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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.
- galaxy.webapps.galaxy.api.depends(dep_type: ~typing.Type[~galaxy.webapps.galaxy.api.T], app=<function get_app_with_request_session>) 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=Depends(get_session_manager), security: IdEncodingHelper = GalaxyTypeDepends(_do_resolve), galaxysession: str = Security(APIKeyCookie)) GalaxySession | None [source]
- galaxy.webapps.galaxy.api.get_api_user(user_manager: UserManager = GalaxyTypeDepends(_do_resolve), key: str = Security(APIKeyQuery), x_api_key: str = Security(APIKeyHeader), bearer_token: HTTPAuthorizationCredentials = Security(HTTPBearer), run_as: int[int] | None = Header(None)) User | None [source]
- galaxy.webapps.galaxy.api.get_user(galaxy_session=Depends(get_session), api_user=Depends(get_api_user)) User | None [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.
- property environ: Environ
Fallback WSGI environ.
This is not a full environ, there is no body. This is only meant to make routes.url_for work.
- property headers
- 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.
- property headers
The response headers.
- galaxy.webapps.galaxy.api.get_current_history_from_session(galaxy_session: GalaxySession | None) History | None [source]
- galaxy.webapps.galaxy.api.fix_url_for(mapper: Mapper, galaxy_request: GalaxyASGIRequest)[source]
- galaxy.webapps.galaxy.api.get_trans(request: Request, response: Response, app: StructuredApp = Depends(get_app_with_request_session), user=Depends(get_user), galaxy_session=Depends(get_session)) SessionRequestContext [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]
-
An enumeration.
- get = 'GET'
- head = 'HEAD'
- post = 'POST'
- put = 'PUT'
- patch = 'PATCH'
- delete = 'DELETE'
- options = 'OPTIONS'
- class galaxy.webapps.galaxy.api.FrameworkRouter(*, prefix: str[str] = '', tags: ~typing.List[str | enum.Enum] | None[~typing.List[str | ~enum.Enum] | None] | None = None, dependencies: ~typing.Sequence[fastapi.params.Depends] | None[~typing.Sequence[~fastapi.params.Depends] | None] | None = None, default_response_class: ~typing.Type[starlette.responses.Response][~typing.Type[~starlette.responses.Response]] = <fastapi.datastructures.DefaultPlaceholder object>, responses: ~typing.Dict[int | str, Dict[str, Any]] | None[~typing.Dict[int | str, ~typing.Dict[str, ~typing.Any]] | None] | None = None, callbacks: ~typing.List[starlette.routing.BaseRoute] | None[~typing.List[~starlette.routing.BaseRoute] | None] | None = None, routes: ~typing.List[starlette.routing.BaseRoute] | None[~typing.List[~starlette.routing.BaseRoute] | None] | None = None, redirect_slashes: bool[bool] = True, default: ~typing.Callable[[MutableMapping[str, Any], Callable[[], Awaitable[MutableMapping[str, Any]]], Callable[[MutableMapping[str, Any]], Awaitable[None]]], Awaitable[None]] | None[~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] | None = None, dependency_overrides_provider: ~typing.Any | None[~typing.Any | None] | None = None, route_class: ~typing.Type[fastapi.routing.APIRoute][~typing.Type[~fastapi.routing.APIRoute]] = <class 'fastapi.routing.APIRoute'>, on_startup: ~typing.Sequence[Callable[[], Any]] | None[~typing.Sequence[~typing.Callable[[], ~typing.Any]] | None] | None = None, on_shutdown: ~typing.Sequence[Callable[[], Any]] | None[~typing.Sequence[~typing.Callable[[], ~typing.Any]] | None] | None = None, lifespan: ~typing.Callable[[Any], AbstractAsyncContextManager[None]] | Callable[[Any], AbstractAsyncContextManager[Mapping[str, Any]]] | None[~typing.Callable[[~typing.Any], ~typing.AbstractAsyncContextManager[None]] | ~typing.Callable[[~typing.Any], ~typing.AbstractAsyncContextManager[~typing.Mapping[str, ~typing.Any]]] | None] | None = None, deprecated: ~typing.bool | None[bool | None] | None = None, include_in_schema: bool[bool] = True, generate_unique_id_function: ~typing.Callable[[fastapi.routing.APIRoute], str][~typing.Callable[[~fastapi.routing.APIRoute], str]] = <fastapi.datastructures.DefaultPlaceholder object>)[source]
Bases:
APIRouter
A FastAPI Router tailored to Galaxy.
- wrap_with_alias(verb: RestVerb, *args, alias: str | None = 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.
- options(*args, **kwd)[source]
Add a path operation using an HTTP OPTIONS operation.
## Example
```python from fastapi import APIRouter, FastAPI
app = FastAPI() router = APIRouter()
@router.options(“/items/”) def get_item_options():
return {“additions”: [“Aji”, “Guacamole”]}
- head(*args, **kwd)[source]
Add a path operation using an HTTP HEAD operation.
## Example
```python from fastapi import APIRouter, FastAPI from pydantic import BaseModel
- class Item(BaseModel):
name: str description: str | None = None
app = FastAPI() router = APIRouter()
@router.head(“/items/”, status_code=204) def get_items_headers(response: Response):
response.headers[“X-Cat-Dog”] = “Alone in the world”
- 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.Router(*, prefix: str[str] = '', tags: ~typing.List[str | enum.Enum] | None[~typing.List[str | ~enum.Enum] | None] | None = None, dependencies: ~typing.Sequence[fastapi.params.Depends] | None[~typing.Sequence[~fastapi.params.Depends] | None] | None = None, default_response_class: ~typing.Type[starlette.responses.Response][~typing.Type[~starlette.responses.Response]] = <fastapi.datastructures.DefaultPlaceholder object>, responses: ~typing.Dict[int | str, Dict[str, Any]] | None[~typing.Dict[int | str, ~typing.Dict[str, ~typing.Any]] | None] | None = None, callbacks: ~typing.List[starlette.routing.BaseRoute] | None[~typing.List[~starlette.routing.BaseRoute] | None] | None = None, routes: ~typing.List[starlette.routing.BaseRoute] | None[~typing.List[~starlette.routing.BaseRoute] | None] | None = None, redirect_slashes: bool[bool] = True, default: ~typing.Callable[[MutableMapping[str, Any], Callable[[], Awaitable[MutableMapping[str, Any]]], Callable[[MutableMapping[str, Any]], Awaitable[None]]], Awaitable[None]] | None[~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] | None = None, dependency_overrides_provider: ~typing.Any | None[~typing.Any | None] | None = None, route_class: ~typing.Type[fastapi.routing.APIRoute][~typing.Type[~fastapi.routing.APIRoute]] = <class 'fastapi.routing.APIRoute'>, on_startup: ~typing.Sequence[Callable[[], Any]] | None[~typing.Sequence[~typing.Callable[[], ~typing.Any]] | None] | None = None, on_shutdown: ~typing.Sequence[Callable[[], Any]] | None[~typing.Sequence[~typing.Callable[[], ~typing.Any]] | None] | None = None, lifespan: ~typing.Callable[[Any], AbstractAsyncContextManager[None]] | Callable[[Any], AbstractAsyncContextManager[Mapping[str, Any]]] | None[~typing.Callable[[~typing.Any], ~typing.AbstractAsyncContextManager[None]] | ~typing.Callable[[~typing.Any], ~typing.AbstractAsyncContextManager[~typing.Mapping[str, ~typing.Any]]] | None] | None = None, deprecated: ~typing.bool | None[bool | None] | None = None, include_in_schema: bool[bool] = True, generate_unique_id_function: ~typing.Callable[[fastapi.routing.APIRoute], str][~typing.Callable[[~fastapi.routing.APIRoute], str]] = <fastapi.datastructures.DefaultPlaceholder object>)[source]
Bases:
FrameworkRouter
- class galaxy.webapps.galaxy.api.APIContentTypeRoute(path: str, endpoint: ~typing.Callable[[...], ~typing.Any], *, response_model: ~typing.Any = <fastapi.datastructures.DefaultPlaceholder object>, status_code: int | None = None, tags: ~typing.List[str | ~enum.Enum] | None = None, dependencies: ~typing.Sequence[~fastapi.params.Depends] | None = None, summary: str | None = None, description: str | None = None, response_description: str = 'Successful Response', responses: ~typing.Dict[int | str, ~typing.Dict[str, ~typing.Any]] | None = None, deprecated: bool | None = None, name: str | None = None, methods: ~typing.Set[str] | ~typing.List[str] | None = None, operation_id: str | None = None, response_model_include: ~typing.Set[int] | ~typing.Set[str] | ~typing.Dict[int, ~typing.Any] | ~typing.Dict[str, ~typing.Any] | None = None, response_model_exclude: ~typing.Set[int] | ~typing.Set[str] | ~typing.Dict[int, ~typing.Any] | ~typing.Dict[str, ~typing.Any] | None = 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.Type[~starlette.responses.Response] | ~fastapi.datastructures.DefaultPlaceholder = <fastapi.datastructures.DefaultPlaceholder object>, dependency_overrides_provider: ~typing.Any | None = None, callbacks: ~typing.List[~starlette.routing.BaseRoute] | None = None, openapi_extra: ~typing.Dict[str, ~typing.Any] | None = None, generate_unique_id_function: ~typing.Callable[[~fastapi.routing.APIRoute], str] | ~fastapi.datastructures.DefaultPlaceholder = <fastapi.datastructures.DefaultPlaceholder object>)[source]
Bases:
APIRoute
Determines endpoint to match using content-type.
- 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) Any | None [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
- galaxy.webapps.galaxy.api.search_query_param(model_name: str, tags: list, free_text_fields: list) str | None [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
- 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'
- history_manager: HistoryManager = GalaxyTypeDepends(_do_resolve)
- class galaxy.webapps.galaxy.api.annotations.HistoryContentAnnotationsController(app: StructuredApp)[source]
Bases:
BaseAnnotationsController
- controller_name = 'history_content_annotations'
- hda_manager: HDAManager = GalaxyTypeDepends(_do_resolve)
- class galaxy.webapps.galaxy.api.annotations.WorkflowAnnotationsController(app: StructuredApp)[source]
Bases:
BaseAnnotationsController
- controller_name = 'workflow_annotations'
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.
- class galaxy.webapps.galaxy.api.authenticate.FastAPIAuthenticate(*, authentication_service: AuthenticationService = GalaxyTypeDepends(_do_resolve))[source]
Bases:
object
- authentication_service: AuthenticationService = GalaxyTypeDepends(_do_resolve)
- get_api_key(*, request: Request) APIKeyResponse [source]
galaxy.webapps.galaxy.api.cloud module
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:
- 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:
- 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: str | None = None, keys: str | None = None, default_view: str | None = None, **_) SerializationParams [source]
- galaxy.webapps.galaxy.api.common.query_serialization_params(view: str | None[str | None] | None = None, keys: str | None = Query(None)) SerializationParams [source]
- galaxy.webapps.galaxy.api.common.get_value_filter_query_params(q: List[str] | None = Query(None), qv: List[str] | None = 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: List[str] | None = Query(None), qv: List[str] | None = Query(None), offset: int | None = Query(0), limit: int | None = Query(None), order: str | None = 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 thealias
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)) UserModel | None [source]
Return information about the current authenticated user.
- index(*, trans: ProvidesUserContext = Depends(get_trans), view: str | None[str | None] | None = None, keys: str | None = 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.
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’
- 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:
- 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.
- 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:
- 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:
- 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
galaxy.webapps.galaxy.api.datasets module
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
- async index(*, extension_only: bool | None = Query(True), upload_only: bool | None = Query(True)) 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: bool | None = Query(True), upload_only: bool | None = Query(True)) DatatypesCombinedMap [source]
Combines the datatype information from (/api/datatypes) and the mapping information from (/api/datatypes/mapping) into a single response.
- 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_formats_detailed()[source]
Gets a map of datatypes and their corresponding EDAM formats. EDAM formats contain the EDAM iri, label, and definition.
- async edam_data() Dict[str, str] [source]
Gets a map of datatypes and their corresponding EDAM data.
galaxy.webapps.galaxy.api.display_applications module
API operations on annotations.
- class galaxy.webapps.galaxy.api.display_applications.FastAPIDisplay(*, manager: DisplayApplicationsManager = GalaxyTypeDepends(_do_resolve))[source]
Bases:
object
- manager: DisplayApplicationsManager = GalaxyTypeDepends(_do_resolve)
- index() List[DisplayApplication] [source]
Returns the list of display applications.
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.
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
]
- class galaxy.webapps.galaxy.api.extended_metadata.LibraryDatasetExtendMetadataController(app: StructuredApp)[source]
Bases:
BaseExtendedMetadataController
[LibraryDatasetDatasetAssociation
]- controller_name = 'library_dataset_extended_metadata'
- class galaxy.webapps.galaxy.api.extended_metadata.HistoryDatasetExtendMetadataController(app: StructuredApp)[source]
Bases:
BaseExtendedMetadataController
[HistoryDatasetAssociation
]- controller_name = 'history_dataset_extended_metadata'
- hda_manager: HDAManager = GalaxyTypeDepends(_do_resolve)
galaxy.webapps.galaxy.api.folder_contents module
API operations on the contents of a library folder.
- class galaxy.webapps.galaxy.api.folder_contents.FastAPILibraryFoldersContents(*, service: LibraryFolderContentsService = GalaxyTypeDepends(_do_resolve))[source]
Bases:
object
- service: LibraryFolderContentsService = GalaxyTypeDepends(_do_resolve)
- index(*, folder_id: int[int], trans: ProvidesUserContext = Depends(get_trans), limit: int = Query(10), offset: int = Query(0), search_text: str | None = Query(None), include_deleted: bool | None = Query(False), order_by: typing_extensions.Literal[name, description, type, size, update_time] = Query(name), sort_desc: bool | None = Query(False))[source]
Returns a list of a folder’s contents (files and sub-folders).
Additional metadata for the folder is provided in the response as a separate object containing data for breadcrumb path building, permissions and other folder’s details.
Note: When sorting, folders always have priority (they show-up before any dataset regardless of the sorting).
Security note: - Accessing a library folder or sub-folder requires only access to the parent library. - Deleted folders can only be accessed by admins or users with MODIFY permission. - Datasets may be public, private or restricted (to a group of users). Listing deleted datasets has the same requirements as folders.
- create(*, folder_id: int[int], trans: ProvidesUserContext = Depends(get_trans), payload: CreateLibraryFilePayload = Body(PydanticUndefined))[source]
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(*, id: int[int], trans: ProvidesUserContext = Depends(get_trans)) LibraryFolderDetails [source]
Returns detailed information about the library folder with the given ID.
- create(*, id: int[int], trans: ProvidesUserContext = Depends(get_trans), payload: CreateLibraryFolderPayload = Body(PydanticUndefined)) LibraryFolderDetails [source]
Returns detailed information about the newly created library folder.
- update(*, id: int[int], trans: ProvidesUserContext = Depends(get_trans), payload: UpdateLibraryFolderPayload = Body(PydanticUndefined)) LibraryFolderDetails [source]
Updates the information of an existing library folder.
- delete(*, id: int[int], undelete: bool | None[bool | None] | None = None, trans: ProvidesUserContext = Depends(get_trans)) LibraryFolderDetails [source]
Marks the specified library folder as deleted (or undeleted).
- get_permissions(*, id: int[int], trans: ProvidesUserContext = Depends(get_trans), scope: LibraryPermissionScope | None = Query(None), page: int = Query(1), page_limit: int = Query(10), q: str | None = Query(None)) 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(*, id: int[int], trans: ProvidesUserContext = Depends(get_trans), action: LibraryFolderPermissionAction | None = Query(None), payload: LibraryFolderPermissionsPayload = Body(PydanticUndefined)) LibraryFolderCurrentPermissions [source]
Sets the permissions to manage a library folder.
galaxy.webapps.galaxy.api.forms module
API operations on FormDefinition objects.
- class galaxy.webapps.galaxy.api.forms.FastAPIForms(*, form_manager: FormManager = GalaxyTypeDepends(_do_resolve))[source]
Bases:
object
- form_manager: FormManager = GalaxyTypeDepends(_do_resolve)
- delete(*, id: int[int], trans: ProvidesUserContext = Depends(get_trans))[source]
- undelete(*, id: int[int], trans: ProvidesUserContext = Depends(get_trans))[source]
- class galaxy.webapps.galaxy.api.forms.FormDefinitionAPIController(app: StructuredApp)[source]
Bases:
BaseGalaxyAPIController
galaxy.webapps.galaxy.api.genomes module
- 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(PydanticUndefined), 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(*, trans: ProvidesUserContext = Depends(get_trans), id: str = Path(PydanticUndefined), type: str = Query(fasta_indexes), format: str = Query(None)) Any [source]
galaxy.webapps.galaxy.api.group_roles module
API operations on Group objects.
- galaxy.webapps.galaxy.api.group_roles.group_role_to_model(trans, group_id: int, role) GroupRoleResponse [source]
- class galaxy.webapps.galaxy.api.group_roles.FastAPIGroupRoles(*, manager: GroupRolesManager = GalaxyTypeDepends(_do_resolve))[source]
Bases:
object
- manager: GroupRolesManager = GalaxyTypeDepends(_do_resolve)
- index(*, group_id: int[int], trans: ProvidesAppContext = Depends(get_trans)) GroupRoleListResponse [source]
- show(*, group_id: int[int], role_id: int[int], trans: ProvidesAppContext = Depends(get_trans)) GroupRoleResponse [source]
- update(*, group_id: int[int], role_id: int[int], trans: ProvidesAppContext = Depends(get_trans)) GroupRoleResponse [source]
- delete(*, group_id: int[int], role_id: int[int], trans: ProvidesAppContext = Depends(get_trans)) GroupRoleResponse [source]
galaxy.webapps.galaxy.api.group_users module
API operations on Group objects.
- galaxy.webapps.galaxy.api.group_users.group_user_to_model(trans, group_id, user) GroupUserResponse [source]
- class galaxy.webapps.galaxy.api.group_users.FastAPIGroupUsers(*, manager: GroupUsersManager = GalaxyTypeDepends(_do_resolve))[source]
Bases:
object
- manager: GroupUsersManager = GalaxyTypeDepends(_do_resolve)
- index(*, group_id: int[int], trans: ProvidesAppContext = Depends(get_trans)) GroupUserListResponse [source]
GET /api/groups/{encoded_group_id}/users Displays a collection (list) of groups.
- show(*, group_id: int[int], user_id: int[int], trans: ProvidesAppContext = Depends(get_trans)) GroupUserResponse [source]
Displays information about a group user.
- update(*, group_id: int[int], user_id: int[int], trans: ProvidesAppContext = Depends(get_trans)) GroupUserResponse [source]
PUT /api/groups/{encoded_group_id}/users/{encoded_user_id} Adds a user to a group
- delete(*, group_id: int[int], user_id: int[int], trans: ProvidesAppContext = Depends(get_trans)) GroupUserResponse [source]
DELETE /api/groups/{encoded_group_id}/users/{encoded_user_id} Removes a user from a group
galaxy.webapps.galaxy.api.groups module
API operations on Group objects.
- class galaxy.webapps.galaxy.api.groups.FastAPIGroups(*, manager: GroupsManager = GalaxyTypeDepends(_do_resolve))[source]
Bases:
object
- manager: GroupsManager = GalaxyTypeDepends(_do_resolve)
- index(*, trans: ProvidesAppContext = Depends(get_trans)) GroupListResponse [source]
- create(*, payload: GroupCreatePayload[GroupCreatePayload], trans: ProvidesAppContext = Depends(get_trans)) GroupListResponse [source]
- show(*, group_id: int[int], trans: ProvidesAppContext = Depends(get_trans)) GroupResponse [source]
- update(*, group_id: int[int], payload: GroupUpdatePayload[GroupUpdatePayload], trans: ProvidesAppContext = Depends(get_trans)) GroupResponse [source]
- delete(*, group_id: int[int], trans: ProvidesAppContext = Depends(get_trans))[source]
- purge(*, group_id: int[int], trans: ProvidesAppContext = Depends(get_trans))[source]
- undelete(*, group_id: int[int], trans: ProvidesAppContext = Depends(get_trans))[source]
galaxy.webapps.galaxy.api.histories module
galaxy.webapps.galaxy.api.history_contents module
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: ProvidesAppContext, 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:
- ..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:
- ..note:
This API method is intended only for consumption by job runners, not end users.
- Return type:
- Returns:
an okay message
- tus_patch(trans, **kwds)[source]
Exposed as PATCH /api/job_files/resumable_upload.
I think based on the docs, a separate tusd server is needed for job files if also hosting one for use facing uploads.
Setting up tusd for job files should just look like (I think):
tusd -host localhost -port 1080 -upload-dir=<galaxy_root>/database/tmp
See more discussion of checking upload access, but we shouldn’t need the API key and session stuff the user upload tusd server should be configured with.
Also shouldn’t need a hooks endpoint for this reason but if you want to add one the target CLI entry would be -hooks-http=<galaxy_url>/api/job_files/tus_hooks and the action is featured below.
I would love to check the job state with __authorize_job_access on the first POST but it seems like TusMiddleware doesn’t default to coming in here for that initial POST the way it does for the subsequent PATCHes. Ultimately, the upload is still authorized before the write done with POST /api/jobs/<job_id>/files so I think there is no route here to mess with user data - the worst of the security issues that can be caused is filling up the sever with needless files that aren’t acted on. Since this endpoint is not meant for public consumption - all the job files stuff and the TUS server should be blocked to public IPs anyway and restricted to your Pulsar servers and similar targeting could be accomplished with a user account and the user facing upload endpoints.
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(PydanticUndefined)) 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’
galaxy.webapps.galaxy.api.jobs module
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: bool | None = 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(*, id: int[int], trans: ProvidesUserContext = Depends(get_trans)) LibrarySummary [source]
Returns summary information about a particular library.
- create(*, trans: ProvidesUserContext = Depends(get_trans), payload: CreateLibraryPayload = Body(PydanticUndefined)) 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(PydanticUndefined)) List[LibrarySummary] [source]
- update(*, id: int[int], trans: ProvidesUserContext = Depends(get_trans), payload: UpdateLibraryPayload = Body(PydanticUndefined)) LibrarySummary [source]
Updates the information of an existing library.
- delete(*, id: int[int], trans: ProvidesUserContext = Depends(get_trans), undelete: bool | None = Query(None), payload: DeleteLibraryPayload | None = Body(None)) LibrarySummary [source]
Marks the specified library as deleted (or undeleted). Currently, only admin users can delete or restore libraries.
- get_permissions(*, id: int[int], trans: ProvidesUserContext = Depends(get_trans), scope: LibraryPermissionScope | None = Query(None), is_library_access: bool | None = Query(None), page: int = Query(1), page_limit: int = Query(10), q: str | None = Query(None)) 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(*, id: int[int], trans: ProvidesUserContext = Depends(get_trans), action: LibraryPermissionAction | None = Query(None), payload: LibraryPermissionsPayload | LegacyLibraryPermissionsPayload = Body(PydanticUndefined)) LibraryLegacySummary | LibraryCurrentPermissions [source]
Sets the permissions to access and manipulate a library.
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:
- 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.
- 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 infrom_hda_id
(and optionallyldda_message
).To copy an HDCA into a library send
create_type
of ‘file’ and the HDCA’s encoded id infrom_hdca_id
(and optionallyldda_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) oruser_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:
- update(trans, id, library_id, payload, **kwd)[source]
PUT /api/libraries/{library_id}/contents/{id}
Create an ImplicitlyConvertedDatasetAssociation.
- delete(trans, library_id, id, **kwd)[source]
DELETE /api/libraries/{library_id}/contents/{id}
Delete the LibraryDataset with the given
id
.- Parameters:
- Return type:
- 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(PydanticUndefined)) 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/).
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(PydanticUndefined)) Any [source]
Record any metrics sent and return some status object.
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:
- 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(*, response: Response, trans: ProvidesUserContext = Depends(get_trans), deleted: bool = Query(False), limit: int = Query(100), offset: int = Query(0), search: str | None = Query(None), show_own: bool = Query(True), show_published: bool = Query(True), show_shared: bool = Query(False), sort_by: typing_extensions.Literal[create_time, title, update_time, username] = Query(update_time), sort_desc: bool = Query(False), user_id: int[int] | None = Query(None)) PageSummaryList [source]
Get a list with summary information of all Pages available to the user.
- create(*, trans: ProvidesUserContext = Depends(get_trans), payload: CreatePagePayload = Body(PydanticUndefined)) PageSummary [source]
Get a list with details of all Pages available to the user.
- async delete(*, id: int[int], trans: ProvidesUserContext = Depends(get_trans))[source]
Marks the Page with the given ID as deleted.
- async undelete(*, id: int[int], trans: ProvidesUserContext = Depends(get_trans))[source]
Marks the Page with the given ID as undeleted.
- async show_pdf(*, id: int[int], trans: ProvidesUserContext = Depends(get_trans))[source]
Return a PDF document of the last revision of the Page.
This feature may not be available in this Galaxy.
- async prepare_pdf(*, id: int[int], trans: ProvidesUserContext = Depends(get_trans)) 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(*, id: int[int], trans: ProvidesUserContext = Depends(get_trans)) PageDetails [source]
Return summary information about a specific Page and the content of the last revision.
- sharing(*, id: int[int], trans: ProvidesUserContext = Depends(get_trans)) SharingStatus [source]
Return the sharing status of the item.
- enable_link_access(*, id: int[int], trans: ProvidesUserContext = Depends(get_trans)) SharingStatus [source]
Makes this item accessible by a URL link and return the current sharing status.
- disable_link_access(*, id: int[int], trans: ProvidesUserContext = Depends(get_trans)) SharingStatus [source]
Makes this item inaccessible by a URL link and return the current sharing status.
- publish(*, id: int[int], trans: ProvidesUserContext = Depends(get_trans)) SharingStatus [source]
Makes this item publicly available by a URL link and return the current sharing status.
- unpublish(*, id: int[int], trans: ProvidesUserContext = Depends(get_trans)) SharingStatus [source]
Removes this item from the published list and return the current sharing status.
Shares this item with specific users and return the current sharing status.
- set_slug(*, id: int[int], trans: ProvidesUserContext = Depends(get_trans), payload: SetSlugPayload = Body(PydanticUndefined))[source]
Sets a new slug to access this item by URL. The new slug must be unique.
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)
galaxy.webapps.galaxy.api.provenance module
API operations provenance
- class galaxy.webapps.galaxy.api.provenance.BaseProvenanceController(app: StructuredApp)[source]
Bases:
BaseGalaxyAPIController
- 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(*, id: int[int], trans: ProvidesUserContext = Depends(get_trans)) QuotaDetails [source]
Displays details on a particular active quota.
- show_deleted(*, id: int[int], trans: ProvidesUserContext = Depends(get_trans)) 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(*, id: int[int], payload: UpdateQuotaParams, trans: ProvidesUserContext = Depends(get_trans)) str [source]
Updates an existing quota.
- delete(*, id: int[int], trans: ProvidesUserContext = Depends(get_trans), payload: DeleteQuotaPayload = Body(None)) str [source]
Deletes an existing quota.
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: RemoteFilesFormat | None = Query(uri), recursive: bool | None = Query(None), disable: RemoteFilesDisableMode | None = Query(None), writeable: bool | None = Query(None)) ListUriResponse | ListJstreeResponse [source]
Lists all remote files available to the user from different sources.
- async plugins(*, user_ctx: ProvidesUserContext = Depends(get_trans), browsable_only: bool | None = Query(True), include_kind: List[galaxy.files.sources.PluginKind] | None[List[PluginKind] | None] | None = None, exclude_kind: List[galaxy.files.sources.PluginKind] | None[List[PluginKind] | None] | None = None) FilesSourcePluginList [source]
Display plugin information for each of the gxfiles:// URI targets available.
- async create_entry(*, user_ctx: ProvidesUserContext = Depends(get_trans), payload: CreateEntryPayload = Body(PydanticUndefined)) CreatedEntryResponse [source]
Creates a new entry on the remote files source.
galaxy.webapps.galaxy.api.roles module
API operations on Role objects.
- 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)) RoleListResponse [source]
- show(*, id: int[int], trans: ProvidesUserContext = Depends(get_trans)) RoleModelResponse [source]
- create(*, trans: ProvidesUserContext = Depends(get_trans), role_definition_model: RoleDefinitionModel = Body(PydanticUndefined)) RoleModelResponse [source]
- delete(*, id: int[int], trans: ProvidesUserContext = Depends(get_trans)) RoleModelResponse [source]
- purge(*, id: int[int], trans: ProvidesUserContext = Depends(get_trans)) RoleModelResponse [source]
- undelete(*, id: int[int], trans: ProvidesUserContext = Depends(get_trans)) RoleModelResponse [source]
galaxy.webapps.galaxy.api.sanitize_allow module
API operations allowing clients to retrieve and modify the HTML sanitization allow list.
galaxy.webapps.galaxy.api.search module
galaxy.webapps.galaxy.api.short_term_storage module
API operations around galaxy.short_term_storage infrastructure.
galaxy.webapps.galaxy.api.tasks module
API Controller providing experimental access to Celery Task State.
galaxy.webapps.galaxy.api.tool_data module
- class galaxy.webapps.galaxy.api.tool_data.ImportToolDataBundle(*, source: ImportToolDataBundleDatasetSource | ImportToolDataBundleUriSource)[source]
Bases:
BaseModel
- model_config: ClassVar[ConfigDict] = {}
Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].
- model_fields: ClassVar[dict[str, FieldInfo]] = {'source': FieldInfo(annotation=Union[ImportToolDataBundleDatasetSource, ImportToolDataBundleUriSource], required=True, discriminator='src')}
Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].
This replaces Model.__fields__ from Pydantic V1.
- 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 create(*, tool_data_file_path: str | None = None, import_bundle_model: ImportToolDataBundle = Body(PydanticUndefined)) AsyncTaskResultSummary [source]
- async show(*, table_name: str = Path(PydanticUndefined)) ToolDataDetails [source]
Get details of a given tool data table.
- async reload(*, table_name: str = Path(PydanticUndefined)) ToolDataDetails [source]
Reloads a data table and return its details.
- async show_field(*, table_name: str = Path(PydanticUndefined), field_name: str = Path(PydanticUndefined)) ToolDataField [source]
Reloads a data table and return its details.
- async download_field_file(*, table_name: str = Path(PydanticUndefined), field_name: str = Path(PydanticUndefined), file_name: str = Path(PydanticUndefined))[source]
Download a file associated with the data table field.
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:
- Returns:
a dictified description of the dependency, with attribute
dependency_type: None
if no match was found.
- install_dependency(trans: ProvidesAppContext, id: str | None = 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:
- 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:
- 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.
- 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.
- clean(trans: ProvidesAppContext, id=None, **kwds)[source]
POST /api/dependency_resolvers/{index}/clean
Cleans up intermediate files created by resolvers during the dependency installation.
- 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:
- 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:
- 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
- class galaxy.webapps.galaxy.api.tool_shed_repositories.ToolShedRepositoriesController(app: StructuredApp)[source]
Bases:
BaseGalaxyAPIController
RESTful controller for interactions with tool shed repositories.
- service: ToolShedRepositoriesService = GalaxyTypeDepends(_do_resolve)
- 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
- class galaxy.webapps.galaxy.api.tool_shed_repositories.FastAPIToolShedRepositories(*, service: ToolShedRepositoriesService = GalaxyTypeDepends(_do_resolve))[source]
Bases:
object
- service: ToolShedRepositoriesService = GalaxyTypeDepends(_do_resolve)
- index(*, name: str | None = Query(None), owner: str | None = Query(None), changeset: str | None = Query(None), deleted: bool | None = Query(None), uninstalled: bool | None = Query(None)) List[InstalledToolShedRepository] [source]
- show(*, id: int[int]) InstalledToolShedRepository [source]
galaxy.webapps.galaxy.api.tools module
- class galaxy.webapps.galaxy.api.tools.FormDataApiRoute(path: str, endpoint: ~typing.Callable[[...], ~typing.Any], *, response_model: ~typing.Any = <fastapi.datastructures.DefaultPlaceholder object>, status_code: int | None = None, tags: ~typing.List[str | ~enum.Enum] | None = None, dependencies: ~typing.Sequence[~fastapi.params.Depends] | None = None, summary: str | None = None, description: str | None = None, response_description: str = 'Successful Response', responses: ~typing.Dict[int | str, ~typing.Dict[str, ~typing.Any]] | None = None, deprecated: bool | None = None, name: str | None = None, methods: ~typing.Set[str] | ~typing.List[str] | None = None, operation_id: str | None = None, response_model_include: ~typing.Set[int] | ~typing.Set[str] | ~typing.Dict[int, ~typing.Any] | ~typing.Dict[str, ~typing.Any] | None = None, response_model_exclude: ~typing.Set[int] | ~typing.Set[str] | ~typing.Dict[int, ~typing.Any] | ~typing.Dict[str, ~typing.Any] | None = 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.Type[~starlette.responses.Response] | ~fastapi.datastructures.DefaultPlaceholder = <fastapi.datastructures.DefaultPlaceholder object>, dependency_overrides_provider: ~typing.Any | None = None, callbacks: ~typing.List[~starlette.routing.BaseRoute] | None = None, openapi_extra: ~typing.Dict[str, ~typing.Any] | None = None, generate_unique_id_function: ~typing.Callable[[~fastapi.routing.APIRoute], str] | ~fastapi.datastructures.DefaultPlaceholder = <fastapi.datastructures.DefaultPlaceholder object>)[source]
Bases:
APIContentTypeRoute
- class galaxy.webapps.galaxy.api.tools.JsonApiRoute(path: str, endpoint: ~typing.Callable[[...], ~typing.Any], *, response_model: ~typing.Any = <fastapi.datastructures.DefaultPlaceholder object>, status_code: int | None = None, tags: ~typing.List[str | ~enum.Enum] | None = None, dependencies: ~typing.Sequence[~fastapi.params.Depends] | None = None, summary: str | None = None, description: str | None = None, response_description: str = 'Successful Response', responses: ~typing.Dict[int | str, ~typing.Dict[str, ~typing.Any]] | None = None, deprecated: bool | None = None, name: str | None = None, methods: ~typing.Set[str] | ~typing.List[str] | None = None, operation_id: str | None = None, response_model_include: ~typing.Set[int] | ~typing.Set[str] | ~typing.Dict[int, ~typing.Any] | ~typing.Dict[str, ~typing.Any] | None = None, response_model_exclude: ~typing.Set[int] | ~typing.Set[str] | ~typing.Dict[int, ~typing.Any] | ~typing.Dict[str, ~typing.Any] | None = 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.Type[~starlette.responses.Response] | ~fastapi.datastructures.DefaultPlaceholder = <fastapi.datastructures.DefaultPlaceholder object>, dependency_overrides_provider: ~typing.Any | None = None, callbacks: ~typing.List[~starlette.routing.BaseRoute] | None = None, openapi_extra: ~typing.Dict[str, ~typing.Any] | None = None, generate_unique_id_function: ~typing.Callable[[~fastapi.routing.APIRoute], str] | ~fastapi.datastructures.DefaultPlaceholder = <fastapi.datastructures.DefaultPlaceholder object>)[source]
Bases:
APIContentTypeRoute
- 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(PydanticUndefined), trans: ProvidesHistoryContext = Depends(get_trans))[source]
- async fetch_form(*, request: Request, payload: FetchDataFormPayload = Depends(_as_form), files: List[UploadFile] | None = None, trans: ProvidesHistoryContext = Depends(get_trans))[source]
- 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
- panel_views(trans: GalaxyWebTransaction, **kwds)[source]
GET /api/tool_panels returns a dictionary of available tool panel views and default view
- panel_view(trans: GalaxyWebTransaction, view, **kwds)[source]
GET /api/tool_panels/{view}
returns a dictionary of tools and tool sections for the given view
- Parameters:
trackster – if true, only tools that are compatible with Trackster are returned
- 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.
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)
- show(*, tour_id: str) TourDetails [source]
Return a tour definition.
- update_tour(*, tour_id: str) TourDetails [source]
Return a tour definition.
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.
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.
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
galaxy.webapps.galaxy.api.users module
API operations on User objects.
- class galaxy.webapps.galaxy.api.users.FastAPIUsers(*, service: UsersService = GalaxyTypeDepends(_do_resolve), user_serializer: UserSerializer = GalaxyTypeDepends(_do_resolve))[source]
Bases:
object
- service: UsersService = GalaxyTypeDepends(_do_resolve)
- user_serializer: UserSerializer = GalaxyTypeDepends(_do_resolve)
- recalculate_disk_usage(*, trans: ProvidesUserContext = Depends(get_trans))[source]
This route will be removed in a future version.
Please use /api/users/current/recalculate_disk_usage instead.
- recalculate_disk_usage_by_user_id(*, user_id: int[int], trans: ProvidesUserContext = Depends(get_trans))[source]
- index_deleted(*, trans: ProvidesUserContext = Depends(get_trans), f_email: str | None = Query(None), f_name: str | None = Query(None), f_any: str | None = Query(None)) List[UserModel | LimitedUserModel] [source]
- undelete(*, user_id: int[int], trans: ProvidesHistoryContext = Depends(get_trans)) DetailedUserModel [source]
- show_deleted(*, user_id: int[int], trans: ProvidesHistoryContext = Depends(get_trans)) DetailedUserModel | AnonUserModel [source]
- get_or_create_api_key(*, user_id: int[int], trans: ProvidesUserContext = Depends(get_trans)) str [source]
- get_api_key(*, user_id: int[int], trans: ProvidesUserContext = Depends(get_trans))[source]
- delete_api_key(*, user_id: int[int], trans: ProvidesUserContext = Depends(get_trans))[source]
- usage(*, trans: ProvidesUserContext = Depends(get_trans), user_id: int[int] | typing_extensions.Literal[current] = Path(PydanticUndefined)) List[UserQuotaUsage] [source]
- usage_for(*, trans: ProvidesUserContext = Depends(get_trans), user_id: int[int] | typing_extensions.Literal[current] = Path(PydanticUndefined), label: str = Path(PydanticUndefined)) UserQuotaUsage | None [source]
- get_beacon(*, user_id: int[int], trans: ProvidesUserContext = Depends(get_trans)) UserBeaconSetting [source]
Warning: This endpoint is experimental and might change or disappear in future versions.
- set_beacon(*, user_id: int[int], trans: ProvidesUserContext = Depends(get_trans), payload: UserBeaconSetting = Body(PydanticUndefined)) UserBeaconSetting [source]
Warning: This endpoint is experimental and might change or disappear in future versions.
- remove_favorite(*, user_id: int[int], trans: ProvidesUserContext = Depends(get_trans), object_type: FavoriteObjectType = Path(PydanticUndefined), object_id: str = Path(PydanticUndefined)) FavoriteObjectsSummary [source]
- set_favorite(*, user_id: int[int], trans: ProvidesUserContext = Depends(get_trans), object_type: FavoriteObjectType = Path(PydanticUndefined), payload: FavoriteObject = Body(PydanticUndefined)) FavoriteObjectsSummary [source]
- set_theme(*, user_id: int[int], trans: ProvidesUserContext = Depends(get_trans), theme: str = Path(PydanticUndefined)) str [source]
- add_custom_builds(*, user_id: int[int], key: str = Path(PydanticUndefined), trans: ProvidesUserContext = Depends(get_trans), payload: CustomBuildCreationPayload = Body(PydanticUndefined)) Any [source]
- get_custom_builds(*, user_id: int[int], trans: ProvidesHistoryContext = Depends(get_trans)) CustomBuildsCollection [source]
- delete_custom_builds(*, user_id: int[int], key: str = Path(PydanticUndefined), trans: ProvidesUserContext = Depends(get_trans)) DeletedCustomBuild [source]
- create(*, trans: ProvidesUserContext = Depends(get_trans), payload: UserCreationPayload | RemoteUserCreationPayload = Body(PydanticUndefined)) CreatedUserModel [source]
- index(*, trans: ProvidesUserContext = Depends(get_trans), deleted: bool = Query(False), f_email: str | None = Query(None), f_name: str | None = Query(None), f_any: str | None = Query(None)) List[UserModel | LimitedUserModel] [source]
- show(*, trans: ProvidesHistoryContext = Depends(get_trans), user_id: int[int] | typing_extensions.Literal[current] = Path(PydanticUndefined), deleted: bool | None = Query(None)) DetailedUserModel | AnonUserModel [source]
- update(*, trans: ProvidesUserContext = Depends(get_trans), user_id: int[int] | typing_extensions.Literal[current] = Path(PydanticUndefined), payload: Dict[Any, Any] = Body(PydanticUndefined), deleted: bool | None = Query(None)) DetailedUserModel [source]
- delete(*, user_id: int[int], trans: ProvidesUserContext = Depends(get_trans), purge: bool[bool] = False, payload: UserDeletionPayload | None = None) DetailedUserModel [source]
- send_activation_email(*, user_id: int[int], trans: ProvidesUserContext = Depends(get_trans))[source]
- class galaxy.webapps.galaxy.api.users.UserAPIController(app: StructuredApp)[source]
Bases:
BaseGalaxyAPIController
,UsesTagsMixin
,BaseUIController
,UsesFormDefinitionsMixin
- service: UsersService = GalaxyTypeDepends(_do_resolve)
- user_manager: UserManager = GalaxyTypeDepends(_do_resolve)
- 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.
- 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
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)
- async index(*, response: Response, trans: ProvidesUserContext = Depends(get_trans), deleted: bool = Query(False), limit: int | None = Query(None), offset: int | None = Query(0), user_id: int[int] | None = Query(None), show_own: bool = Query(True), show_published: bool = Query(True), show_shared: bool = Query(False), sort_by: typing_extensions.Literal[create_time, title, update_time, username] = Query(update_time), sort_desc: bool = Query(True), search: str | None = Query(None)) VisualizationSummaryList [source]
- sharing(*, id: int[int], trans: ProvidesUserContext = Depends(get_trans)) SharingStatus [source]
Return the sharing status of the item.
- enable_link_access(*, id: int[int], trans: ProvidesUserContext = Depends(get_trans)) SharingStatus [source]
Makes this item accessible by a URL link and return the current sharing status.
- disable_link_access(*, id: int[int], trans: ProvidesUserContext = Depends(get_trans)) SharingStatus [source]
Makes this item inaccessible by a URL link and return the current sharing status.
- publish(*, id: int[int], trans: ProvidesUserContext = Depends(get_trans)) SharingStatus [source]
Makes this item publicly available by a URL link and return the current sharing status.
- unpublish(*, id: int[int], trans: ProvidesUserContext = Depends(get_trans)) SharingStatus [source]
Removes this item from the published list and return the current sharing status.
Shares this item with specific users and return the current sharing status.
- set_slug(*, id: int[int], trans: ProvidesUserContext = Depends(get_trans), payload: SetSlugPayload = Body(PydanticUndefined))[source]
Sets a new slug to access this item by URL. The new slug must be unique.
- 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)
- 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.