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Source code for galaxy.webapps.galaxy.api.libraries

"""
API operations on a data library.
"""

import logging
from typing import (
    List,
    Optional,
    Union,
)

from fastapi import (
    Body,
    Query,
)

from galaxy.managers.context import ProvidesUserContext
from galaxy.schema.schema import (
    CreateLibrariesFromStore,
    CreateLibraryPayload,
    DeleteLibraryPayload,
    LegacyLibraryPermissionsPayload,
    LibraryAvailablePermissions,
    LibraryCurrentPermissions,
    LibraryLegacySummary,
    LibraryPermissionAction,
    LibraryPermissionScope,
    LibraryPermissionsPayload,
    LibrarySummary,
    LibrarySummaryList,
    UpdateLibraryPayload,
)
from galaxy.webapps.galaxy.api import (
    depends,
    DependsOnTrans,
    Router,
)
from galaxy.webapps.galaxy.api.common import LibraryIdPathParam
from galaxy.webapps.galaxy.services.libraries import LibrariesService

log = logging.getLogger(__name__)

router = Router(tags=["libraries"])

DeletedQueryParam: Optional[bool] = Query(
    default=None, title="Display deleted", description="Whether to include deleted libraries in the result."
)

UndeleteQueryParam: Optional[bool] = Query(
    default=None, title="Undelete", description="Whether to restore a deleted library."
)


[docs]@router.cbv class FastAPILibraries: service: LibrariesService = depends(LibrariesService)
[docs] @router.get( "/api/libraries", summary="Returns a list of summary data for all libraries.", ) def index( self, trans: ProvidesUserContext = DependsOnTrans, deleted: Optional[bool] = DeletedQueryParam, ) -> LibrarySummaryList: """Returns a list of summary data for all libraries.""" return self.service.index(trans, deleted)
[docs] @router.get( "/api/libraries/deleted", summary="Returns a list of summary data for all libraries marked as deleted.", ) def index_deleted( self, trans: ProvidesUserContext = DependsOnTrans, ) -> LibrarySummaryList: """Returns a list of summary data for all libraries marked as deleted.""" return self.service.index(trans, True)
[docs] @router.get( "/api/libraries/{id}", summary="Returns summary information about a particular library.", ) def show( self, id: LibraryIdPathParam, trans: ProvidesUserContext = DependsOnTrans, ) -> LibrarySummary: """Returns summary information about a particular library.""" return self.service.show(trans, id)
[docs] @router.post( "/api/libraries", summary="Creates a new library and returns its summary information.", require_admin=True, ) def create( self, trans: ProvidesUserContext = DependsOnTrans, payload: CreateLibraryPayload = Body(...), ) -> LibrarySummary: """Creates a new library and returns its summary information. Currently, only admin users can create libraries.""" return self.service.create(trans, payload)
[docs] @router.post( "/api/libraries/from_store", summary="Create libraries from a model store.", require_admin=True, ) def create_from_store( self, trans: ProvidesUserContext = DependsOnTrans, payload: CreateLibrariesFromStore = Body(...), ) -> List[LibrarySummary]: return self.service.create_from_store(trans, payload)
[docs] @router.patch( "/api/libraries/{id}", summary="Updates the information of an existing library.", ) def update( self, id: LibraryIdPathParam, trans: ProvidesUserContext = DependsOnTrans, payload: UpdateLibraryPayload = Body(...), ) -> LibrarySummary: """ Updates the information of an existing library. """ return self.service.update(trans, id, payload)
[docs] @router.delete( "/api/libraries/{id}", summary="Marks the specified library as deleted (or undeleted).", require_admin=True, ) def delete( self, id: LibraryIdPathParam, trans: ProvidesUserContext = DependsOnTrans, undelete: Optional[bool] = UndeleteQueryParam, payload: Optional[DeleteLibraryPayload] = Body(default=None), ) -> LibrarySummary: """Marks the specified library as deleted (or undeleted). Currently, only admin users can delete or restore libraries.""" if payload: undelete = payload.undelete return self.service.delete(trans, id, undelete)
[docs] @router.get( "/api/libraries/{id}/permissions", summary="Gets the current or available permissions of a particular library.", ) def get_permissions( self, id: LibraryIdPathParam, trans: ProvidesUserContext = DependsOnTrans, scope: Optional[LibraryPermissionScope] = Query( None, title="Scope", description="The scope of the permissions to retrieve. Either the `current` permissions or the `available`.", ), is_library_access: Optional[bool] = Query( None, title="Is Library Access", description="Indicates whether the roles available for the library access are requested.", ), page: int = Query( default=1, title="Page", description="The page number to retrieve when paginating the available roles." ), page_limit: int = Query( default=10, title="Page Limit", description="The maximum number of permissions per page when paginating." ), q: Optional[str] = Query( None, title="Query", description="Optional search text to retrieve only the roles matching this query." ), ) -> Union[LibraryCurrentPermissions, LibraryAvailablePermissions]: """Gets the current or available permissions of a particular library. The results can be paginated and additionally filtered by a query.""" return self.service.get_permissions( trans, id, scope, is_library_access, page, page_limit, q, )
[docs] @router.post( "/api/libraries/{id}/permissions", summary="Sets the permissions to access and manipulate a library.", ) def set_permissions( self, id: LibraryIdPathParam, trans: ProvidesUserContext = DependsOnTrans, action: Optional[LibraryPermissionAction] = Query( default=None, title="Action", description="Indicates what action should be performed on the Library.", ), payload: Union[ LibraryPermissionsPayload, LegacyLibraryPermissionsPayload, ] = Body(...), ) -> Union[LibraryLegacySummary, LibraryCurrentPermissions]: # Old legacy response """Sets the permissions to access and manipulate a library.""" payload_dict = payload.model_dump(by_alias=True) if isinstance(payload, LibraryPermissionsPayload) and action is not None: payload_dict["action"] = action return self.service.set_permissions(trans, id, payload_dict)