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feat: Roche Cedex BioHT - Add support for mM unit (mmol/L) #1119

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Merged
joshua-benchling merged 2 commits into from
Nov 11, 2025
Merged

feat: Roche Cedex BioHT - Add support for mM unit (mmol/L) #1119

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52e205a
add support for mM unit
joshua-benchling Nov 4, 2025
dc0ddf5
Merge branch 'main' into jherna/roche_cedex_extend_support_mm_unit
joshua-benchling Nov 11, 2025
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27 changes: 18 additions & 9 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 @@ -28,6 +28,12 @@
from allotropy.parsers.utils.pandas import map_rows, SeriesData
from allotropy.parsers.utils.uuids import random_uuid_str

# Maps source units to (target_unit, conversion_multiplier)
UNIT_CONVERSIONS: dict[str, tuple[str, float]] = {
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"mg/L": ("g/L", 0.001),
"mM": ("mmol/L", 1.0),
}


@dataclass(frozen=True)
class Title:
Expand Down Expand Up @@ -111,15 +117,18 @@ def create(data: SeriesData) -> RawMeasurement:

@staticmethod
def _get_value_and_unit(value: JsonFloat, unit: str) -> tuple[JsonFloat, str]:
multiplier = 1.0
if unit == "mg/L":
unit = "g/L"
multiplier = 1 / 1000

if isinstance(value, int | float):
value = value * multiplier

return value, unit
normalized_unit = unit.strip()

# Check if unit needs conversion
if normalized_unit in UNIT_CONVERSIONS:
target_unit, multiplier = UNIT_CONVERSIONS[normalized_unit]
if isinstance(value, int | float):
converted_value: JsonFloat = value * multiplier
else:
converted_value = value
return converted_value, target_unit

return value, normalized_unit


def create_measurements(data: pd.DataFrame) -> dict[str, dict[str, RawMeasurement]]:
Expand Down
4 changes: 2 additions & 2 deletions tests/parsers/roche_cedex_bioht/testdata/roche_cedex_bioht_example01.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
40 2023-09-15 16:55:51 SMPL1 SAM GLN2B mmol/L 2.45 0.17138 R
40 2023-09-15 16:55:53 SMPL1 SAM ODB OD 6.32 1.05394 R
40 2023-09-15 16:56:18 SMPL1 SAM LDH2B U/L 88.09 0.00728 R
40 2023-09-15 16:56:26 SMPL1 SAM NH3B mmol/L 1.846 0.05333 R
40 2023-09-15 16:56:26 SMPL1 SAM NH3B mM 1.846 0.05333 R
40 2023-09-15 16:56:37 SMPL1 SAM LAC2B g/L 0.02 0.01567 R
40 2023-09-15 16:56:48 SMPL1 SAM TP2LB g/L 4.6 0.14883 R
40 2023-09-15 16:56:58 SMPL2 SAM GLN2B mmol/L 2.40 0.16787 R
Expand All @@ -20,7 +20,7 @@
40 2023-09-15 16:59:16 SMPL3 SAM LAC2B g/L < TEST RNG < 0.00 0.00329 R
40 2023-09-15 16:59:38 SMPL3 SAM TP2D g/L < TEST RNG < 40.0 0.02702 R
40 2023-09-15 17:00:52 SMPL3 SAM TP2LB g/L 4.8 0.15436 R
40 2023-09-16 10:12:10 SMPL4 SAM GLN2B mmol/L 2.07 0.14503 R
40 2023-09-16 10:12:10 SMPL4 SAM GLN2B mM 2.07 0.14503 R
40 2023-09-16 10:12:12 SMPL4 SAM ODB OD 4.09 0.68160 R
40 2023-09-16 10:13:29 SMPL4 SAM LDH2B U/L 334.84 0.02665 R
40 2023-09-16 10:13:37 SMPL4 SAM NH3B mmol/L 3.788 0.11415 R
Expand Down
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