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[23.1] Handle missing indexer for a dataset #17736

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merged 2 commits into from
Mar 18, 2024
Merged

[23.1] Handle missing indexer for a dataset #17736

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b84f945
[23.1] Handle missing indexer for a dataset
ahmedhamidawan Mar 14, 2024
d6914b7
exception without the `try/catch` block
ahmedhamidawan Mar 15, 2024
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16 changes: 11 additions & 5 deletions lib/galaxy/webapps/galaxy/services/datasets.py
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Original file line number Diff line number Diff line change
Expand Up @@ -863,12 +863,11 @@ def _data(

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:
Expand All @@ -878,7 +877,7 @@ def _data(
# 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.
Expand Down Expand Up @@ -928,8 +927,7 @@ def _data(
)

# 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"]

Expand Down Expand Up @@ -981,3 +979,11 @@ def _raw_data(
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
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