Commit 8412cb53 authored by John Chilton's avatar John Chilton
Browse files

Type and bug fixes for api/extended_metadata.py.

parent 14fb067c

lib/galaxy/webapps/galaxy/api/extended_metadata.py

+16 −23
Original line number Diff line number Diff line
@@ -2,13 +2,14 @@ 
API operations on annotations.

"""

import logging

from typing import Generic, Optional, TypeVar



from galaxy import (

    managers,

    web

    model,

    web,

)

from galaxy.webapps.base.controller import (

    HTTPNotImplemented,

    UsesExtendedMetadataMixin,

    UsesLibraryMixinItems,

    UsesStoredWorkflowMixin
@@ -17,10 +18,16 @@ from . import BaseGalaxyAPIController, depends 


log = logging.getLogger(__name__)



T = TypeVar('T')



class BaseExtendedMetadataController(BaseGalaxyAPIController, UsesExtendedMetadataMixin, UsesLibraryMixinItems, UsesStoredWorkflowMixin):



    @web.legacy_expose_api

class BaseExtendedMetadataController(BaseGalaxyAPIController, UsesExtendedMetadataMixin, UsesLibraryMixinItems, UsesStoredWorkflowMixin, Generic[T]):

    exmeta_item_id: str



    def _get_item_from_id(self, trans, idstr, check_writable=True) -> Optional[T]:

        ...



    @web.expose_api

    def index(self, trans, **kwd):

        idnum = kwd[self.exmeta_item_id]

        item = self._get_item_from_id(trans, idnum, check_writable=False)
@@ -29,7 +36,7 @@ class BaseExtendedMetadataController(BaseGalaxyAPIController, UsesExtendedMetada 
            if ex_meta is not None:

                return ex_meta.data



    @web.legacy_expose_api

    @web.expose_api

    def create(self, trans, payload, **kwd):

        idnum = kwd[self.exmeta_item_id]

        item = self._get_item_from_id(trans, idnum, check_writable=True)
@@ -41,26 +48,12 @@ class BaseExtendedMetadataController(BaseGalaxyAPIController, UsesExtendedMetada 
            ex_obj = self.create_extended_metadata(trans, payload)

            self.set_item_extended_metadata_obj(trans, item, ex_obj)



    @web.legacy_expose_api

    def delete(self, trans, **kwd):

        idnum = kwd[self.tagged_item_id]

        item = self._get_item_from_id(trans, idnum, check_writable=True)

        if item is not None:

            ex_obj = self.get_item_extended_metadata_obj(trans, item)

            if ex_obj is not None:

                self.unset_item_extended_metadata_obj(trans, item)

                self.delete_extended_metadata(trans, ex_obj)



    @web.legacy_expose_api

    def undelete(self, trans, **kwd):

        raise HTTPNotImplemented()





class LibraryDatasetExtendMetadataController(BaseExtendedMetadataController):

class LibraryDatasetExtendMetadataController(BaseExtendedMetadataController[model.LibraryDatasetDatasetAssociation]):

    controller_name = "library_dataset_extended_metadata"

    exmeta_item_id = "library_content_id"



    def _get_item_from_id(self, trans, idstr, check_writable=True):

    def _get_item_from_id(self, trans, idstr, check_writable=True) -> Optional[model.LibraryDatasetDatasetAssociation]:

        if check_writable:

            item = self.get_library_dataset_dataset_association(trans, idstr)

            if trans.app.security_agent.can_modify_library_item(trans.get_current_user_roles(), item):
@@ -72,12 +65,12 @@ class LibraryDatasetExtendMetadataController(BaseExtendedMetadataController): 
        return None





class HistoryDatasetExtendMetadataController(BaseExtendedMetadataController):

class HistoryDatasetExtendMetadataController(BaseExtendedMetadataController[model.HistoryDatasetAssociation]):

    controller_name = "history_dataset_extended_metadata"

    exmeta_item_id = "history_content_id"

    hda_manager: managers.hdas.HDAManager = depends(managers.hdas.HDAManager)



    def _get_item_from_id(self, trans, idstr, check_writable=True):

    def _get_item_from_id(self, trans, idstr, check_writable=True) -> Optional[model.HistoryDatasetAssociation]:

        decoded_idstr = self.decode_id(idstr)

        if check_writable:

            return self.hda_manager.get_owned(decoded_idstr, trans.user, current_history=trans.history)

setup.cfg

+0 −2
Original line number Diff line number Diff line
@@ -751,8 +751,6 @@ check_untyped_defs = False 
check_untyped_defs = False

[mypy-galaxy.webapps.galaxy.api.genomes]

check_untyped_defs = False

[mypy-galaxy.webapps.galaxy.api.extended_metadata]

check_untyped_defs = False

[mypy-galaxy.webapps.galaxy.api.datasets]

check_untyped_defs = False

[mypy-galaxy.webapps.galaxy.api.authenticate]