidesUserContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis), undelete: Optional[bool] = Query(None), payload: Optional[DeleteLibraryPayload] = Body(None)) → LibrarySummary[source]¶: 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: EncodedDatabaseIdField = 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][source]¶: 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: EncodedDatabaseIdField = Path(Ellipsis), action: Optional[LibraryPermissionAction] = Query(None), payload: Union[LibraryPermissionsPayload, LegacyLibraryPermissionsPayload] = Body(Ellipsis)) → Union[LibraryLegacySummary, LibraryCurrentPermissions][source]¶: 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)[source]¶

Bases: BaseGalaxyAPIController, UsesLibraryMixinItems, UsesFormDefinitionsMixin, LibraryActions

__init__(app: StructuredApp, hda_manager: HDAManager)[source]¶: Initialize an interface for application ‘app’

index(trans, library_id, **kwd)[source]¶

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)[source]¶

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

create(trans, library_id, payload, **kwd)[source]¶

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)[source]¶

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

Create an 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)[source]¶

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)[source]¶

Bases: BaseGalaxyAPIController, UsesVisualizationMixin, LibraryActions

__init__(app: StructuredApp)[source]¶: Initialize an interface for application ‘app’

show(trans, id, **kwd)[source]¶

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)[source]¶

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)[source]¶

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)[source]¶

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)[source]¶

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)[source]¶

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)[source]¶

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)[source]¶

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))[source]¶

Bases: object

licenses_manager: LicensesManager = GalaxyTypeDepends(_do_resolve)¶

async index() → List[LicenseMetadataModel][source]¶: Returns an index with all the available [SPDX licenses](https://spdx.org/licenses/).

async get(*, id=Path(Ellipsis)) → LicenseMetadataModel[source]¶: 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))[source]¶

Bases: object

manager: MetricsManager = GalaxyTypeDepends(_do_resolve)¶

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

Bases: BaseGalaxyAPIController

manager: PageManager = GalaxyTypeDepends(_do_resolve)¶

index(self, trans, page_id, **kwd)[source]¶

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)[source]¶

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))[source]¶

Bases: object

service: PagesService = GalaxyTypeDepends(_do_resolve)¶

async index(*, trans: ProvidesUserContext = Depends(get_trans), deleted: bool = Query(False), user_id: Optional[EncodedDatabaseIdField] = 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[source]¶: Get a list with summary information of all Pages available to the user.

create(*, trans: ProvidesUserContext = Depends(get_trans), payload: CreatePagePayload = Body(Ellipsis)) → PageSummary[source]¶: Get a list with details of all Pages available to the user.

async delete(*, trans: ProvidesUserContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis))[source]¶: Marks the Page with the given ID as deleted.

async show_pdf(*, trans: ProvidesUserContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis))[source]¶

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: EncodedDatabaseIdField = Path(Ellipsis)) → AsyncFile[source]¶

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: EncodedDatabaseIdField = Path(Ellipsis)) → PageDetails[source]¶: Return summary information about a specific Page and the content of the last revision.

sharing(*, trans: ProvidesUserContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis)) → SharingStatus[source]¶: Return the sharing status of the item.

enable_link_access(*, trans: ProvidesUserContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis)) → SharingStatus[source]¶: Makes this item accessible by a URL link and return the current sharing status.

disable_link_access(*, trans: ProvidesUserContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis)) → SharingStatus[source]¶: Makes this item inaccessible by a URL link and return the current sharing status.

publish(*, trans: ProvidesUserContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis)) → SharingStatus[source]¶: Makes this item publicly available by a URL link and return the current sharing status.

unpublish(*, trans: ProvidesUserContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis)) → SharingStatus[source]¶: Removes this item from the published list and return the current sharing status.

share_with_users(*, trans: ProvidesUserContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis), payload: ShareWithPayload = Body(Ellipsis)) → ShareWithStatus[source]¶: Shares this item with specific users and return the current sharing status.

set_slug(*, trans: ProvidesUserContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis), payload: SetSlugPayload = Body(Ellipsis))[source]¶: 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)[source]¶

Bases: BaseGalaxyAPIController

RESTful controller for interactions with plugins.

hda_manager: HDAManager = GalaxyTypeDepends(_do_resolve)¶

history_manager: HistoryManager = GalaxyTypeDepends(_do_resolve)¶

index(trans, **kwargs)[source]¶: GET /api/plugins:

show(trans, id, **kwargs)[source]¶: GET /api/plugins/{id}:

galaxy.webapps.galaxy.api.provenance module¶

API operations provenance

class galaxy.webapps.galaxy.api.provenance.BaseProvenanceController(app: StructuredApp)[source]¶

Bases: BaseGalaxyAPIController

index(trans, **kwd)[source]¶

show(trans, elem_name, **kwd)[source]¶

create(trans, tag_name, payload=None, **kwd)[source]¶

delete(trans, tag_name, **kwd)[source]¶

class galaxy.webapps.galaxy.api.provenance.HDAProvenanceController(app: StructuredApp)[source]¶

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)[source]¶

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))[source]¶

Bases: object

service: QuotasService = GalaxyTypeDepends(_do_resolve)¶

index(*, trans: ProvidesUserContext = Depends(get_trans)) → QuotaSummaryList[source]¶: Displays a list with information of quotas that are currently active.

index_deleted(*, trans: ProvidesUserContext = Depends(get_trans)) → QuotaSummaryList[source]¶: Displays a list with information of quotas that have been deleted.

show(*, trans: ProvidesUserContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis)) → QuotaDetails[source]¶: Displays details on a particular active quota.

show_deleted(*, trans: ProvidesUserContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis)) → QuotaDetails[source]¶: Displays details on a particular quota that has been deleted.

create(*, payload: CreateQuotaParams, trans: ProvidesUserContext = Depends(get_trans)) → CreateQuotaResult[source]¶: Creates a new quota.

update(*, payload: UpdateQuotaParams, id: EncodedDatabaseIdField = Path(Ellipsis), trans: ProvidesUserContext = Depends(get_trans)) → str[source]¶: Updates an existing quota.

delete(*, id: EncodedDatabaseIdField = Path(Ellipsis), trans: ProvidesUserContext = Depends(get_trans), payload: DeleteQuotaPayload = Body(None)) → str[source]¶: Deletes an existing quota.

undelete(*, id: EncodedDatabaseIdField = Path(Ellipsis), trans: ProvidesUserContext = Depends(get_trans)) → str[source]¶: 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))[source]¶

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]][source]¶: Lists all remote files available to the user from different sources.

async plugins(*, user_ctx: ProvidesUserContext = Depends(get_trans)) → FilesSourcePluginList[source]¶: 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(trans, role)[source]¶

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

Bases: object

role_manager: RoleManager = GalaxyTypeDepends(_do_resolve)¶

index(*, trans: ProvidesUserContext = Depends(get_trans)) → RoleListModel[source]¶

show(*, id: EncodedDatabaseIdField, trans: ProvidesUserContext = Depends(get_trans)) → RoleModel[source]¶

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

__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)[source]¶

Bases: BaseAPIController

index(trans, **kwd)[source]¶: GET /api/sanitize_allow Return an object showing the current state of the toolbox and allow list.

create(trans, tool_id, **kwd)[source]¶: PUT /api/sanitize_allow Add a new tool_id to the allowlist.

delete(trans, tool_id, **kwd)[source]¶: 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)[source]¶

Bases: BaseGalaxyAPIController, SharableItemSecurityMixin

create(trans: ProvidesUserContext, payload: dict, **kwd)[source]¶: 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))[source]¶

Bases: object

short_term_storage_monitor: ShortTermStorageMonitor = GalaxyTypeDepends(_do_resolve)¶

is_ready(*, storage_request_id: str) → bool[source]¶

serve(*, storage_request_id: str)[source]¶

__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))[source]¶

Bases: object

manager: TagsManager = GalaxyTypeDepends(_do_resolve)¶

update(*, trans: ProvidesUserContext = Depends(get_trans), payload: ItemTagsPayload = Body(Ellipsis))[source]¶

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[source]¶

Bases: object

state(*, task_id: str) → str[source]¶

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

galaxy.webapps.galaxy.api.tool_data module¶

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

Bases: object

tool_data_manager: ToolDataManager = GalaxyTypeDepends(_do_resolve)¶

async index() → ToolDataEntryList[source]¶: Get the list of all available data tables.

async show(*, table_name: str = Path(Ellipsis)) → ToolDataDetails[source]¶: Get details of a given tool data table.

async reload(*, table_name: str = Path(Ellipsis)) → ToolDataDetails[source]¶: Reloads a data table and return its details.

async show_field(*, table_name: str = Path(Ellipsis), field_name: str = Path(Ellipsis)) → ToolDataField[source]¶: 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))[source]¶: Download a file associated with the data table field.

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

Bases: BaseGalaxyAPIController

__init__(app: StructuredApp)[source]¶: Initialize an interface for application ‘app’

index(trans: ProvidesAppContext, **kwd)[source]¶: GET /api/dependency_resolvers

show(trans: ProvidesAppContext, id: str)[source]¶: GET /api/dependency_resolvers/<id>

update(trans)[source]¶

PUT /api/dependency_resolvers

Reload tool dependency resolution configuration.

resolver_dependency(trans: ProvidesAppContext, id: str, **kwds)[source]¶

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)[source]¶

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)[source]¶

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)[source]¶

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)[source]¶

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)[source]¶

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)[source]¶

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)[source]¶

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)[source]¶

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)[source]¶: GET /api/dependency_resolvers/unused_paths

delete_unused_dependency_paths(trans: ProvidesAppContext, payload, **kwds)[source]¶: 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)[source]¶

Bases: BaseGalaxyAPIController

__init__(app: StructuredApp)[source]¶: Initialize an interface for application ‘app’

index(trans: ProvidesUserContext, running=False, job_id=None, **kwd)[source]¶

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)[source]¶

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)[source]¶: 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()[source]¶

class galaxy.webapps.galaxy.api.tool_shed_repositories.ToolShedRepositoriesController(app: StructuredApp)[source]¶

Bases: BaseGalaxyAPIController

RESTful controller for interactions with tool shed repositories.

index(trans: ProvidesUserContext, **kwd)[source]¶: GET /api/tool_shed_repositories Display a list of dictionaries containing information about installed tool shed repositories.

install_repository_revision(trans: ProvidesUserContext, payload, **kwd)[source]¶

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 simultaneously).
(optional) – Set to True if you want to install repository dependencies defined for the specified repository being installed. The default setting is False.
(optional) – Set to True if you want to install tool dependencies defined for the specified repository being installed. The default setting is False.
(optional) – The shed-related tool panel configuration file configured in the “tool_config_file” setting in the Galaxy config file (e.g., galaxy.ini). At least one shed-related tool panel config file is required to be configured. Setting this parameter to a specific file enables you to choose where the specified repository will be installed because the tool_path attribute of the <toolbox> from the specified file is used as the installation location (e.g., <toolbox tool_path=”database/shed_tools”>). If this parameter is not set, a shed-related tool panel configuration file will be selected automatically.

install_repository_revisions(trans, payload, **kwd)[source]¶

POST /api/tool_shed_repositories/install_repository_revisions Install one or more specified repository revisions from one or more specified tool sheds into Galaxy. The received parameters must be ordered lists so that positional values in tool_shed_urls, names, owners and changeset_revisions are associated.

It’s questionable whether this method is needed as the above method for installing a single repository can probably cover all desired scenarios. We’ll keep this one around just in case…

Parameters: key – the current Galaxy admin user’s API key

The following parameters are included in the payload. :param tool_shed_urls: the base URLs of the Tool Sheds from which to install a specified Repository :param names: the names of the Repositories to be installed :param owners: the owners of the Repositories to be installed :param changeset_revisions: the changeset_revisions of each RepositoryMetadata object associated with each Repository to be installed :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, as both cannot be used.

Parameters

tool_panel_section_id – optional id of the Galaxy tool panel section in which to load tools contained in the Repository. If not set, 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, as both cannot be used.
(optional) (shed_tool_conf) – Set to True if you want to install repository dependencies defined for the specified repository being installed. The default setting is False.
(optional) – Set to True if you want to install tool dependencies defined for the specified repository being installed. The default setting is False.
(optional) – The shed-related tool panel configuration file configured in the “tool_config_file” setting in the Galaxy config file (e.g., galaxy.ini). At least one shed-related tool panel config file is required to be configured. Setting this parameter to a specific file enables you to choose where the specified repository will be installed because the tool_path attribute of the <toolbox> from the specified file is used as the installation location (e.g., <toolbox tool_path=”database/shed_tools”>). If this parameter is not set, a shed-related tool panel configuration file will be selected automatically.

uninstall_repository(trans, id=None, **kwd)[source]¶

DELETE /api/tool_shed_repositories/id DELETE /api/tool_shed_repositories/

Parameters

id – encoded repository id. Either id or name, owner, changeset_revision and tool_shed_url need to be supplied
kwd – ‘remove_from_disk’: Remove repository from disk or deactivate repository. Defaults to True (= remove repository from disk). ‘name’: Repository name ‘owner’: Repository owner ‘changeset_revision’: Changeset revision to uninstall ‘tool_shed_url’: Tool Shed URL

check_for_updates(trans, **kwd)[source]¶

GET /api/tool_shed_repositories/check_for_updates Check for updates to the specified repository, or all installed repositories.

Parameters: id – the encoded repository id

reset_metadata_on_selected_installed_repositories(trans, **kwd)[source]¶

reset_metadata_on_installed_repositories(trans, payload, **kwd)[source]¶

PUT /api/tool_shed_repositories/reset_metadata_on_installed_repositories

Resets all metadata on all repositories installed into Galaxy in an “orderly fashion”.

Parameters: key – the API key of the Galaxy admin user.

show(trans, id, **kwd)[source]¶

GET /api/tool_shed_repositories/{encoded_tool_shed_repsository_id}

Display a dictionary containing information about a specified tool_shed_repository.

{
    id: (string) Galaxy ID
    status: (string) Installation status
    name: (string) Repository name
    deleted: (bool) Repository deleted
    ctx_rev: (int) Changeset revision number (0, 1, 2...)
    error_message: (string) Installation error message
    installed_changeset_revision: (string) Initially installed changeset revision. Used to construct path to repository within Galaxies filesystem. Does not change if a repository is updated.
    tool_shed: (string) Repository toolshed hostname
    dist_to_shed: (bool)
    url: (string) API url of repository
    uninstalled: (bool) Tool has been uninstalled
    owner: (string) Repository owner within toolshed
    changeset_revision: (string) Changeset revision of repository
    include_datatypes: (bool) Repository includes installed datatypes
    tool_shed_status: (dict) See https://github.com/galaxyproject/galaxy/issues/10453
        latest_installable_revision: (string) Most recent version available on toolshed
        revision_update: (string)
        revision_upgrade: (string)
        repository_deprecated: (string) Repository has been depreciated
}

Parameters: id – the encoded id of the ToolShedRepository object

galaxy.webapps.galaxy.api.tools module¶

class galaxy.webapps.galaxy.api.tools.FormDataApiRoute(path: str, endpoint: ~typing.Callable[[...], ~typing.Any], *, response_model: ~typing.Optional[~typing.Type[~typing.Any]] = None, 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>)[source]¶

Bases: APIContentTypeRoute

match_content_type: str = 'multipart/form-data'¶

methods: Set[str]¶

secure_cloned_response_field: Optional[ModelField]¶

response_fields: Dict[Union[int, str], ModelField]¶

class galaxy.webapps.galaxy.api.tools.JsonApiRoute(path: str, endpoint: ~typing.Callable[[...], ~typing.Any], *, response_model: ~typing.Optional[~typing.Type[~typing.Any]] = None, 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>)[source]¶

Bases: APIContentTypeRoute

match_content_type: str = 'application/json'¶

methods: Set[str]¶

secure_cloned_response_field: Optional[ModelField]¶

response_fields: Dict[Union[int, str], ModelField]¶

class galaxy.webapps.galaxy.api.tools.FetchTools(*, service: ToolsService = GalaxyTypeDepends(_do_resolve))[source]¶

Bases: object

service: ToolsService = GalaxyTypeDepends(_do_resolve)¶

async fetch_json(*, payload: FetchDataPayload = Body(Ellipsis), trans: ProvidesHistoryContext = Depends(get_trans))[source]¶

async fetch_form(*, request: Request, payload: FetchDataFormPayload = Depends(_as_form), files: Optional[List[UploadFile]] = None, trans: ProvidesHistoryContext = Depends(get_trans))[source]¶

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

class galaxy.webapps.galaxy.api.tools.ToolsController(app: StructuredApp)[source]¶

Bases: BaseGalaxyAPIController, UsesVisualizationMixin

RESTful controller for interactions with tools.

history_manager: HistoryManager = GalaxyTypeDepends(_do_resolve)¶

hda_manager: HDAManager = GalaxyTypeDepends(_do_resolve)¶

hdca_manager: DatasetCollectionManager = GalaxyTypeDepends(_do_resolve)¶

service: ToolsService = GalaxyTypeDepends(_do_resolve)¶

index(trans: GalaxyWebTransaction, **kwds)[source]¶

GET /api/tools

returns a list of tools defined by parameters

Parameters

in_panel – if true, tools are returned in panel structure, including sections and labels
view – ToolBox view to apply (default is ‘default’)
trackster – if true, only tools that are compatible with Trackster are returned
q – if present search on the given query will be performed
tool_id – if present the given tool_id will be searched for all installed versions

show(trans: GalaxyWebTransaction, id, **kwd)[source]¶

GET /api/tools/{tool_id}

Returns tool information

parameters:

io_details - if true, parameters and inputs are returned link_details - if true, hyperlink to the tool is returned tool_version - if provided return this tool version

build(trans: GalaxyWebTransaction, id, **kwd)[source]¶: GET /api/tools/{tool_id}/build Returns a tool model including dynamic parameters and updated values, repeats block etc.

test_data_path(trans: GalaxyWebTransaction, id, **kwd)[source]¶: GET /api/tools/{tool_id}/test_data_path?tool_version={tool_version}

test_data_download(trans: GalaxyWebTransaction, id, **kwd)[source]¶: GET /api/tools/{tool_id}/test_data_download?tool_version={tool_version}&filename={filename}

tests_summary(trans: GalaxyWebTransaction, **kwd)[source]¶

GET /api/tools/tests_summary

Fetch summary information for each tool and version combination with tool tests defined. This summary information currently includes tool name and a count of the tests.

Fetch complete test data for each tool with /api/tools/{tool_id}/test_data?tool_version=<tool_version>

test_data(trans: GalaxyWebTransaction, id, **kwd)[source]¶

GET /api/tools/{tool_id}/test_data?tool_version={tool_version}

This API endpoint is unstable and experimental. In particular the format of the response has not been entirely nailed down (it exposes too many Galaxy internals/Pythonisms in a rough way). If this endpoint is being used from outside of scripts shipped with Galaxy let us know and please be prepared for the response from this API to change its format in some ways.

If tool version is not passed, it is assumed to be latest. Tool version can be set as ‘*’ to get tests for all configured versions.

reload(trans: GalaxyWebTransaction, id, **kwd)[source]¶: GET /api/tools/{tool_id}/reload Reload specified tool.

all_requirements(trans: GalaxyWebTransaction, **kwds)[source]¶: GET /api/tools/all_requirements Return list of unique requirements for all tools.

requirements(trans: GalaxyWebTransaction, id, **kwds)[source]¶: GET /api/tools/{tool_id}/requirements Return the resolver status for a specific tool id. [{“status”: “installed”, “name”: “hisat2”, “versionless”: false, “resolver_type”: “conda”, “version”: “2.0.3”, “type”: “package”}]

install_dependencies(trans: GalaxyWebTransaction, id, **kwds)[source]¶

POST /api/tools/{tool_id}/dependencies

This endpoint is also available through POST /api/tools/{tool_id}/install_dependencies, but will be deprecated in the future.

Attempts to install requirements via the dependency resolver

parameters:

index:: index of dependency resolver to use when installing dependency. Defaults to using the highest ranking resolver

resolver_type: Use the dependency resolver of this resolver_type to install dependency. build_dependency_cache: If true, attempts to cache dependencies for this tool force_rebuild: If true and cache dir exists, attempts to delete cache dir

uninstall_dependencies(trans: GalaxyWebTransaction, id, **kwds)[source]¶

DELETE /api/tools/{tool_id}/dependencies

Attempts to uninstall requirements via the dependency resolver

parameters:

index:

index of dependency resolver to use when installing dependency. Defaults to using the highest ranking resolver

resolver_type: Use the dependency resolver of this resolver_type to install dependency

build_dependency_cache(trans: GalaxyWebTransaction, id, **kwds)[source]¶

POST /api/tools/{tool_id}/build_dependency_cache Attempts to cache installed dependencies.

parameters:: force_rebuild: If true and chache dir exists, attempts to delete cache dir

diagnostics(trans: GalaxyWebTransaction, id, **kwd)[source]¶: GET /api/tools/{tool_id}/diagnostics Return diagnostic information to help debug panel and dependency related problems.

citations(trans: GalaxyWebTransaction, id, **kwds)[source]¶

conversion(trans: GalaxyWebTransaction, tool_id, payload, **kwd)[source]¶

xrefs(trans: GalaxyWebTransaction, id, **kwds)[source]¶

download(trans: GalaxyWebTransaction, id, **kwds)[source]¶

raw_tool_source(trans: GalaxyWebTransaction, id, **kwds)[source]¶: Returns tool source. language is included in the response header.

error_stack(trans: GalaxyWebTransaction, **kwd)[source]¶: GET /api/tools/error_stack Returns global tool error stack

create(trans: GalaxyWebTransaction, payload, **kwd)[source]¶

POST /api/tools Execute tool with a given parameter payload

Parameters: input_format (str) – input format for the payload. Possible values are the default ‘legacy’ (where inputs nested inside conditionals or repeats are identified with e.g. ‘<conditional_name>|<input_name>’) or ‘21.01’ (where inputs inside conditionals or repeats are nested elements).

galaxy.webapps.galaxy.api.toolshed module¶

class galaxy.webapps.galaxy.api.toolshed.ToolShedController(app: StructuredApp)[source]¶

Bases: BaseGalaxyAPIController

RESTful controller for interactions with Toolsheds.

index(trans, **kwd)[source]¶: GET /api/tool_shed Interact with the Toolshed registry of this instance.

request(trans, **params)[source]¶: GET /api/tool_shed/request

galaxy.webapps.galaxy.api.tours module¶

API Controller providing Galaxy Tours

class galaxy.webapps.galaxy.api.tours.FastAPITours(*, registry: ToursRegistry = GalaxyTypeDepends(_do_resolve))[source]¶

Bases: object

registry: ToursRegistry = GalaxyTypeDepends(_do_resolve)¶

index() → TourList[source]¶: Return list of available tours.

show(*, tour_id: str) → TourDetails[source]¶: Return a tour definition.

update_tour(*, tour_id: str) → TourDetails[source]¶: Return a tour definition.

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

galaxy.webapps.galaxy.api.trs_consumer module¶

Proxy requests to GA4GH TRS servers (e.g. Dockstore).

Information on TRS can be found at https://github.com/ga4gh/tool-registry-service-schemas.

class galaxy.webapps.galaxy.api.trs_consumer.TrsConsumeAPIController(app: StructuredApp)[source]¶

Bases: BaseGalaxyAPIController

Controller for TRS proxying.

get_servers(trans, *args, **kwd)[source]¶

get_tool(trans, *args, **kwd)[source]¶

get_versions(trans, *args, **kwd)[source]¶

get_version(trans, *args, **kwd)[source]¶

galaxy.webapps.galaxy.api.trs_search module¶

Proxy requests to GA4GH TRS servers (e.g. Dockstore).

Information on TRS can be found at https://github.com/ga4gh/tool-registry-service-schemas.

class galaxy.webapps.galaxy.api.trs_search.TrsSearchAPIController(app: StructuredApp)[source]¶

Bases: BaseGalaxyAPIController

Controller for TRS searching.

Not trying to emulate the actual underlying GA4GH API interface so throwing the search functionality into a different controller than the trs_consumer.

index(trans, trs_server=None, query=None, **kwd)[source]¶

GET /api/trs_search

Search a TRS server.

Parameters: query (str) – search query

galaxy.webapps.galaxy.api.uploads module¶

API operations for uploaded files in storage.

class galaxy.webapps.galaxy.api.uploads.UploadsAPIController(app: StructuredApp)[source]¶

Bases: BaseGalaxyAPIController

READ_CHUNK_SIZE = 65536¶

hooks(trans, **kwds)[source]¶: Exposed as POST /api/upload/hooks and /api/upload/resumable_upload

index(trans, **kwd)[source]¶

create(trans, payload, **kwd)[source]¶: POST /api/uploads/

galaxy.webapps.galaxy.api.users module¶

API operations on User objects.

class galaxy.webapps.galaxy.api.users.FastAPIHistories(*, service: UsersService = GalaxyTypeDepends(_do_resolve))[source]¶

Bases: object

service: UsersService = GalaxyTypeDepends(_do_resolve)¶

recalculate_disk_usage(*, trans: ProvidesUserContext = Depends(get_trans))[source]¶

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

class galaxy.webapps.galaxy.api.users.UserAPIController(app: StructuredApp)[source]¶

Bases: BaseGalaxyAPIController, UsesTagsMixin, BaseUIController, UsesFormDefinitionsMixin

user_manager: UserManager = GalaxyTypeDepends(_do_resolve)¶

user_serializer: UserSerializer = GalaxyTypeDepends(_do_resolve)¶

user_deserializer: UserDeserializer = GalaxyTypeDepends(_do_resolve)¶

api_key_manager: ApiKeyManager = GalaxyTypeDepends(_do_resolve)¶

index(trans: ProvidesUserContext, deleted='False', f_email=None, f_name=None, f_any=None, **kwd)[source]¶

GET /api/users GET /api/users/deleted Displays a collection (list) of users.

Parameters

deleted (bool) – (optional) If true, show deleted users
f_email (str) – (optional) An email address to filter on. (Non-admin users can only use this if expose_user_email is True in galaxy.ini)
f_name (str) – (optional) A username to filter on. (Non-admin users can only use this if expose_user_name is True in galaxy.ini)
f_any (str) – (optional) Filter on username OR email. (Non-admin users can use this, the email filter and username filter will only be active if their corresponding expose_user_* is True in galaxy.ini)

show(trans: ProvidesUserContext, id, deleted='False', **kwd)[source]¶: GET /api/users/{encoded_id} GET /api/users/deleted/{encoded_id} GET /api/users/current Displays information about a user.

create(trans: GalaxyWebTransaction, payload: dict, **kwd)[source]¶: POST /api/users Creates a new Galaxy user.

update(self, trans, id, payload, **kwd)[source]¶

PUT /api/users/{id}
updates the values for the item with the given id

Parameters

id (str) – the encoded id of the item to update
payload (dict) – a dictionary of new attribute values

Return type

dict

Returns

an error object if an error occurred or a dictionary containing the serialized item after any changes

delete(trans, id, **kwd)[source]¶

DELETE /api/users/{id} delete the user with the given id Functionality restricted based on admin status

Parameters

id (str) – the encoded id of the user to delete
purge (bool) – (optional) if True, purge the user

undelete(trans, id, **kwd)[source]¶

POST /api/users/deleted/{id}/undelete Undelete the user with the given id

Parameters: id (str) – the encoded id of the user to be undeleted

anon_user_api_value(trans)[source]¶: Return data for an anonymous user, truncated to only usage and quota_percent

get_information(trans, id, **kwd)[source]¶

GET /api/users/{id}/information/inputs Return user details such as username, email, addresses etc.

Parameters: id (str) – the encoded id of the user

set_information(trans, id, payload=None, **kwd)[source]¶

PUT /api/users/{id}/information/inputs Save a user’s email, username, addresses etc.

Parameters

id (str) – the encoded id of the user
payload (dict) – data with new settings

set_favorite(trans, id, object_type, payload=None, **kwd)[source]¶

Add the object to user’s favorites PUT /api/users/{id}/favorites/{object_type}

Parameters

id (str) – the encoded id of the user
object_type (str) – the object type that users wants to favorite
object_id (str) – the id of an object that users wants to favorite

remove_favorite(trans, id, object_type, object_id, payload=None, **kwd)[source]¶

Remove the object from user’s favorites DELETE /api/users/{id}/favorites/{object_type}/{object_id:.*?}

Parameters

id (str) – the encoded id of the user
object_type (str) – the object type that users wants to favorite
object_id (str) – the id of an object that users wants to remove from favorites

get_password(trans, id, payload=None, **kwd)[source]¶: Return available password inputs.

set_password(trans, id, payload=None, **kwd)[source]¶: Allows to the logged-in user to change own password.

get_permissions(trans, id, payload=None, **kwd)[source]¶: Get the user’s default permissions for the new histories

set_permissions(trans, id, payload=None, **kwd)[source]¶: Set the user’s default permissions for the new histories

get_toolbox_filters(trans, id, payload=None, **kwd)[source]¶: API call for fetching toolbox filters data. Toolbox filters are specified in galaxy.ini. The user can activate them and the choice is stored in user_preferences.

set_toolbox_filters(trans, id, payload=None, **kwd)[source]¶: API call to update toolbox filters data.

api_key(trans, id, payload=None, **kwd)[source]¶: Create API key.

get_or_create_api_key(trans, id, payload=None, **kwd)[source]¶: Unified ‘get or create’ for API key

get_api_key(trans, id, payload=None, **kwd)[source]¶: Get API key inputs.

set_api_key(trans, id, payload=None, **kwd)[source]¶: Get API key inputs with new API key.

get_custom_builds(trans, id, payload=None, **kwd)[source]¶

GET /api/users/{id}/custom_builds Returns collection of custom builds.

Parameters: id (str) – the encoded id of the user

add_custom_builds(trans, id, key, payload=None, **kwd)[source]¶

PUT /api/users/{id}/custom_builds/{key} Add new custom build.

Parameters

id (str) – the encoded id of the user
id – custom build key
payload (dict) – data with new build details

delete_custom_builds(trans, id, key, payload=None, **kwd)[source]¶

DELETE /api/users/{id}/custom_builds/{key} Delete a custom build.

Parameters

id (str) – the encoded id of the user
id – custom build key to be deleted

galaxy.webapps.galaxy.api.visualizations module¶

Visualizations resource control over the API.

NOTE!: this is a work in progress and functionality and data structures may change often.

class galaxy.webapps.galaxy.api.visualizations.FastAPIVisualizations(*, service: VisualizationsService = GalaxyTypeDepends(_do_resolve))[source]¶

Bases: object

service: VisualizationsService = GalaxyTypeDepends(_do_resolve)¶

sharing(*, trans: ProvidesUserContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis)) → SharingStatus[source]¶: Return the sharing status of the item.

enable_link_access(*, trans: ProvidesUserContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis)) → SharingStatus[source]¶: Makes this item accessible by a URL link and return the current sharing status.

disable_link_access(*, trans: ProvidesUserContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis)) → SharingStatus[source]¶: Makes this item inaccessible by a URL link and return the current sharing status.

publish(*, trans: ProvidesUserContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis)) → SharingStatus[source]¶: Makes this item publicly available by a URL link and return the current sharing status.

unpublish(*, trans: ProvidesUserContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis)) → SharingStatus[source]¶: Removes this item from the published list and return the current sharing status.

share_with_users(*, trans: ProvidesUserContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis), payload: ShareWithPayload = Body(Ellipsis)) → ShareWithStatus[source]¶: Shares this item with specific users and return the current sharing status.

set_slug(*, trans: ProvidesUserContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis), payload: SetSlugPayload = Body(Ellipsis))[source]¶: Sets a new slug to access this item by URL. The new slug must be unique.

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

class galaxy.webapps.galaxy.api.visualizations.VisualizationsController(app: StructuredApp)[source]¶

Bases: BaseGalaxyAPIController, UsesVisualizationMixin, UsesAnnotations

RESTful controller for interactions with visualizations.

service: VisualizationsService = GalaxyTypeDepends(_do_resolve)¶

index(trans: GalaxyWebTransaction, **kwargs)[source]¶: GET /api/visualizations:

show(trans: GalaxyWebTransaction, id: str, **kwargs)[source]¶: GET /api/visualizations/{viz_id}

create(trans: GalaxyWebTransaction, payload: dict, **kwargs)[source]¶

POST /api/visualizations creates a new visualization using the given payload

POST /api/visualizations?import_id={encoded_visualization_id} imports a copy of an existing visualization into the user’s workspace

update(trans: GalaxyWebTransaction, id: str, payload: dict, **kwargs)[source]¶: PUT /api/visualizations/{encoded_visualization_id}

galaxy.webapps.galaxy.api.webhooks module¶

API Controller providing Galaxy Webhooks

class galaxy.webapps.galaxy.api.webhooks.WebhooksController(app: StructuredApp)[source]¶

Bases: BaseGalaxyAPIController

all_webhooks(trans: GalaxyWebTransaction, **kwd)[source]¶

GET /api/webhooks/

Return all webhooks.

webhook_data(trans: Any, webhook_id, **kwd)[source]¶

GET /api/webhooks/{webhook_id}/data/{params}

Return the result of executing helper function.

galaxy.webapps.galaxy.api.workflows module¶

API operations for Workflows

class galaxy.webapps.galaxy.api.workflows.CreateInvocationFromStore(*, store_content_uri: str = None, store_dict: Dict[str, Any] = None, model_store_format: ModelStoreFormat = None, history_id: str = None, **extra_data: Any)[source]¶

Bases: StoreContentSource

history_id: Optional[str]¶

class Config[source]¶

Bases: object

extra = 'allow'¶

class galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController(app: StructuredApp)[source]¶

Bases: BaseGalaxyAPIController, UsesStoredWorkflowMixin, UsesAnnotations, SharableMixin, ServesExportStores, ConsumesModelStores

service: WorkflowsService = GalaxyTypeDepends(_do_resolve)¶

invocations_service: InvocationsService = GalaxyTypeDepends(_do_resolve)¶

__init__(app: StructuredApp)[source]¶: Initialize an interface for application ‘app’

get_workflow_menu(trans: ProvidesUserContext, **kwd)[source]¶: Get workflows present in the tools panel GET /api/workflows/menu

set_workflow_menu(trans: GalaxyWebTransaction, payload=None, **kwd)[source]¶: Save workflow menu to be shown in the tool panel PUT /api/workflows/menu

get_workflows_list(trans: ProvidesUserContext, missing_tools=False, show_published=None, show_shared=None, show_hidden=False, show_deleted=False, **kwd)[source]¶

Displays a collection of workflows.

Parameters

show_published (boolean) – Optional boolean to include published workflows If unspecified this behavior depends on whether the request is coming from an authenticated session. The default is true for annonymous API requests and false otherwise.
show_hidden (boolean) – if True, show hidden workflows
show_deleted (boolean) – if True, show deleted workflows
show_shared – Optional boolean to include shared workflows. If unspecified this behavior depends on show_deleted/show_hidden. Defaulting to false if show_hidden or show_deleted is true or else false.
missing_tools (boolean) – if True, include a list of missing tools per workflow

show(trans: GalaxyWebTransaction, id, **kwd)[source]¶

GET /api/workflows/{encoded_workflow_id}

Parameters: instance (boolean) – true if fetch by Workflow ID instead of StoredWorkflow id, false by default.

Displays information needed to run a workflow.

show_versions(trans: GalaxyWebTransaction, workflow_id, **kwds)[source]¶

GET /api/workflows/{encoded_workflow_id}/versions

Parameters: instance (boolean) – true if fetch by Workflow ID instead of StoredWorkflow id, false by default.

Lists all versions of this workflow.

create(trans: GalaxyWebTransaction, payload=None, **kwd)[source]¶

POST /api/workflows

Create workflows in various ways.

Parameters

from_history_id (str) – Id of history to extract a workflow from.
job_ids (str) – If from_history_id is set - optional list of jobs to include when extracting a workflow from history
dataset_ids (str) – If from_history_id is set - optional list of HDA “hid”s corresponding to workflow inputs when extracting a workflow from history
dataset_collection_ids (str) – If from_history_id is set - optional list of HDCA “hid”s corresponding to workflow inputs when extracting a workflow from history
workflow_name (str) – If from_history_id is set - name of the workflow to create when extracting a workflow from history

workflow_dict(trans: GalaxyWebTransaction, workflow_id, **kwd)[source]¶

GET /api/workflows/{encoded_workflow_id}/download

Returns a selected workflow.

Parameters

style (str) – Style of export. The default is ‘export’, which is the meant to be used with workflow import endpoints. Other formats such as ‘instance’, ‘editor’, ‘run’ are more tied to the GUI and should not be considered stable APIs. The default format for ‘export’ is specified by the admin with the default_workflow_export_format config option. Style can be specified as either ‘ga’ or ‘format2’ directly to be explicit about which format to download.
instance (boolean) – true if fetch by Workflow ID instead of StoredWorkflow id, false by default.

delete(trans: ProvidesUserContext, id, **kwd)[source]¶

DELETE /api/workflows/{encoded_workflow_id} Deletes a specified workflow Author: rpark

copied from galaxy.web.controllers.workflows.py (delete)

import_new_workflow_deprecated(trans: GalaxyWebTransaction, payload, **kwd)[source]¶

POST /api/workflows/upload Importing dynamic workflows from the api. Return newly generated workflow id. Author: rpark

# currently assumes payload[‘workflow’] is a json representation of a workflow to be inserted into the database

Deprecated in favor to POST /api/workflows with encoded ‘workflow’ in payload the same way.

update(trans: GalaxyWebTransaction, id, payload, **kwds)[source]¶

PUT /api/workflows/{id}

Update the workflow stored with id.

Parameters

id (str) – the encoded id of the workflow to update
instance (boolean) – true if fetch by Workflow ID instead of StoredWorkflow id, false by default.
payload (dict) –
a dictionary containing any or all the

workflow

the json description of the workflow as would be produced by GET workflows/<id>/download or given to POST workflows

The workflow contents will be updated to target this.

name

optional string name for the workflow, if not present in payload, name defaults to existing name

annotation

optional string annotation for the workflow, if not present in payload, annotation defaults to existing annotation

menu_entry

optional boolean marking if the workflow should appear in the user’s menu, if not present, workflow menu entries are not modified

tags

optional list containing list of tags to add to the workflow (overwriting existing tags), if not present, tags are not modified

from_tool_form

True iff encoded state coming in is encoded for the tool form.

Return type

dict

Returns

serialized version of the workflow

refactor(trans, id, payload, **kwds)[source]¶

PUT /api/workflows/{id}/refactor
updates the workflow stored with id

Parameters

id (str) – the encoded id of the workflow to update
instance (boolean) – true if fetch by Workflow ID instead of StoredWorkflow id, false by default.
payload (dict) – a dictionary containing list of actions to apply.

Return type

dict

Returns

serialized version of the workflow

build_module(trans: GalaxyWebTransaction, payload=None)[source]¶: POST /api/workflows/build_module Builds module models for the workflow editor.

get_tool_predictions(trans: ProvidesUserContext, payload, **kwd)[source]¶

POST /api/workflows/get_tool_predictions

Fetch predicted tools for a workflow

Parameters: payload (dict) – a dictionary containing two parameters ‘tool_sequence’ - comma separated sequence of tool ids ‘remote_model_url’ - (optional) path to the deep learning model

import_shared_workflow_deprecated(trans: GalaxyWebTransaction, payload, **kwd)[source]¶

POST /api/workflows/import Import a workflow shared by other users.

Parameters: workflow_id (str) – the workflow id (required)
Raises: exceptions.MessageException, exceptions.ObjectNotFound

invoke(trans: GalaxyWebTransaction, workflow_id, payload, **kwd)[source]¶

POST /api/workflows/{encoded_workflow_id}/invocations

Schedule the workflow specified by workflow_id to run.

Note

This method takes the same arguments as galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController.create() above.

Raises: exceptions.MessageException, exceptions.RequestParameterInvalidException

index_invocations(trans: GalaxyWebTransaction, **kwd)[source]¶

GET /api/workflows/{workflow_id}/invocations GET /api/invocations

Get the list of a user’s workflow invocations. If workflow_id is supplied (either via URL or query parameter) it should be an encoded StoredWorkflow id and returned invocations will be restricted to that workflow. history_id (an encoded History id) can be used to further restrict the query. If neither a workflow_id or history_id is supplied, all the current user’s workflow invocations will be indexed (as determined by the invocation being executed on one of the user’s histories).

Parameters

workflow_id (str) – an encoded stored workflow id to restrict query to
instance (boolean) – true if fetch by Workflow ID instead of StoredWorkflow id, false by default.
history_id (str) – an encoded history id to restrict query to
job_id (str) – an encoded job id to restrict query to
user_id (str) – an encoded user id to restrict query to, must be own id if not admin user
view (str) – level of detail to return per invocation ‘element’ or ‘collection’.
step_details (bool) – If ‘view’ is ‘element’, also include details on individual steps.

Raises

exceptions.MessageException, exceptions.ObjectNotFound

create_invocations_from_store(trans, payload, **kwd)[source]¶

POST /api/invocations/from_store

Create invocation(s) from a supplied model store.

Input can be an archive describing a Galaxy model store containing an workflow invocation - for instance one created with with write_store or prepare_store_download endpoint.

show_invocation(trans: GalaxyWebTransaction, invocation_id, **kwd)[source]¶

GET /api/workflows/{workflow_id}/invocations/{invocation_id} GET /api/invocations/{invocation_id}

Get detailed description of workflow invocation

Parameters

invocation_id (str) – the invocation id (required)
step_details (bool) – fetch details about individual invocation steps and populate a steps attribute in the resulting dictionary. Defaults to false.
legacy_job_state (bool) – If step_details is true, and this is set to true populate the invocation step state with the job state instead of the invocation step state. This will also produce one step per job in mapping jobs to mimic the older behavior with respect to collections. Partially scheduled steps may provide incomplete information and the listed steps outputs are the mapped over step outputs but the individual job outputs when this is set - at least for now.

Raises

exceptions.MessageException, exceptions.ObjectNotFound

cancel_invocation(trans: ProvidesUserContext, invocation_id, **kwd)[source]¶

DELETE /api/workflows/{workflow_id}/invocations/{invocation_id} DELETE /api/invocations/{invocation_id} Cancel the specified workflow invocation.

Parameters: invocation_id (str) – the usage id (required)
Raises: exceptions.MessageException, exceptions.ObjectNotFound

show_invocation_report(trans: GalaxyWebTransaction, invocation_id, **kwd)[source]¶

GET /api/workflows/{workflow_id}/invocations/{invocation_id}/report GET /api/invocations/{invocation_id}/report

Get JSON summarizing invocation for reporting.

show_invocation_report_pdf(trans: GalaxyWebTransaction, invocation_id, **kwd)[source]¶

GET /api/workflows/{workflow_id}/invocations/{invocation_id}/report.pdf GET /api/invocations/{invocation_id}/report.pdf

Get JSON summarizing invocation for reporting.

export_invocation_bco(trans: GalaxyWebTransaction, invocation_id, **kwd)[source]¶

GET /api/invocations/{invocations_id}/biocompute

Return a BioCompute Object for the workflow invocation.

The BioCompute Object endpoints are in beta - important details such as how inputs and outputs are represented, how the workflow is encoded, and how author and version information is encoded, and how URLs are generated will very likely change in important ways over time.

download_invocation_bco(trans: GalaxyWebTransaction, invocation_id, **kwd)[source]¶

GET /api/invocations/{invocations_id}/biocompute/download

Returns a selected BioCompute Object as a file for download (HTTP headers configured with filename and such).

The BioCompute Object endpoints are in beta - important details such as how inputs and outputs are represented, how the workflow is encoded, and how author and version information is encoded, and how URLs are generated will very likely change in important ways over time.

invocation_step(trans, invocation_id, step_id, **kwd)[source]¶

GET /api/workflows/{workflow_id}/invocations/{invocation_id}/steps/{step_id} GET /api/invocations/{invocation_id}/steps/{step_id}

Parameters

invocation_id (str) – the invocation id (required)
step_id (str) – encoded id of the WorkflowInvocationStep (required)
payload – payload containing update action information for running workflow.

Raises

exceptions.MessageException, exceptions.ObjectNotFound

invocation_step_jobs_summary(trans: GalaxyWebTransaction, invocation_id, **kwd)[source]¶

GET /api/workflows/{workflow_id}/invocations/{invocation_id}/step_jobs_summary GET /api/invocations/{invocation_id}/step_jobs_summary

return job state summary info aggregated across per step of the workflow invocation

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.

Parameters: invocation_id (str) – the invocation id (required)
Return type: dict[]
Returns: an array of job summary object dictionaries for each step

invocation_jobs_summary(trans: GalaxyWebTransaction, invocation_id, **kwd)[source]¶

GET /api/workflows/{workflow_id}/invocations/{invocation_id}/jobs_summary GET /api/invocations/{invocation_id}/jobs_summary

return job state summary info aggregated across all current jobs of workflow invocation

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.

Parameters: invocation_id (str) – the invocation id (required)
Return type: dict
Returns: a job summary object merged for all steps in workflow invocation

update_invocation_step(trans: GalaxyWebTransaction, invocation_id, step_id, payload, **kwd)[source]¶

PUT /api/workflows/{workflow_id}/invocations/{invocation_id}/steps/{step_id} PUT /api/invocations/{invocation_id}/steps/{step_id}

Update state of running workflow step invocation - still very nebulous but this would be for stuff like confirming paused steps can proceed etc….

Parameters

invocation_id (str) – the usage id (required)
step_id (str) – encoded id of the WorkflowInvocationStep (required)

Raises

exceptions.MessageException, exceptions.ObjectNotFound

class galaxy.webapps.galaxy.api.workflows.FastAPIWorkflows(*, service: WorkflowsService = GalaxyTypeDepends(_do_resolve), invocations_service: InvocationsService = GalaxyTypeDepends(_do_resolve))[source]¶

Bases: object

service: WorkflowsService = GalaxyTypeDepends(_do_resolve)¶

invocations_service: InvocationsService = GalaxyTypeDepends(_do_resolve)¶

index(*, response: Response, trans: ProvidesUserContext = Depends(get_trans), show_deleted: bool = Query(False), show_hidden: bool = Query(False), missing_tools: bool = Query(False), show_published: Optional[bool] = Query(None), show_shared: Optional[bool] = Query(None), sort_by: Optional[WorkflowSortByEnum] = Query(None), sort_desc: Optional[bool] = Query(None), limit: Optional[int] = Query(None), offset: Optional[int] = Query(0), search: Optional[str] = Query(None), skip_step_counts: bool = Query(False)) → List[Dict[str, Any]][source]¶: Lists stored workflows viewable by the user.

sharing(*, trans: ProvidesUserContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis)) → SharingStatus[source]¶: Return the sharing status of the item.

enable_link_access(*, trans: ProvidesUserContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis)) → SharingStatus[source]¶: Makes this item accessible by a URL link and return the current sharing status.

disable_link_access(*, trans: ProvidesUserContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis)) → SharingStatus[source]¶: Makes this item inaccessible by a URL link and return the current sharing status.

publish(*, trans: ProvidesUserContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis)) → SharingStatus[source]¶: Makes this item publicly available by a URL link and return the current sharing status.

unpublish(*, trans: ProvidesUserContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis)) → SharingStatus[source]¶: Removes this item from the published list and return the current sharing status.

share_with_users(*, trans: ProvidesUserContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis), payload: ShareWithPayload = Body(Ellipsis)) → ShareWithStatus[source]¶: Shares this item with specific users and return the current sharing status.

set_slug(*, trans: ProvidesUserContext = Depends(get_trans), id: EncodedDatabaseIdField = Path(Ellipsis), payload: SetSlugPayload = Body(Ellipsis))[source]¶: Sets a new slug to access this item by URL. The new slug must be unique.

prepare_store_download(*, trans: ProvidesUserContext = Depends(get_trans), invocation_id: EncodedDatabaseIdField = Path(Ellipsis), payload: PrepareStoreDownloadPayload = Body(Ellipsis)) → AsyncFile[source]¶

write_store(*, trans: ProvidesUserContext = Depends(get_trans), invocation_id: EncodedDatabaseIdField = Path(Ellipsis), payload: WriteStoreToPayload = Body(Ellipsis)) → AsyncTaskResultSummary[source]¶

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