Commit b84f9459 authored by Ahmed Awan's avatar Ahmed Awan
Browse files

[23.1] Handle missing indexer for a dataset 

In case a dataset does not have an indexer, raise an exception.
Fixes the bug mentioned in https://github.com/galaxyproject/galaxy/pull/17639#issuecomment-1995990448
parent a3c14eaa

lib/galaxy/webapps/galaxy/services/datasets.py

+12 −3
Original line number Diff line number Diff line
@@ -868,7 +868,7 @@ class DatasetsService(ServiceBase, UsesVisualizationMixin): 
        # Coverage mode uses index data.

        if mode == "Coverage":

            # Get summary using minimal cutoffs.

            indexer = self.data_provider_registry.get_data_provider(trans, original_dataset=dataset, source="index")

            indexer = self._get_indexer(trans, dataset)

            return indexer.get_data(chrom, low, high, **kwargs)



        # TODO:
@@ -878,7 +878,7 @@ class DatasetsService(ServiceBase, UsesVisualizationMixin): 
        # If mode is Auto, need to determine what type of data to return.

        if mode == "Auto":

            # Get stats from indexer.

            indexer = self.data_provider_registry.get_data_provider(trans, original_dataset=dataset, source="index")

            indexer = self._get_indexer(trans, dataset)

            stats = indexer.get_data(chrom, low, high, stats=True)



            # If stats were requested, return them.
@@ -929,7 +929,7 @@ class DatasetsService(ServiceBase, UsesVisualizationMixin): 


            # Get mean depth.

            if not indexer:

                indexer = self.data_provider_registry.get_data_provider(trans, original_dataset=dataset, source="index")

                indexer = self._get_indexer(trans, dataset)

            stats = indexer.get_data(chrom, low, high, stats=True)

            mean_depth = stats["data"]["mean"]
@@ -981,3 +981,12 @@ class DatasetsService(ServiceBase, UsesVisualizationMixin): 
        data = data_provider.get_data(**kwargs)



        return data



    def _get_indexer(self, trans, dataset):

        try:

            indexer = self.data_provider_registry.get_data_provider(trans, original_dataset=dataset, source="index")

            if indexer is None:

                raise Exception("No indexer available for this dataset")

            return indexer

        except Exception as e:

            raise galaxy_exceptions.ObjectNotFound(f"Error getting indexer: {util.unicodify(e)}")