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Merge pull request #18248 from mvdbeek/enable_transparent_use_of_comp…
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…ressed_datasets_in_DatasetDataProvider

[24.0] Transparently open compressed files in DatasetDataProvider
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jmchilton authored May 30, 2024
2 parents 0daf36d + dea0d52 commit 1dd31f0
Showing 1 changed file with 2 additions and 1 deletion.
3 changes: 2 additions & 1 deletion lib/galaxy/datatypes/dataproviders/dataset.py
Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@
)

from galaxy.util import sqlite
from galaxy.util.compression_utils import get_fileobj
from . import (
base,
column,
Expand Down Expand Up @@ -54,7 +55,7 @@ def __init__(self, dataset, **kwargs):
# this dataset file is obviously the source
# TODO: this might be a good place to interface with the object_store...
mode = "rb" if dataset.datatype.is_binary else "r"
super().__init__(open(dataset.get_file_name(), mode))
super().__init__(get_fileobj(dataset.get_file_name(), mode))

# TODO: this is a bit of a mess
@classmethod
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