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fix: Surface previously skipped columns as custom info in NovaBio Flex2 parser #1236

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Merged
nathan-stender merged 1 commit into from
Jun 29, 2026
Merged

fix: Surface previously skipped columns as custom info in NovaBio Flex2 parser #1236

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4 changes: 0 additions & 4 deletions src/allotropy/parsers/novabio_flex2/novabio_flex2_structure.py
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Original file line number Diff line number Diff line change
Expand Up @@ -89,10 +89,6 @@ def create(cls, units: SeriesData, data: SeriesData) -> Sample:
cell_density_dilution = cell_density_dilution.split(":")[0]

unused_keys = {
"Sample Time",
"PCO2 @ Temp",
"PO2 @ Temp",
"pH @ Temp",
"Operator",
"Osm",
}
Expand Down
76 changes: 44 additions & 32 deletions tests/parsers/novabio_flex2/testdata/SampleResults2022-06-28_142558.json
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Original file line number Diff line number Diff line change
@@ -1,6 +1,19 @@
{
"$asm.manifest": "http://purl.allotrope.org/manifests/solution-analyzer/BENCHLING/2024/09/solution-analyzer.manifest",
"solution analyzer aggregate document": {
"data system document": {
"ASM file identifier": "SampleResults2022-06-28_142558.json",
"data system instance identifier": "N/A",
"ASM converter name": "allotropy_novabio_flex2",
"ASM converter version": "0.1.138",
"file name": "SampleResults2022-06-28_142558.csv",
"software name": "NovaBio Flex",
"UNC path": "tests/parsers/novabio_flex2/testdata/SampleResults2022-06-28_142558.csv"
},
"device system document": {
"model number": "Flex2",
"product manufacturer": "Nova Biomedical"
},
"solution analyzer document": [
{
"measurement aggregate document": {
Expand All @@ -9,13 +22,13 @@
"device control aggregate document": {
"device control document": [
{
"device type": "solution-analyzer",
"detection type": "metabolite-detection",
"device type": "solution-analyzer",
"custom information document": {
"Vessel Pressure (psi)": 0.0,
"Sparging O2%": 20.9,
"Chemistry Flow Time": 6.67,
"pH / Gas Flow Time": 3.65
"Vessel Pressure (psi)": 0.0,
"pH / Gas Flow Time": 3.65,
"Sparging O2%": 20.9
}
}
]
Expand All @@ -27,9 +40,13 @@
"batch identifier": "BATCH_123",
"description": "Spent Media",
"custom information document": {
"Vessel ID": "3L Bioreactor",
"Cell Type": "Workhog",
"Sample Time": "24-6-2022 14:34:52",
"pH @ Temp": 7.4,
"Chemistry Dilution Ratio": "1:1",
"Cell Type": "Workhog"
"Vessel ID": "3L Bioreactor",
"PCO2 @ Temp": 46.8,
"PO2 @ Temp": 191.6
}
},
"analyte aggregate document": {
Expand Down Expand Up @@ -104,13 +121,13 @@
"device control aggregate document": {
"device control document": [
{
"device type": "solution-analyzer",
"detection type": "blood-gas-detection",
"device type": "solution-analyzer",
"custom information document": {
"Vessel Pressure (psi)": 0.0,
"Sparging O2%": 20.9,
"Chemistry Flow Time": 6.67,
"pH / Gas Flow Time": 3.65
"Vessel Pressure (psi)": 0.0,
"pH / Gas Flow Time": 3.65,
"Sparging O2%": 20.9
}
}
]
Expand All @@ -122,9 +139,13 @@
"batch identifier": "BATCH_123",
"description": "Spent Media",
"custom information document": {
"Vessel ID": "3L Bioreactor",
"Cell Type": "Workhog",
"Sample Time": "24-6-2022 14:34:52",
"pH @ Temp": 7.4,
"Chemistry Dilution Ratio": "1:1",
"Cell Type": "Workhog"
"Vessel ID": "3L Bioreactor",
"PCO2 @ Temp": 46.8,
"PO2 @ Temp": 191.6
}
},
"pO2": {
Expand All @@ -148,13 +169,13 @@
"device control aggregate document": {
"device control document": [
{
"device type": "solution-analyzer",
"detection type": "ph-detection",
"device type": "solution-analyzer",
"custom information document": {
"Vessel Pressure (psi)": 0.0,
"Sparging O2%": 20.9,
"Chemistry Flow Time": 6.67,
"pH / Gas Flow Time": 3.65
"Vessel Pressure (psi)": 0.0,
"pH / Gas Flow Time": 3.65,
"Sparging O2%": 20.9
}
}
]
Expand All @@ -166,9 +187,13 @@
"batch identifier": "BATCH_123",
"description": "Spent Media",
"custom information document": {
"Vessel ID": "3L Bioreactor",
"Cell Type": "Workhog",
"Sample Time": "24-6-2022 14:34:52",
"pH @ Temp": 7.4,
"Chemistry Dilution Ratio": "1:1",
"Cell Type": "Workhog"
"Vessel ID": "3L Bioreactor",
"PCO2 @ Temp": 46.8,
"PO2 @ Temp": 191.6
}
},
"pH": {
Expand All @@ -185,19 +210,6 @@
},
"analyst": "ANALYST1"
}
],
"data system document": {
"ASM file identifier": "SampleResults2022-06-28_142558.json",
"data system instance identifier": "N/A",
"file name": "SampleResults2022-06-28_142558.csv",
"UNC path": "tests/parsers/novabio_flex2/testdata/SampleResults2022-06-28_142558.csv",
"ASM converter name": "allotropy_novabio_flex2",
"ASM converter version": "0.1.105",
"software name": "NovaBio Flex"
},
"device system document": {
"model number": "Flex2",
"product manufacturer": "Nova Biomedical"
}
]
}
}
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