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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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[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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15 changes: 12 additions & 3 deletions lib/galaxy/webapps/galaxy/services/datasets.py
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Original file line number Diff line number Diff line change
Expand Up @@ -868,7 +868,7 @@ def _data(
# 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 +878,7 @@ 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 @@ -929,7 +929,7 @@ 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)
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stats = indexer.get_data(chrom, low, high, stats=True)
mean_depth = stats["data"]["mean"]

Expand Down Expand Up @@ -981,3 +981,12 @@ def _raw_data(
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")
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return indexer
except Exception as e:
raise galaxy_exceptions.ObjectNotFound(f"Error getting indexer: {util.unicodify(e)}")
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