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fix: Surface previously skipped columns as custom info in NovaBio Flex2 parser (#1236)
## Summary - `Sample Time`, `PCO2 @ Temp`, `PO2 @ Temp`, and `pH @ Temp` were incorrectly marked as `unused_keys` in the NovaBio Flex2 parser (introduced in #1070) - These fields are not duplicates of already-mapped ASM fields — they were skipped by mistake during the PR review categorization - Removed them from `unused_keys` so they now flow through to `custom_info` in the output - `Operator` and `Osm` remain suppressed since they are consumed elsewhere (as `analyst` and `osmolality` respectively) ## Test plan - [x] All 13 NovaBio Flex2 tests pass - [x] discover_vendor tests pass - [x] Lint clean (ruff, black, mypy) 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>
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‎src/allotropy/parsers/novabio_flex2/novabio_flex2_structure.py‎

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@@ -89,10 +89,6 @@ def create(cls, units: SeriesData, data: SeriesData) -> Sample:
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cell_density_dilution = cell_density_dilution.split(":")[0]
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unused_keys = {
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"Sample Time",
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"PCO2 @ Temp",
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"PO2 @ Temp",
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"pH @ Temp",
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"Operator",
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"Osm",
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}

‎tests/parsers/novabio_flex2/testdata/SampleResults2022-06-28_142558.json‎

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@@ -1,6 +1,19 @@
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{
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"$asm.manifest": "http://purl.allotrope.org/manifests/solution-analyzer/BENCHLING/2024/09/solution-analyzer.manifest",
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"solution analyzer aggregate document": {
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"data system document": {
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"ASM file identifier": "SampleResults2022-06-28_142558.json",
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"data system instance identifier": "N/A",
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"ASM converter name": "allotropy_novabio_flex2",
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"ASM converter version": "0.1.138",
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"file name": "SampleResults2022-06-28_142558.csv",
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"software name": "NovaBio Flex",
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"UNC path": "tests/parsers/novabio_flex2/testdata/SampleResults2022-06-28_142558.csv"
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},
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"device system document": {
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"model number": "Flex2",
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"product manufacturer": "Nova Biomedical"
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},
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"solution analyzer document": [
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{
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"measurement aggregate document": {
@@ -9,13 +22,13 @@
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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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"detection type": "metabolite-detection",
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"device type": "solution-analyzer",
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"custom information document": {
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"Vessel Pressure (psi)": 0.0,
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"Sparging O2%": 20.9,
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"Chemistry Flow Time": 6.67,
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"pH / Gas Flow Time": 3.65
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"Vessel Pressure (psi)": 0.0,
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"pH / Gas Flow Time": 3.65,
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"Sparging O2%": 20.9
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}
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}
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]
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"batch identifier": "BATCH_123",
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"description": "Spent Media",
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"custom information document": {
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"Vessel ID": "3L Bioreactor",
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"Cell Type": "Workhog",
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"Sample Time": "24-6-2022 14:34:52",
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"pH @ Temp": 7.4,
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"Chemistry Dilution Ratio": "1:1",
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"Cell Type": "Workhog"
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"Vessel ID": "3L Bioreactor",
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"PCO2 @ Temp": 46.8,
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"PO2 @ Temp": 191.6
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}
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},
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"analyte aggregate document": {
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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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"detection type": "blood-gas-detection",
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"device type": "solution-analyzer",
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"custom information document": {
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"Vessel Pressure (psi)": 0.0,
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"Sparging O2%": 20.9,
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"Chemistry Flow Time": 6.67,
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"pH / Gas Flow Time": 3.65
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"Vessel Pressure (psi)": 0.0,
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"pH / Gas Flow Time": 3.65,
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"Sparging O2%": 20.9
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}
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}
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]
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"batch identifier": "BATCH_123",
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"description": "Spent Media",
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"custom information document": {
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"Vessel ID": "3L Bioreactor",
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"Cell Type": "Workhog",
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"Sample Time": "24-6-2022 14:34:52",
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"pH @ Temp": 7.4,
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"Chemistry Dilution Ratio": "1:1",
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"Cell Type": "Workhog"
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"Vessel ID": "3L Bioreactor",
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"PCO2 @ Temp": 46.8,
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"PO2 @ Temp": 191.6
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}
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},
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"pO2": {
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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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"detection type": "ph-detection",
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"device type": "solution-analyzer",
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"custom information document": {
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"Vessel Pressure (psi)": 0.0,
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"Sparging O2%": 20.9,
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"Chemistry Flow Time": 6.67,
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"pH / Gas Flow Time": 3.65
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"Vessel Pressure (psi)": 0.0,
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"pH / Gas Flow Time": 3.65,
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"Sparging O2%": 20.9
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}
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}
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]
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"batch identifier": "BATCH_123",
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"description": "Spent Media",
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"custom information document": {
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"Vessel ID": "3L Bioreactor",
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"Cell Type": "Workhog",
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"Sample Time": "24-6-2022 14:34:52",
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"pH @ Temp": 7.4,
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"Chemistry Dilution Ratio": "1:1",
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"Cell Type": "Workhog"
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"Vessel ID": "3L Bioreactor",
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"PCO2 @ Temp": 46.8,
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"PO2 @ Temp": 191.6
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}
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},
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"pH": {
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},
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"analyst": "ANALYST1"
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}
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],
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"data system document": {
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"ASM file identifier": "SampleResults2022-06-28_142558.json",
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"data system instance identifier": "N/A",
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"file name": "SampleResults2022-06-28_142558.csv",
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"UNC path": "tests/parsers/novabio_flex2/testdata/SampleResults2022-06-28_142558.csv",
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"ASM converter name": "allotropy_novabio_flex2",
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"ASM converter version": "0.1.105",
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"software name": "NovaBio Flex"
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},
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"device system document": {
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"model number": "Flex2",
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"product manufacturer": "Nova Biomedical"
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}
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]
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}
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}

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