opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity

Merge branch 'release_23.2' into release_24.0

Browse Source
This commit is contained in:
mvdbeek
2024-03-18 11:32:07 +01:00
parent 7b88bcd091 5d7a18e964
commit 44b77b1c22
1 changed files with 11 additions and 5 deletions
Download Patch File Download Diff File Expand all files Collapse all files
lib/galaxy/webapps/galaxy/services/datasets.py
+11 -5
View File
@@ -891,12 +891,11 @@ 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:
@@ -906,7 +905,7 @@ 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.
@@ -956,8 +955,7 @@ 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"]
@@ -1008,3 +1006,11 @@ 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