fix: NovaBio Flex2 - do not emit pH measurement when only vessel temperature is present

[slopez-b]

Summary

Converting a NovaBio BioProfile Flex2 SampleResults.csv failed schema validation and aborted the entire file whenever any row had a Vessel Temperature (°C) value but a blank pH. Reported by a customer (CUST-12475) whose failing sample had a vessel temperature of 37 °C and no pH reading.

Root cause

DETECTION_PROPERTY_MAPPING["ph-detection"] groups ph and temperature into a single measurement, and _get_measurements() emitted that measurement whenever any of its properties was non-None:

if any(value is not None for value in kwargs.values()):
    measurements.append(_create_measurement(sample, detection_type=..., **kwargs))

A row with a temperature but no pH therefore produced a ph-detection measurement carrying only a temperature. The Allotrope pH-detector schema (adm/ph/REC/2024/09/ph-detector.schema.json, measurementDocumentItems) marks pH as required and temperature as optional, so the measurement failed the anyOf validation:

AllotropeValidationError: Failed to validate allotrope model against schema:
{'device control aggregate document': {'device control document': [{'detection type': 'ph-detection', ...}]},
 ... 'temperature': {'value': 37.0, 'unit': 'degC'}} is not valid under any of the given schemas
Failed validating 'anyOf' in schema[...]['measurement document']['items']['allOf'][1]

Fix

Skip a detection type when its schema-required measured value is absent. Implemented as a small mapping rather than a one-off if detection_type == "ph-detection" check, so the same guard can cover other detection types later:

# Detection types whose ASM measurement schema requires a specific measured value; a
# measurement must not be emitted when that value is absent.
REQUIRED_PROPERTY_BY_DETECTION_TYPE = {"ph-detection": "ph"}

The guard sits at the top of the loop body, so it also avoids building kwargs needlessly.
Temperature-only samples now simply produce no pH measurement; every other detection type on the sample is unaffected.

Test plan

• New parametrized test_ph_detection_requires_ph_value covers all four pH/temperature combinations: temperature-only and empty samples yield no ph-detection, while both pH cases still do.
• New SampleResults2025-02-09_104000.csv fixture (plus generated .json snapshot) exercises full file conversion across three samples: temperature-without-pH, pH-with-temperature, and pH-without-temperature. The first yields only metabolite and blood-gas measurements; the other two retain ph-detection.
• Both new tests confirmed to fail on the unpatched parser and pass with the fix.
• The three pre-existing NovaBio Flex2 snapshots are byte-identical, so samples that do have pH are provably unchanged.
• Full suite green: 1128 tests passed.
• ruff, black, and mypy clean on the changed files.

Manual validation

Before the fix this raised AllotropeValidationError; after the fix it converts and validates cleanly, keeping the metabolite detection:

CONVERTED OK
detection types: ['metabolite-detection']

Out of scope

Two pre-existing behaviors are deliberately left alone, as neither is the reported scenario and both need a different remedy:

1. A sample with only a temperature and no other measurable data still fails, because an empty metabolite-detection measurement is emitted.
2. When a file has a units row, po2_unit/pco2_unit are populated from that row even when the PO2/PCO2 values are blank, making the any(value is not None ...) guard true and emitting a valueless blood-gas-detection measurement that fails validation the same way. This has the same shape as the bug fixed here, but the trigger is a units-only measurement rather than a missing required field. The new fixture supplies gas values on every row to avoid it.

[ajcariaga16]

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