Merge pull request #17736 from ahmedhamidawan/dataset_handle_missing_indexer (4b3bc550) · Commits · NDIP / Galaxy

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

+11 −5

Original line number	Diff line number	Diff line
		@@ -863,12 +863,11 @@ class DatasetsService(ServiceBase, UsesVisualizationMixin):

		extra_info = None
		mode = kwargs.get("mode", "Auto")
		indexer = None

		# 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 +877,7 @@ 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.
		@@ -928,8 +927,7 @@ 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 +979,11 @@ class DatasetsService(ServiceBase, UsesVisualizationMixin):
		data = data_provider.get_data(**kwargs)

		return data

		def _get_indexer(self, trans, dataset):
		indexer = self.data_provider_registry.get_data_provider(trans, original_dataset=dataset, source="index")
		if indexer is None:
		msg = f"No indexer available for dataset {self.encode_id(dataset.id)}"
		log.exception(msg)
		raise galaxy_exceptions.ObjectNotFound(msg)
		return indexer