Unverified Commit 90281980 authored by mvdbeek's avatar mvdbeek
Browse files

Avoid hitting disk if file_size is zero

parent 907c9195

lib/galaxy/managers/datasets.py

+3 −3
Original line number Diff line number Diff line
@@ -190,7 +190,7 @@ class DatasetSerializer(base.ModelSerializer[DatasetManager], deletable.Purgable 
            "extra_files_path": self.serialize_extra_files_path,

            "permissions": self.serialize_permissions,

            "total_size": lambda item, key, **context: int(item.get_total_size()),

            "file_size": lambda item, key, **context: int(item.get_size()),

            "file_size": lambda item, key, **context: int(item.get_size(calculate_size=False)),

        }

        self.serializers.update(serializers)
@@ -522,9 +522,9 @@ class _UnflattenedMetadataDatasetAssociationSerializer(base.ModelSerializer[T], 
            "extra_files_path": self._proxy_to_dataset(serializer=self.dataset_serializer.serialize_extra_files_path),

            "permissions": self._proxy_to_dataset(serializer=self.dataset_serializer.serialize_permissions),

            # TODO: do the sizes proxy accurately/in the same way?

            "size": lambda item, key, **context: int(item.get_size()),

            "size": lambda item, key, **context: int(item.get_size(calculate_size=False)),

            "file_size": lambda item, key, **context: self.serializers["size"](item, key, **context),

            "nice_size": lambda item, key, **context: item.get_size(nice_size=True),

            "nice_size": lambda item, key, **context: item.get_size(nice_size=True, calculate_size=False),

            # common to lddas and hdas - from mapping.py

            "copied_from_history_dataset_association_id": self.serialize_id,

            "copied_from_library_dataset_dataset_association_id": self.serialize_id,

lib/galaxy/managers/library_datasets.py

+1 −1
Original line number Diff line number Diff line
@@ -242,7 +242,7 @@ class LibraryDatasetsManager(datasets.DatasetAssociationManager): 
        rval["deleted"] = ld.deleted

        rval["folder_id"] = f"F{rval['folder_id']}"

        rval["full_path"] = full_path

        rval["file_size"] = util.nice_size(int(ldda.get_size()))

        rval["file_size"] = util.nice_size(int(ldda.get_size(calculate_size=False)))

        rval["date_uploaded"] = ldda.create_time.isoformat()

        rval["update_time"] = ldda.update_time.isoformat()

        rval["can_user_modify"] = trans.user_is_admin or trans.app.security_agent.can_modify_library_item(

lib/galaxy/model/__init__.py

+8 −5
Original line number Diff line number Diff line
@@ -3568,18 +3568,21 @@ class Dataset(Base, StorableObject, Serializable, _HasTable): 
        else:

            return self.object_store.size(self)



    def get_size(self, nice_size=False):

    def get_size(self, nice_size=False, calculate_size=True):

        """Returns the size of the data on disk"""

        if self.file_size:

            if nice_size:

                return galaxy.util.nice_size(self.file_size)

            else:

                return self.file_size

        else:

        elif calculate_size:

            # Hopefully we only reach this branch in sessionless mode

            if nice_size:

                return galaxy.util.nice_size(self._calculate_size())

            else:

                return self._calculate_size()

        else:

            return self.file_size or 0



    def set_size(self, no_extra_files=False):

        """Sets the size of the data on disk.
@@ -4018,11 +4021,11 @@ class DatasetInstance(UsesCreateAndUpdateTime, _HasTable): 
        self.clear_associated_files()

        _get_datatypes_registry().change_datatype(self, new_ext)



    def get_size(self, nice_size=False):

    def get_size(self, nice_size=False, calculate_size=True):

        """Returns the size of the data on disk"""

        if nice_size:

            return galaxy.util.nice_size(self.dataset.get_size())

        return self.dataset.get_size()

            return galaxy.util.nice_size(self.dataset.get_size(calculate_size=calculate_size))

        return self.dataset.get_size(calculate_size=calculate_size)



    def set_size(self, **kwds):

        """Sets and gets the size of the data on disk"""

lib/galaxy/webapps/galaxy/api/library_datasets.py

+3 −1
Original line number Diff line number Diff line
@@ -357,7 +357,9 @@ class LibraryDatasetsController(BaseGalaxyAPIController, UsesVisualizationMixin, 
        trans.sa_session.flush()



        rval = trans.security.encode_all_ids(library_dataset.to_dict())

        nice_size = util.nice_size(int(library_dataset.library_dataset_dataset_association.get_size()))

        nice_size = util.nice_size(

            int(library_dataset.library_dataset_dataset_association.get_size(calculate_size=False))

        )

        rval["file_size"] = nice_size

        rval["update_time"] = library_dataset.update_time.strftime("%Y-%m-%d %I:%M %p")

        rval["deleted"] = library_dataset.deleted

lib/galaxy/webapps/galaxy/services/library_folder_contents.py

+1 −1
Original line number Diff line number Diff line
@@ -128,7 +128,7 @@ class LibraryFolderContentsService(ServiceBase, UsesLibraryMixinItems): 
                        current_user_roles, content_item.library_dataset_dataset_association.dataset

                    )

                )

                raw_size = int(content_item.library_dataset_dataset_association.get_size())

                raw_size = int(content_item.library_dataset_dataset_association.get_size(calculate_size=False))

                nice_size = util.nice_size(raw_size)

                update_time = content_item.library_dataset_dataset_association.update_time.isoformat()