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Decompress phenio source #158

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merged 3 commits into from
Nov 26, 2024
Merged

Decompress phenio source #158

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8b92123
Update poetry lock
caufieldjh Nov 26, 2024
0f78946
Update phenio source to phenio.owl.tar.gz in download config
caufieldjh Nov 26, 2024
76a6695
Update phenio transform to use tar.gz
caufieldjh Nov 26, 2024
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4 changes: 2 additions & 2 deletions download.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -10,8 +10,8 @@
# phenio.owl
#
-
url: https://github.com/monarch-initiative/phenio/releases/latest/download/phenio.owl
local_name: phenio.owl
url: https://github.com/monarch-initiative/phenio/releases/latest/download/phenio.owl.tar.gz
local_name: phenio.owl.tar.gz

#
# phenio.owl test file
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13 changes: 9 additions & 4 deletions kg_phenio/transform_utils/phenio/phenio_transform.py
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Original file line number Diff line number Diff line change
Expand Up @@ -67,7 +67,7 @@ def run(self, data_file: Optional[str] = None) -> None:
data_file = os.path.join(self.input_base_dir, data_file)
self.parse(k, data_file, k)
else:
# load all ontologies
# Load PHENIO
for k in ONTO_FILES.keys():
data_file = os.path.join(self.input_base_dir, ONTO_FILES[k])
self.parse(k, data_file, k)
Expand All @@ -82,10 +82,13 @@ def parse(self, name: str, data_file: str, source: str) -> None:
Returns:
None.
"""
# Check if it needs to be decompressed first,
# and it probably does.
if not os.path.exists(data_file):
if os.path.exists(data_file + ".tar.gz"):
print(f"Decompressing {data_file}")
with tarfile.open(data_file) as compfile:
comp_data_file = data_file + ".tar.gz"
print(f"Decompressing {comp_data_file}")
with tarfile.open(comp_data_file) as compfile:
compfile.extractall(self.input_base_dir)
else:
print(f"Found ontology at {data_file}")
Expand Down Expand Up @@ -145,7 +148,9 @@ def parse(self, name: str, data_file: str, source: str) -> None:
if not os.path.exists(data_file_tsv):
if self.config:
if name == "PhenioTransformTest":
print(f"Transforming to KGX TSV with test config in {self.test_config}...")
print(
f"Transforming to KGX TSV with test config in {self.test_config}..."
)
tx_config = self.test_config
else:
print(f"Transforming to KGX TSV with config in {self.config}...")
Expand Down
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