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felipenarvnathan-stender
felipenarv
and
nathan-stender
authored
feat: Roche Cedex BioHT - Added support for mg/L (#1028)
Co-authored-by: Nathan Stender <nathan.stender@benchling.com>
1 parent ac47580 commit ef8a064

3 files changed

Lines changed: 327 additions & 2 deletions

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‎src/allotropy/parsers/roche_cedex_bioht/roche_cedex_bioht_structure.py‎

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@@ -64,14 +64,27 @@ def create(data: SeriesData) -> RawMeasurement:
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if BELOW_TEST_RANGE in error
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else data.get(float, "concentration value", NaN)
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)
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value, unit = RawMeasurement._get_value_and_unit(
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concentration_value, data[str, "concentration unit"]
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)
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return RawMeasurement(
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data[str, "analyte name"],
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data[str, "measurement time"],
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concentration_value,
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data[str, "concentration unit"],
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value,
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unit,
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error or None,
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)
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@staticmethod
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def _get_value_and_unit(value: JsonFloat, unit: str) -> tuple[JsonFloat, str]:
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if isinstance(value, int | float):
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if unit == "mg/L":
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return value / 1000, "g/L"
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return value, unit
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def create_measurements(data: pd.DataFrame) -> dict[str, dict[str, RawMeasurement]]:
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measurements = sorted(

‎tests/parsers/roche_cedex_bioht/testdata/roche_cedex_bioht_example_with_mg_L.json‎

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{
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"$asm.manifest": "http://purl.allotrope.org/manifests/solution-analyzer/REC/2024/09/solution-analyzer.manifest",
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"solution analyzer aggregate document": {
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"solution analyzer document": [
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{
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"measurement aggregate document": {
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"measurement document": [
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{
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"device control aggregate document": {
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"device control document": [
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{
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"device type": "solution-analyzer"
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}
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]
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},
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"measurement identifier": "ROCHE_CEDEX_BIOHT_TEST_ID_0",
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"measurement time": "2023-09-15T16:55:51+00:00",
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"sample document": {
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"sample identifier": "SMPL1"
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},
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"absorbance": {
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"value": 6.32,
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"unit": "mAU"
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}
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},
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{
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"device control aggregate document": {
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"device control document": [
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{
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"device type": "solution-analyzer"
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}
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]
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},
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"measurement identifier": "ROCHE_CEDEX_BIOHT_TEST_ID_1",
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"measurement time": "2023-09-15T16:55:51+00:00",
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"sample document": {
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"sample identifier": "SMPL1"
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},
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"analyte aggregate document": {
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"analyte document": [
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{
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"analyte name": "ammonia",
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"molar concentration": {
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"value": 1.846,
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"unit": "mmol/L"
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}
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},
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{
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"analyte name": "glutamine",
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"molar concentration": {
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"value": 2.45,
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"unit": "mmol/L"
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}
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},
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{
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"analyte name": "lactate",
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"mass concentration": {
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"value": 2e-05,
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"unit": "g/L"
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}
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},
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{
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"analyte name": "ldh",
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"molar concentration": {
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"value": 1.471103,
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"unit": "mmol/L"
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}
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},
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{
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"analyte name": "total protein",
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"mass concentration": {
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"value": 0.0046,
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"unit": "g/L"
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}
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}
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]
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}
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}
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],
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"data processing time": "2023-09-17T13:04:06+00:00"
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},
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"analyst": "ADMIN"
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},
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{
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"measurement aggregate document": {
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"measurement document": [
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{
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"device control aggregate document": {
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"device control document": [
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{
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"device type": "solution-analyzer"
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}
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]
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},
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"measurement identifier": "ROCHE_CEDEX_BIOHT_TEST_ID_2",
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"measurement time": "2023-09-15T16:56:58+00:00",
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"sample document": {
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"sample identifier": "SMPL2"
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},
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"analyte aggregate document": {
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"analyte document": [
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{
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"analyte name": "ammonia",
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"molar concentration": {
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"value": 1.87,
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"unit": "mmol/L"
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}
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},
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{
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"analyte name": "glutamine",
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"molar concentration": {
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"value": 2.4,
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"unit": "mmol/L"
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}
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},
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{
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"analyte name": "total protein",
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"mass concentration": {
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"value": 0.0047,
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"unit": "g/L"
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}
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}
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]
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}
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}
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],
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"data processing time": "2023-09-17T13:04:06+00:00"
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},
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"analyst": "ADMIN"
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},
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{
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"measurement aggregate document": {
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"measurement document": [
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{
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"device control aggregate document": {
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"device control document": [
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{
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"device type": "solution-analyzer"
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}
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]
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},
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"measurement identifier": "ROCHE_CEDEX_BIOHT_TEST_ID_3",
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"measurement time": "2023-09-15T16:58:34+00:00",
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"sample document": {
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"sample identifier": "SMPL3"
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},
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"absorbance": {
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"value": 6.71,
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"unit": "mAU"
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}
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},
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{
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"device control aggregate document": {
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"device control document": [
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{
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"device type": "solution-analyzer"
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}
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]
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},
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"measurement identifier": "ROCHE_CEDEX_BIOHT_TEST_ID_4",
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"measurement time": "2023-09-15T16:58:34+00:00",
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"sample document": {
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"sample identifier": "SMPL3"
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},
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"analyte aggregate document": {
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"analyte document": [
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{
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"analyte name": "ammonia",
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"molar concentration": {
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"value": 1.817,
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"unit": "mmol/L"
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}
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},
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{
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"analyte name": "glutamine",
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"molar concentration": {
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"value": 2.43,
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"unit": "mmol/L"
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}
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},
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{
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"analyte name": "total protein",
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"mass concentration": {
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"value": 4.8,
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"unit": "g/L"
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}
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}
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]
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}
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}
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],
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"data processing time": "2023-09-17T13:04:06+00:00"
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},
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"analyst": "ADMIN"
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},
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{
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"measurement aggregate document": {
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"measurement document": [
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{
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"device control aggregate document": {
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"device control document": [
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{
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"device type": "solution-analyzer"
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}
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]
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},
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"measurement identifier": "ROCHE_CEDEX_BIOHT_TEST_ID_5",
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"measurement time": "2023-09-16T10:12:10+00:00",
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"sample document": {
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"sample identifier": "SMPL4"
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},
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"absorbance": {
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"value": 4.09,
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"unit": "mAU"
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}
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},
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{
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"device control aggregate document": {
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"device control document": [
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{
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"device type": "solution-analyzer"
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}
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]
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},
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"measurement identifier": "ROCHE_CEDEX_BIOHT_TEST_ID_6",
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"measurement time": "2023-09-16T10:12:10+00:00",
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"sample document": {
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"sample identifier": "SMPL4"
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},
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"analyte aggregate document": {
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"analyte document": [
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{
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"analyte name": "ammonia",
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"molar concentration": {
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"value": 3.788,
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"unit": "mmol/L"
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}
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},
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{
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"analyte name": "glutamine",
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"molar concentration": {
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"value": 2.07,
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"unit": "mmol/L"
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}
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},
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{
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"analyte name": "lactate",
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"mass concentration": {
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"value": 0.00189,
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"unit": "g/L"
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}
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},
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{
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"analyte name": "ldh",
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"molar concentration": {
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"value": 5.591828,
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"unit": "mmol/L"
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}
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}
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]
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}
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}
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],
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"data processing time": "2023-09-17T13:04:06+00:00"
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},
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"analyst": "ADMIN"
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}
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],
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"data system document": {
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"ASM file identifier": "roche_cedex_bioht_example_with_mg_L.json",
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"data system instance identifier": "N/A",
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"file name": "roche_cedex_bioht_example_with_mg_L.txt",
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"UNC path": "tests/parsers/roche_cedex_bioht/testdata/roche_cedex_bioht_example_with_mg_L.txt",
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"ASM converter name": "allotropy_roche_cedex_bioht",
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"ASM converter version": "0.1.97",
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"software name": "CEDEX BIO HT",
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"software version": "6.0.0.1905 (1905)"
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},
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"device system document": {
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"device identifier": "N/A",
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"equipment serial number": "123456",
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"model number": "CEDEX BIO HT"
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}
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}
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}

‎tests/parsers/roche_cedex_bioht/testdata/roche_cedex_bioht_example_with_mg_L.txt‎

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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
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40 2023-09-15 16:55:51 SMPL1 SAM GLN2B mmol/L 2.45 0.17138 R
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40 2023-09-15 16:55:53 SMPL1 SAM ODB OD 6.32 1.05394 R
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40 2023-09-15 16:56:18 SMPL1 SAM LDH2B U/L 88.09 0.00728 R
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40 2023-09-15 16:56:26 SMPL1 SAM NH3B mmol/L 1.846 0.05333 R
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40 2023-09-15 16:56:37 SMPL1 SAM LAC2B mg/L 0.02 0.01567 R
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40 2023-09-15 16:56:48 SMPL1 SAM TP2LB mg/L 4.6 0.14883 R
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40 2023-09-15 16:56:58 SMPL2 SAM GLN2B mmol/L 2.40 0.16787 R
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40 2023-09-15 16:57:09 SMPL2 SAM ODB OD < TEST RNG 6.71 1.11766 R
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40 2023-09-15 16:57:19 SMPL2 SAM LDH2B U/L < TEST RNG < 20.00 0.00060 R
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40 2023-09-15 16:57:30 SMPL2 SAM NH3B mmol/L 1.870 0.05408 R
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40 2023-09-15 16:57:41 SMPL2 SAM LAC2B mg/L < TEST RNG < 0.00 0.00310 R
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40 2023-09-15 16:57:51 SMPL2 SAM TP2B mg/L < TEST RNG < 4.0 0.03322 R
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40 2023-09-15 16:58:02 SMPL2 SAM TP2D mg/L < TEST RNG < 40.0 0.02653 R
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40 2023-09-15 16:58:23 SMPL2 SAM TP2LB mg/L 4.7 0.15217 R
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40 2023-09-15 16:58:34 SMPL3 SAM GLN2B mmol/L 2.43 0.17049 R
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40 2023-09-15 16:58:45 SMPL3 SAM ODB OD 6.71 1.11813 R
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40 2023-09-15 16:58:55 SMPL3 SAM LDH2B U/L < TEST RNG < 20.00 0.00076 R
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40 2023-09-15 16:59:06 SMPL3 SAM NH3B mmol/L 1.817 0.05242 R
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40 2023-09-15 16:59:16 SMPL3 SAM LAC2B mg/L < TEST RNG < 0.00 0.00329 R
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40 2023-09-15 16:59:38 SMPL3 SAM TP2D mg/L < TEST RNG < 40.0 0.02702 R
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40 2023-09-15 17:00:52 SMPL3 SAM TP2LB g/L 4.8 0.15436 R
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40 2023-09-16 10:12:10 SMPL4 SAM GLN2B mmol/L 2.07 0.14503 R
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40 2023-09-16 10:12:12 SMPL4 SAM ODB OD 4.09 0.68160 R
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40 2023-09-16 10:13:29 SMPL4 SAM LDH2B U/L 334.84 0.02665 R
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40 2023-09-16 10:13:37 SMPL4 SAM NH3B mmol/L 3.788 0.11415 R
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40 2023-09-16 10:22:55 SMPL4 SAM LAC2B mg/L v 1.89 0.15187 R

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