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chore: Refactor custom data block in roche bioht parser #1089

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Merged
nathan-stender merged 1 commit into from
Sep 26, 2025
Merged

chore: Refactor custom data block in roche bioht parser #1089

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60 changes: 26 additions & 34 deletions src/allotropy/parsers/roche_cedex_bioht/roche_cedex_bioht_structure.py
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Original file line number Diff line number Diff line change
Expand Up @@ -75,48 +75,40 @@ def create(data: SeriesData) -> RawMeasurement:
if error == BELOW_TEST_RANGE:
error = data.get(str, "original concentration value", error)

custom_info = data.get_custom_keys(
{"detection kit", "detection kit range", "analyte code"}
)
custom_info["record type"] = data.get(str, "row type", None)
data.mark_read(
{
"sample identifier",
"batch identifier",
"col4",
"col5",
"col6",
"col8",
"col10",
"col11",
"col12",
"col13",
"original concentration value",
"sample role type",
}
)

if error:
custom_info["flag"] = error

measurement = RawMeasurement(
return RawMeasurement(
data[str, "analyte name"],
data[str, "measurement time"],
value,
unit,
data[str, "analyte code"],
error,
{},
custom_info=dict(
sorted(
{
**{
# analyte code is read to generate the analyte id, but is not saved to a field, so include in custom data.
"analyte code": data.get(str, "analyte code"),
"record type": data.get(str, "row type"),
"flag": error or None,
},
**data.get_unread(
skip={
# Sample and batch identifier are read in groupby operation.
"sample identifier",
"batch identifier",
# Read by reader
"sample role type",
# Only read if there is an error.
"original concentration value",
# Skip unidentified columns (col1, col2, etc)
r"col[\d]+",
}
),
}.items()
)
),
)

if isinstance(measurement.custom_info, dict):
custom_info.update(data.get_unread())
custom_info_sorted = dict(sorted(custom_info.items()))

measurement.custom_info.update(custom_info_sorted)

return measurement

@staticmethod
def _get_value_and_unit(value: JsonFloat, unit: str) -> tuple[JsonFloat, str]:
multiplier = 1.0
Expand Down
16 changes: 8 additions & 8 deletions tests/parsers/roche_cedex_bioht/roche_cedex_bioht_structure_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -113,7 +113,7 @@ def test_create_measurements() -> None:
"g/L",
"LAC2B",
None,
{"analyte code": "LAC2B", "record type": None},
{"analyte code": "LAC2B", "record type": None, "flag": None},
),
"glutamine_GLN2B": RawMeasurement(
"glutamine",
Expand All @@ -122,7 +122,7 @@ def test_create_measurements() -> None:
"mmol/L",
"GLN2B",
None,
{"analyte code": "GLN2B", "record type": None},
{"analyte code": "GLN2B", "record type": None, "flag": None},
),
"osmolality_OSM2B": RawMeasurement(
"osmolality",
Expand All @@ -131,7 +131,7 @@ def test_create_measurements() -> None:
"mosm/kg",
"OSM2B",
None,
{"analyte code": "OSM2B", "record type": None},
{"analyte code": "OSM2B", "record type": None, "flag": None},
),
}
}
Expand Down Expand Up @@ -162,7 +162,7 @@ def test_create_measurements_more_than_one_measurement_docs() -> None:
"g/L",
"LAC2B",
None,
{"analyte code": "LAC2B", "record type": None},
{"analyte code": "LAC2B", "record type": None, "flag": None},
),
"glutamine_GLN2B": RawMeasurement(
"glutamine",
Expand All @@ -171,7 +171,7 @@ def test_create_measurements_more_than_one_measurement_docs() -> None:
"mmol/L",
"GLN2B",
None,
{"analyte code": "GLN2B", "record type": None},
{"analyte code": "GLN2B", "record type": None, "flag": None},
),
},
"2021-05-21T16:57:51+00:00": {
Expand All @@ -182,7 +182,7 @@ def test_create_measurements_more_than_one_measurement_docs() -> None:
"mmol/L",
"GLN2B",
None,
{"analyte code": "GLN2B", "record type": None},
{"analyte code": "GLN2B", "record type": None, "flag": None},
),
},
}
Expand Down Expand Up @@ -242,7 +242,7 @@ def test_create_sample() -> None:
"g/L",
"LAC2B",
None,
{"analyte code": "LAC2B", "record type": None},
{"analyte code": "LAC2B", "record type": None, "flag": None},
),
"glutamine_GLN2B": RawMeasurement(
"glutamine",
Expand All @@ -251,7 +251,7 @@ def test_create_sample() -> None:
"mmol/L",
"GLN2B",
None,
{"analyte code": "GLN2B", "record type": None},
{"analyte code": "GLN2B", "record type": None, "flag": None},
),
}
}
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