Commit 248ec4e8 authored by davelopez's avatar davelopez
Browse files

Allow admin access to datasets API (before refactoring) 

This patch contains the changes in #13060 and it is meant to be applied only to 21.09 do not merge forward this commit into 22.01 since it is already fixed there
parent 6bbf5f65

lib/galaxy/webapps/galaxy/api/datasets.py

+15 −10
Original line number Diff line number Diff line
@@ -46,6 +46,10 @@ class DatasetsController(BaseGalaxyAPIController, UsesVisualizationMixin): 
    def serializer_by_type(self):

        return {'dataset': self.hda_serializer, 'dataset_collection': self.hdca_serializer}



    @property

    def dataset_manager_by_type(self):

        return {'hda': self.hda_manager, 'ldda': self.ldda_manager}



    def _parse_serialization_params(self, kwd, default_view):

        view = kwd.get('view', None)

        keys = kwd.get('keys')
@@ -131,7 +135,8 @@ class DatasetsController(BaseGalaxyAPIController, UsesVisualizationMixin): 
        Displays information about and/or content of a dataset.

        """

        # Get dataset.

        dataset = self.get_hda_or_ldda(trans, hda_ldda=hda_ldda, dataset_id=id)

        decoded_dataset_id = self.decode_id(id)

        dataset = self.dataset_manager_by_type[hda_ldda].get_accessible(decoded_dataset_id, trans.user)



        # Use data type to return particular type of data.

        if data_type == 'state':
@@ -169,7 +174,8 @@ class DatasetsController(BaseGalaxyAPIController, UsesVisualizationMixin): 
        Display user-facing storage details related to the objectstore a

        dataset resides in.

        """

        dataset_instance = self.get_hda_or_ldda(trans, hda_ldda=hda_ldda, dataset_id=dataset_id)

        decoded_dataset_id = self.decode_id(dataset_id)

        dataset_instance = self.dataset_manager_by_type[hda_ldda].get_accessible(decoded_dataset_id, trans.user)

        dataset = dataset_instance.dataset

        object_store = self.app.object_store

        object_store_id = dataset.object_store_id
@@ -198,7 +204,8 @@ class DatasetsController(BaseGalaxyAPIController, UsesVisualizationMixin): 


        For internal use, this endpoint may change without warning.

        """

        dataset_instance = self.get_hda_or_ldda(trans, hda_ldda=hda_ldda, dataset_id=dataset_id)

        decoded_dataset_id = self.decode_id(dataset_id)

        dataset_instance = self.dataset_manager_by_type[hda_ldda].get_accessible(decoded_dataset_id, trans.user)

        inherit_chain = dataset_instance.source_dataset_chain

        result = []

        for dep in inherit_chain:
@@ -218,13 +225,11 @@ class DatasetsController(BaseGalaxyAPIController, UsesVisualizationMixin): 
        if payload:

            kwd.update(payload)

        hda_ldda = kwd.get('hda_ldda', 'hda')

        dataset_assoc = self.get_hda_or_ldda(trans, hda_ldda=hda_ldda, dataset_id=dataset_id)

        if hda_ldda == "hda":

            self.hda_manager.update_permissions(trans, dataset_assoc, **kwd)

            return self.hda_manager.serialize_dataset_association_roles(trans, dataset_assoc)

        else:

            self.ldda_manager.update_permissions(trans, dataset_assoc, **kwd)

            return self.ldda_manager.serialize_dataset_association_roles(trans, dataset_assoc)

        decoded_dataset_id = self.decode_id(dataset_id)

        dataset_manager = self.dataset_manager_by_type[hda_ldda]

        dataset = dataset_manager.get_accessible(decoded_dataset_id, trans.user)

        dataset_manager.update_permissions(trans, dataset, **payload)

        return dataset_manager.serialize_dataset_association_roles(trans, dataset)



    def _dataset_in_use_state(self, dataset):

        """

lib/galaxy_test/api/test_datasets.py

+17 −2
Original line number Diff line number Diff line
@@ -106,8 +106,23 @@ class DatasetsApiTestCase(ApiTestCase): 
        self.dataset_populator.make_private(history_id=self.history_id, dataset_id=hda['id'])

        with self._different_user():

            show_response = self._get(f"datasets/{hda['id']}")

            self._assert_status_code_is(show_response, 400)

            assert show_response.json()['err_msg'] == 'You are not allowed to access this dataset'

            self._assert_status_code_is(show_response, 403)



    def test_admin_can_update_permissions(self):

        # Create private dataset

        hda = self.dataset_populator.new_dataset(self.history_id)

        dataset_id = hda['id']

        self.dataset_populator.make_private(history_id=self.history_id, dataset_id=dataset_id)



        # Admin removes restrictions

        payload = {"action": "remove_restrictions"}

        update_response = self._put(f"datasets/{dataset_id}/permissions", payload, admin=True, json=True)

        self._assert_status_code_is_ok(update_response)



        # Other users can access the dataset

        with self._different_user():

            show_response = self._get(f"datasets/{hda['id']}")

            self._assert_status_code_is_ok(show_response)



    def __assert_matches_hda(self, input_hda, query_hda):

        self._assert_has_keys(query_hda, "id", "name")

lib/galaxy_test/api/test_histories.py

+1 −1
Original line number Diff line number Diff line
@@ -575,7 +575,7 @@ class SharingHistoryTestCase(ApiTestCase, BaseHistories, SharingApiTests): 
        # Other users cannot access the dataset

        with self._different_user():

            show_response = self._get(f"datasets/{hda_id}")

            self._assert_status_code_is(show_response, 400)

            self._assert_status_code_is(show_response, 403)



        sharing_response = self._set_resource_sharing(history_id, "publish")

        assert sharing_response["published"] is True