diff --git a/src/allotropy/parsers/appbio_quantstudio_designandanalysis/appbio_quantstudio_designandanalysis_calculated_documents.py b/src/allotropy/parsers/appbio_quantstudio_designandanalysis/appbio_quantstudio_designandanalysis_calculated_documents.py index 889b88dd4..bf7de9c86 100644 --- a/src/allotropy/parsers/appbio_quantstudio_designandanalysis/appbio_quantstudio_designandanalysis_calculated_documents.py +++ b/src/allotropy/parsers/appbio_quantstudio_designandanalysis/appbio_quantstudio_designandanalysis_calculated_documents.py @@ -391,7 +391,7 @@ def iter_standard_curve_calc_docs( def iter_relative_standard_curve_calc_docs( well_items: list[WellItem], - r_sample: str, + r_sample: str | None, r_target: str | None, ) -> Iterator[CalculatedDocument]: # Y-Intercept, Slope, Quantity, Amp score, Cq confidence, diff --git a/src/allotropy/parsers/appbio_quantstudio_designandanalysis/structure/relative_standard_curve/creator.py b/src/allotropy/parsers/appbio_quantstudio_designandanalysis/structure/relative_standard_curve/creator.py index a83358adc..235ffd6d9 100644 --- a/src/allotropy/parsers/appbio_quantstudio_designandanalysis/structure/relative_standard_curve/creator.py +++ b/src/allotropy/parsers/appbio_quantstudio_designandanalysis/structure/relative_standard_curve/creator.py @@ -22,6 +22,20 @@ ) +def _has_valid_rq_values(reader: DesignQuantstudioReader) -> bool: + """Return True if the RQ Replicate Group Result sheet contains at least one + non-null Rq value. + + When all Rq values are null or nan (e.g. the reference calibrator sample + was not processed or all wells undetermined), the reference sample cannot be + inferred and RQ-derived calculated data documents must be skipped. + """ + sheet = reader.get_non_empty_sheet_or_none("RQ Replicate Group Result") + if sheet is None or "Rq" not in sheet.columns: + return False + return bool(sheet["Rq"].notna().any()) + + class RelativeStandardCurveCreator(Creator): PLUGIN_REGEX: ClassVar[str] = r"Relative Quantification" EXPECTED_SHEETS: ClassVar[list[str]] = [ @@ -34,8 +48,12 @@ def create(cls, reader: DesignQuantstudioReader) -> Data: wells = RelativeStandardCurveWellList.create(reader, header) well_items = wells.get_well_items() - r_sample = Result.get_reference_sample(reader) - r_target = Result.get_reference_target(reader) + if not _has_valid_rq_values(reader): + r_sample = None + r_target = None + else: + r_sample = Result.get_reference_sample(reader) + r_target = Result.get_reference_target(reader) return Data( header, diff --git a/tests/parsers/appbio_quantstudio_designandanalysis/testdata/appbio_quantstudio_designandanalysis_no_RQ_values_example1.json b/tests/parsers/appbio_quantstudio_designandanalysis/testdata/appbio_quantstudio_designandanalysis_no_RQ_values_example1.json new file mode 100644 index 000000000..6262f824d --- /dev/null +++ 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