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Merged
nathan-stender merged 2 commits into from
Jul 7, 2025
Merged

feat: Roche Cedex BioHT - Added support for mg/L #1028

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c570746
Added mg/L to roche cedex bioht
felipenarv Jul 7, 2025
772b1a0
Merge branch 'main' into felipenarv/add_support_for_mgL_roche_cedex_b…
nathan-stender Jul 7, 2025
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17 changes: 15 additions & 2 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 @@ -64,14 +64,27 @@ def create(data: SeriesData) -> RawMeasurement:
if BELOW_TEST_RANGE in error
else data.get(float, "concentration value", NaN)
)

value, unit = RawMeasurement._get_value_and_unit(
concentration_value, data[str, "concentration unit"]
)

return RawMeasurement(
data[str, "analyte name"],
data[str, "measurement time"],
concentration_value,
data[str, "concentration unit"],
value,
unit,
error or None,
)

@staticmethod
def _get_value_and_unit(value: JsonFloat, unit: str) -> tuple[JsonFloat, str]:
if isinstance(value, int | float):
if unit == "mg/L":
return value / 1000, "g/L"

return value, unit


def create_measurements(data: pd.DataFrame) -> dict[str, dict[str, RawMeasurement]]:
measurements = sorted(
Expand Down
285 changes: 285 additions & 0 deletions tests/parsers/roche_cedex_bioht/testdata/roche_cedex_bioht_example_with_mg_L.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,285 @@
{
"$asm.manifest": "http://purl.allotrope.org/manifests/solution-analyzer/REC/2024/09/solution-analyzer.manifest",
"solution analyzer aggregate document": {
"solution analyzer document": [
{
"measurement aggregate document": {
"measurement document": [
{
"device control aggregate document": {
"device control document": [
{
"device type": "solution-analyzer"
}
]
},
"measurement identifier": "ROCHE_CEDEX_BIOHT_TEST_ID_0",
"measurement time": "2023-09-15T16:55:51+00:00",
"sample document": {
"sample identifier": "SMPL1"
},
"absorbance": {
"value": 6.32,
"unit": "mAU"
}
},
{
"device control aggregate document": {
"device control document": [
{
"device type": "solution-analyzer"
}
]
},
"measurement identifier": "ROCHE_CEDEX_BIOHT_TEST_ID_1",
"measurement time": "2023-09-15T16:55:51+00:00",
"sample document": {
"sample identifier": "SMPL1"
},
"analyte aggregate document": {
"analyte document": [
{
"analyte name": "ammonia",
"molar concentration": {
"value": 1.846,
"unit": "mmol/L"
}
},
{
"analyte name": "glutamine",
"molar concentration": {
"value": 2.45,
"unit": "mmol/L"
}
},
{
"analyte name": "lactate",
"mass concentration": {
"value": 2e-05,
"unit": "g/L"
}
},
{
"analyte name": "ldh",
"molar concentration": {
"value": 1.471103,
"unit": "mmol/L"
}
},
{
"analyte name": "total protein",
"mass concentration": {
"value": 0.0046,
"unit": "g/L"
}
}
]
}
}
],
"data processing time": "2023-09-17T13:04:06+00:00"
},
"analyst": "ADMIN"
},
{
"measurement aggregate document": {
"measurement document": [
{
"device control aggregate document": {
"device control document": [
{
"device type": "solution-analyzer"
}
]
},
"measurement identifier": "ROCHE_CEDEX_BIOHT_TEST_ID_2",
"measurement time": "2023-09-15T16:56:58+00:00",
"sample document": {
"sample identifier": "SMPL2"
},
"analyte aggregate document": {
"analyte document": [
{
"analyte name": "ammonia",
"molar concentration": {
"value": 1.87,
"unit": "mmol/L"
}
},
{
"analyte name": "glutamine",
"molar concentration": {
"value": 2.4,
"unit": "mmol/L"
}
},
{
"analyte name": "total protein",
"mass concentration": {
"value": 0.0047,
"unit": "g/L"
}
}
]
}
}
],
"data processing time": "2023-09-17T13:04:06+00:00"
},
"analyst": "ADMIN"
},
{
"measurement aggregate document": {
"measurement document": [
{
"device control aggregate document": {
"device control document": [
{
"device type": "solution-analyzer"
}
]
},
"measurement identifier": "ROCHE_CEDEX_BIOHT_TEST_ID_3",
"measurement time": "2023-09-15T16:58:34+00:00",
"sample document": {
"sample identifier": "SMPL3"
},
"absorbance": {
"value": 6.71,
"unit": "mAU"
}
},
{
"device control aggregate document": {
"device control document": [
{
"device type": "solution-analyzer"
}
]
},
"measurement identifier": "ROCHE_CEDEX_BIOHT_TEST_ID_4",
"measurement time": "2023-09-15T16:58:34+00:00",
"sample document": {
"sample identifier": "SMPL3"
},
"analyte aggregate document": {
"analyte document": [
{
"analyte name": "ammonia",
"molar concentration": {
"value": 1.817,
"unit": "mmol/L"
}
},
{
"analyte name": "glutamine",
"molar concentration": {
"value": 2.43,
"unit": "mmol/L"
}
},
{
"analyte name": "total protein",
"mass concentration": {
"value": 4.8,
"unit": "g/L"
}
}
]
}
}
],
"data processing time": "2023-09-17T13:04:06+00:00"
},
"analyst": "ADMIN"
},
{
"measurement aggregate document": {
"measurement document": [
{
"device control aggregate document": {
"device control document": [
{
"device type": "solution-analyzer"
}
]
},
"measurement identifier": "ROCHE_CEDEX_BIOHT_TEST_ID_5",
"measurement time": "2023-09-16T10:12:10+00:00",
"sample document": {
"sample identifier": "SMPL4"
},
"absorbance": {
"value": 4.09,
"unit": "mAU"
}
},
{
"device control aggregate document": {
"device control document": [
{
"device type": "solution-analyzer"
}
]
},
"measurement identifier": "ROCHE_CEDEX_BIOHT_TEST_ID_6",
"measurement time": "2023-09-16T10:12:10+00:00",
"sample document": {
"sample identifier": "SMPL4"
},
"analyte aggregate document": {
"analyte document": [
{
"analyte name": "ammonia",
"molar concentration": {
"value": 3.788,
"unit": "mmol/L"
}
},
{
"analyte name": "glutamine",
"molar concentration": {
"value": 2.07,
"unit": "mmol/L"
}
},
{
"analyte name": "lactate",
"mass concentration": {
"value": 0.00189,
"unit": "g/L"
}
},
{
"analyte name": "ldh",
"molar concentration": {
"value": 5.591828,
"unit": "mmol/L"
}
}
]
}
}
],
"data processing time": "2023-09-17T13:04:06+00:00"
},
"analyst": "ADMIN"
}
],
"data system document": {
"ASM file identifier": "roche_cedex_bioht_example_with_mg_L.json",
"data system instance identifier": "N/A",
"file name": "roche_cedex_bioht_example_with_mg_L.txt",
"UNC path": "tests/parsers/roche_cedex_bioht/testdata/roche_cedex_bioht_example_with_mg_L.txt",
"ASM converter name": "allotropy_roche_cedex_bioht",
"ASM converter version": "0.1.97",
"software name": "CEDEX BIO HT",
"software version": "6.0.0.1905 (1905)"
},
"device system document": {
"device identifier": "N/A",
"equipment serial number": "123456",
"model number": "CEDEX BIO HT"
}
}
}
27 changes: 27 additions & 0 deletions tests/parsers/roche_cedex_bioht/testdata/roche_cedex_bioht_example_with_mg_L.txt
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Original file line number Diff line number Diff line change
@@ -0,0 +1,27 @@
0 2023-09-17 13:04:06 #ARC-FILE# 1.1a 2021-05-01 2023-09-17 CEDEX BIO HT 123456 6.0.0.1905 (1905) ADMIN
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 16:56:37 SMPL1 SAM LAC2B mg/L 0.02 0.01567 R
40 2023-09-15 16:56:48 SMPL1 SAM TP2LB mg/L 4.6 0.14883 R
40 2023-09-15 16:56:58 SMPL2 SAM GLN2B mmol/L 2.40 0.16787 R
40 2023-09-15 16:57:09 SMPL2 SAM ODB OD < TEST RNG 6.71 1.11766 R
40 2023-09-15 16:57:19 SMPL2 SAM LDH2B U/L < TEST RNG < 20.00 0.00060 R
40 2023-09-15 16:57:30 SMPL2 SAM NH3B mmol/L 1.870 0.05408 R
40 2023-09-15 16:57:41 SMPL2 SAM LAC2B mg/L < TEST RNG < 0.00 0.00310 R
40 2023-09-15 16:57:51 SMPL2 SAM TP2B mg/L < TEST RNG < 4.0 0.03322 R
40 2023-09-15 16:58:02 SMPL2 SAM TP2D mg/L < TEST RNG < 40.0 0.02653 R
40 2023-09-15 16:58:23 SMPL2 SAM TP2LB mg/L 4.7 0.15217 R
40 2023-09-15 16:58:34 SMPL3 SAM GLN2B mmol/L 2.43 0.17049 R
40 2023-09-15 16:58:45 SMPL3 SAM ODB OD 6.71 1.11813 R
40 2023-09-15 16:58:55 SMPL3 SAM LDH2B U/L < TEST RNG < 20.00 0.00076 R
40 2023-09-15 16:59:06 SMPL3 SAM NH3B mmol/L 1.817 0.05242 R
40 2023-09-15 16:59:16 SMPL3 SAM LAC2B mg/L < TEST RNG < 0.00 0.00329 R
40 2023-09-15 16:59:38 SMPL3 SAM TP2D mg/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 10:12:12 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
40 2023-09-16 10:22:55 SMPL4 SAM LAC2B mg/L v 1.89 0.15187 R
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