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fix: Agilent OpenLab CDS - use bytes to read zip file instead of file name #1021

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Merged
nathan-stender merged 3 commits into from
Jun 24, 2025
Merged

fix: Agilent OpenLab CDS - use bytes to read zip file instead of file name #1021

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ed13eba
Use bytes for cds
nathan-stender Jun 23, 2025
3e32d8c
Use bytes for cds
nathan-stender Jun 23, 2025
50f69b9
Use bytes stream
nathan-stender Jun 24, 2025
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4 changes: 2 additions & 2 deletions src/allotropy/parsers/agilent_openlab_cds/agilent_openlab_cds_decoder.py
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Original file line number Diff line number Diff line change
Expand Up @@ -273,7 +273,7 @@ def _get_matching_filenames(zip_ref: zipfile.ZipFile, pattern: str) -> list[str]
]


def decode_data(input_path: str) -> dict[str, Any]:
def decode_data(input_bytes: IO[bytes]) -> dict[str, Any]:
"""
decoded the files in input folder path and returns a structured data
:param input_path: input folder path
Expand All @@ -284,7 +284,7 @@ def decode_data(input_path: str) -> dict[str, Any]:
total_injection_chromatogram_details: list[dict[str, Any]] = []
total_peak_details: list[dict[str, Any]] = []

with zipfile.ZipFile(input_path, "r") as zip_ref:
with zipfile.ZipFile(input_bytes) as zip_ref:
acaml_path = next(iter(_get_matching_filenames(zip_ref, ".*acaml")))
with zip_ref.open(acaml_path) as acaml_file_data:
acaml_file_content = acaml_file_data.read().decode("utf-8-sig")
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2 changes: 1 addition & 1 deletion src/allotropy/parsers/agilent_openlab_cds/agilent_openlab_cds_parser.py
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Expand Up @@ -26,7 +26,7 @@ class AgilentOpenLabCDSParser(VendorParser[Data, Model]):
SCHEMA_MAPPER = Mapper

def create_data(self, named_file_contents: NamedFileContents) -> Data:
structured_data = decode_data(named_file_contents.original_file_path)
structured_data = decode_data(named_file_contents.get_bytes_stream())
return Data(
metadata=create_metadata(structured_data, named_file_contents),
measurement_groups=[create_measurement_groups(structured_data)],
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