From 8eab1175f3ccb39c80a01ac180ef37afd24861c5 Mon Sep 17 00:00:00 2001 From: Javier Ferrer Date: Tue, 19 Nov 2024 13:02:26 +0000 Subject: [PATCH] Fix subcellular location output filename --- pyproject.toml | 2 +- src/ontoform/steps/target.py | 2 +- src/ontoform/transformers/target.py | 4 ++-- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 968d7fb..9b00145 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [project] name = "ontoform" -version = "24.1.0-alpha.3" +version = "24.1.0-alpha.4" description = "Add your description here" readme = "README.md" requires-python = ">=3.12" diff --git a/src/ontoform/steps/target.py b/src/ontoform/steps/target.py index 2d210d9..b856e89 100644 --- a/src/ontoform/steps/target.py +++ b/src/ontoform/steps/target.py @@ -14,7 +14,7 @@ transformations=[ FileTransformation( src_path='input/target-inputs/hpa/subcellular_location.tsv.zip', - dst_path=lambda _, f: f'input/target-inputs/hpa/subcellular_locations.{extension(f)}', + dst_path='input/target-inputs/hpa/subcellular_location.tsv.gz', transformer=SubcellularLocationTransformer, ), FileTransformation( diff --git a/src/ontoform/transformers/target.py b/src/ontoform/transformers/target.py index eea2834..840e35e 100644 --- a/src/ontoform/transformers/target.py +++ b/src/ontoform/transformers/target.py @@ -19,10 +19,10 @@ def transform(self, src: BinaryIO, dst: BinaryIO, output_format: Format) -> None class SubcellularLocationSSLTransformer: - def transform(self, src: BinaryIO, dst: BinaryIO, format: Format) -> None: + def transform(self, src: BinaryIO, dst: BinaryIO, output_format: Format) -> None: # just change output format df = pl.read_csv(src, has_header=True, separator='\t') - write_format(df, dst, format) + write_format(df, dst, output_format) class EssentialityMatricesTransformer: