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feat: AppBio QuantStudio Design & Analysis - remove duplicates and hardcoded values from measurement custom info doc #1088

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Merged
nathan-stender merged 2 commits into from
Sep 30, 2025
Merged

feat: AppBio QuantStudio Design & Analysis - remove duplicates and hardcoded values from measurement custom info doc #1088

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2f3ec44
remove duplicates and hardcoded valios from measurement custom info doc
joshua-benchling Sep 26, 2025
ad8e038
Merge branch 'main' into jherna/quantstudio_designanalysis_duplicated…
nathan-stender Sep 30, 2025
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14 changes: 11 additions & 3 deletions src/allotropy/parsers/appbio_quantstudio/appbio_quantstudio_data_creator.py
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Original file line number Diff line number Diff line change
Expand Up @@ -125,10 +125,19 @@ def _create_processed_data(
data_processing_custom_info = {
"reference dna description": result_metadata.reference_dna_description,
"reference sample description": result_metadata.reference_sample_description,
"Analysis Type": "SinglePlex",
"RQ Min/Max Confidence Level": 0.95,
}

# Add Analysis Type and RQ Min/Max Confidence Level only if present in instrument file
if result_metadata.extra_data:
if "Analysis Type" in result_metadata.extra_data:
data_processing_custom_info["Analysis Type"] = result_metadata.extra_data[
"Analysis Type"
]
if "RQ Min/Max Confidence Level" in result_metadata.extra_data:
data_processing_custom_info[
"RQ Min/Max Confidence Level"
] = result_metadata.extra_data["RQ Min/Max Confidence Level"]

for field in data_processing_field_names:
if field in extra_data:
data_processing_custom_info[field] = extra_data[field]
Expand Down Expand Up @@ -269,7 +278,6 @@ def _create_measurement(
reporter_dye_data_cube=reporter_dye_data_cube,
passive_reference_dye_data_cube=passive_reference_dye_data_cube,
melting_curve_data_cube=_create_melt_curve_data_cube(melt_curve_raw_data),
custom_info=result_metadata.extra_data,
)


Expand Down
13 changes: 11 additions & 2 deletions ...appbio_quantstudio_designandanalysis/appbio_quantstudio_designandanalysis_data_creator.py
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Expand Up @@ -110,11 +110,20 @@ def _create_processed_data(well_item: WellItem, data: Data) -> ProcessedData:
"CQCONF": custom_info.get("CQCONF", "N"),
"NOISE": custom_info.get("NOISE", "N"),
"OUTLIERRG": custom_info.get("OUTLIERRG", "N"),
"Analysis Type": "SinglePlex",
"RQ Min/Max Confidence Level": 0.95,
"Omit": custom_info.get("Omit", False),
}

# Add Analysis Type and RQ Min/Max Confidence Level only if present in instrument file
if data.header.extra_data:
if "Analysis Type" in data.header.extra_data:
data_processing_custom_info["Analysis Type"] = data.header.extra_data[
"Analysis Type"
]
if "RQ Min/Max Confidence Level" in data.header.extra_data:
data_processing_custom_info[
"RQ Min/Max Confidence Level"
] = data.header.extra_data["RQ Min/Max Confidence Level"]

return ProcessedData(
automatic_cycle_threshold_enabled_setting=result.automatic_cycle_threshold_enabled_setting,
cycle_threshold_value_setting=result.cycle_threshold_value_setting,
Expand Down
3,354 changes: 1,197 additions & 2,157 deletions tests/parsers/appbio_quantstudio/testdata/appbio_quantstudio_example01.json
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1,922 changes: 769 additions & 1,153 deletions tests/parsers/appbio_quantstudio/testdata/appbio_quantstudio_example02.json
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4,038 changes: 1,827 additions & 2,211 deletions tests/parsers/appbio_quantstudio/testdata/appbio_quantstudio_example03.json
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952 changes: 381 additions & 571 deletions tests/parsers/appbio_quantstudio/testdata/appbio_quantstudio_example04.json
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926 changes: 331 additions & 595 deletions tests/parsers/appbio_quantstudio/testdata/appbio_quantstudio_example05.json
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146 changes: 55 additions & 91 deletions tests/parsers/appbio_quantstudio/testdata/appbio_quantstudio_example06.json
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1,346 changes: 481 additions & 865 deletions tests/parsers/appbio_quantstudio/testdata/appbio_quantstudio_example07.json
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650 changes: 253 additions & 397 deletions tests/parsers/appbio_quantstudio/testdata/appbio_quantstudio_example08.json
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506 changes: 181 additions & 325 deletions tests/parsers/appbio_quantstudio/testdata/appbio_quantstudio_example09.json
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20 changes: 8 additions & 12 deletions .../parsers/appbio_quantstudio/testdata/appbio_quantstudio_minimal_broken_path_calc_doc.json
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Original file line number Diff line number Diff line change
Expand Up @@ -56,13 +56,13 @@
"custom information document": {
"reference dna description": "RNaseP",
"reference sample description": "800",
"Analysis Type": "SinglePlex",
"RQ Min/Max Confidence Level": 0.95,
"CQCONF": "N",
"BADROX": "N",
"NOISE": "N",
"Analysis Type": "Singleplex",
"RQ Min/Max Confidence Level": 95.0,
"OUTLIERRG": "N",
"omit": false
"BADROX": "N",
"omit": false,
"CQCONF": "N",
"NOISE": "N"
}
},
"cycle threshold result (qPCR)": {
Expand Down Expand Up @@ -126,11 +126,7 @@
}
]
},
"target DNA description": "RNaseP",
"custom information document": {
"RQ Min/Max Confidence Level": 95.0,
"Analysis Type": "Singleplex"
}
"target DNA description": "RNaseP"
}
],
"experimental data identifier": "QuantStudio96-Well Relative Standard Curve Example",
Expand Down Expand Up @@ -221,7 +217,7 @@
"file name": "appbio_quantstudio_minimal_broken_path_calc_doc.txt",
"UNC path": "tests/parsers/appbio_quantstudio/testdata/appbio_quantstudio_minimal_broken_path_calc_doc.txt",
"ASM converter name": "allotropy_appbio_quantstudio_rt_pcr",
"ASM converter version": "0.1.84",
"ASM converter version": "0.1.105",
"software name": "Thermo QuantStudio",
"software version": "1.0"
},
Expand Down
30 changes: 13 additions & 17 deletions tests/parsers/appbio_quantstudio/testdata/appbio_quantstudio_minimal_missing_results.json
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Expand Up @@ -52,15 +52,13 @@
"unit": "#"
},
"custom information document": {
"Analysis Type": "SinglePlex",
"RQ Min/Max Confidence Level": 0.95,
"Method": "Auto",
"omit": false,
"BADROX": "N",
"SNP Assay Name": "CYP19_2",
"CQCONF": "N",
"NOISE": "N",
"omit": false,
"Method": "Auto",
"OUTLIERRG": "N",
"BADROX": "N"
"CQCONF": "N"
}
},
"normalized reporter data cube": {
Expand Down Expand Up @@ -127,12 +125,12 @@
"genotyping qPCR result": "Negative Control (NC)",
"custom information document": {
"Pass.Ref": 846041.75,
"Allele2 Delta Rn": 0.029,
"Allele2 Amp Score": 0.0,
"Allele2 Ct Threshold": 0.132,
"Allele2 Delta Rn": 0.029,
"Allele1 Cq Conf": 0.0,
"Allele2 Cq Conf": 0.0,
"Allele2 Amp Score": 0.0,
"Allele1 Amp Score": 0.0,
"Allele1 Cq Conf": 0.0,
"Quality(%)": 100.0
}
}
Expand Down Expand Up @@ -166,11 +164,11 @@
"custom information document": {
"well identifier": 1,
"sample color": "RGB(238,238,0)",
"Allele2 Color": "RGB(0,139,69)",
"SNP Assay Color": "RGB(176,23,31)",
"Allele1 Color": "RGB(0,0,255)",
"Allele2 Quencher": "NFQ-MGB",
"Allele1 Quencher": "NFQ-MGB",
"Allele2 Quencher": "NFQ-MGB"
"Allele2 Color": "RGB(0,139,69)"
}
},
"processed data aggregate document": {
Expand All @@ -192,13 +190,11 @@
"unit": "#"
},
"custom information document": {
"Analysis Type": "SinglePlex",
"RQ Min/Max Confidence Level": 0.95,
"omit": false,
"CQCONF": "N",
"BADROX": "N",
"NOISE": "N",
"omit": false,
"OUTLIERRG": "N",
"BADROX": "N"
"CQCONF": "N"
}
},
"normalized reporter data cube": {
Expand Down Expand Up @@ -289,7 +285,7 @@
"file name": "appbio_quantstudio_minimal_missing_results.txt",
"UNC path": "tests/parsers/appbio_quantstudio/testdata/appbio_quantstudio_minimal_missing_results.txt",
"ASM converter name": "allotropy_appbio_quantstudio_rt_pcr",
"ASM converter version": "0.1.84",
"ASM converter version": "0.1.105",
"software name": "Thermo QuantStudio",
"software version": "1.0"
},
Expand Down
18 changes: 7 additions & 11 deletions tests/parsers/appbio_quantstudio/testdata/appbio_quantstudio_minimal_test01.json
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Expand Up @@ -57,15 +57,13 @@
"unit": "(unitless)"
},
"custom information document": {
"Analysis Type": "SinglePlex",
"RQ Min/Max Confidence Level": 0.95,
"BADROX": "N",
"noamp": "N",
"expfail": "N",
"CQCONF": "N",
"omit": false,
"BADROX": "N",
"NOISE": "N",
"OUTLIERRG": "N",
"CQCONF": "N"
"expfail": "N"
}
},
"normalized reporter result": {
Expand Down Expand Up @@ -241,15 +239,13 @@
"unit": "(unitless)"
},
"custom information document": {
"Analysis Type": "SinglePlex",
"RQ Min/Max Confidence Level": 0.95,
"BADROX": "N",
"noamp": "N",
"expfail": "N",
"CQCONF": "N",
"omit": false,
"BADROX": "N",
"NOISE": "N",
"OUTLIERRG": "N",
"CQCONF": "N"
"expfail": "N"
}
},
"normalized reporter result": {
Expand Down Expand Up @@ -461,7 +457,7 @@
"file name": "appbio_quantstudio_minimal_test01.txt",
"UNC path": "tests/parsers/appbio_quantstudio/testdata/appbio_quantstudio_minimal_test01.txt",
"ASM converter name": "allotropy_appbio_quantstudio_rt_pcr",
"ASM converter version": "0.1.84",
"ASM converter version": "0.1.105",
"software name": "Thermo QuantStudio",
"software version": "1.0"
},
Expand Down
10 changes: 4 additions & 6 deletions tests/parsers/appbio_quantstudio/testdata/appbio_quantstudio_minimal_test02.json
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Expand Up @@ -55,13 +55,11 @@
"custom information document": {
"reference dna description": "N/A",
"reference sample description": "N/A",
"Analysis Type": "SinglePlex",
"RQ Min/Max Confidence Level": 0.95,
"CQCONF": "N",
"BADROX": "N",
"NOISE": "N",
"OUTLIERRG": "N",
"omit": false
"CQCONF": "N",
"omit": false,
"NOISE": "N"
}
},
"cycle threshold result (qPCR)": {
Expand Down Expand Up @@ -260,7 +258,7 @@
"file name": "appbio_quantstudio_minimal_test02.txt",
"UNC path": "tests/parsers/appbio_quantstudio/testdata/appbio_quantstudio_minimal_test02.txt",
"ASM converter name": "allotropy_appbio_quantstudio_rt_pcr",
"ASM converter version": "0.1.84",
"ASM converter version": "0.1.105",
"software name": "Thermo QuantStudio",
"software version": "1.0"
},
Expand Down
36 changes: 16 additions & 20 deletions tests/parsers/appbio_quantstudio/testdata/appbio_quantstudio_minimal_test03.json
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Expand Up @@ -52,15 +52,13 @@
"unit": "#"
},
"custom information document": {
"Analysis Type": "SinglePlex",
"RQ Min/Max Confidence Level": 0.95,
"NOISE": "N",
"omit": false,
"BADROX": "N",
"SNP Assay Name": "CYP19_2",
"omit": false,
"Method": "Auto",
"OUTLIERRG": "N",
"SNP Assay Name": "CYP19_2",
"CQCONF": "N"
"CQCONF": "N",
"NOISE": "N"
}
},
"normalized reporter data cube": {
Expand Down Expand Up @@ -126,14 +124,14 @@
},
"genotyping qPCR result": "Negative Control (NC)",
"custom information document": {
"Quality(%)": 100.0,
"Allele2 Delta Rn": 0.029,
"Allele1 Cq Conf": 0.0,
"Quality(%)": 100.0,
"Allele2 Cq Conf": 0.0,
"Allele2 Ct Threshold": 0.132,
"Allele1 Amp Score": 0.0,
"Pass.Ref": 846041.75,
"Allele2 Amp Score": 0.0
"Allele2 Ct Threshold": 0.132,
"Allele2 Amp Score": 0.0,
"Allele1 Cq Conf": 0.0,
"Allele1 Amp Score": 0.0
}
}
]
Expand Down Expand Up @@ -166,11 +164,11 @@
"custom information document": {
"well identifier": 1,
"sample color": "RGB(238,238,0)",
"SNP Assay Color": "RGB(176,23,31)",
"Allele2 Quencher": "NFQ-MGB",
"Allele1 Quencher": "NFQ-MGB",
"Allele1 Color": "RGB(0,0,255)",
"SNP Assay Color": "RGB(176,23,31)",
"Allele2 Color": "RGB(0,139,69)",
"Allele1 Quencher": "NFQ-MGB"
"Allele2 Color": "RGB(0,139,69)"
}
},
"processed data aggregate document": {
Expand All @@ -192,13 +190,11 @@
"unit": "#"
},
"custom information document": {
"Analysis Type": "SinglePlex",
"RQ Min/Max Confidence Level": 0.95,
"NOISE": "N",
"omit": false,
"BADROX": "N",
"omit": false,
"OUTLIERRG": "N",
"CQCONF": "N"
"CQCONF": "N",
"NOISE": "N"
}
},
"normalized reporter data cube": {
Expand Down Expand Up @@ -289,7 +285,7 @@
"file name": "appbio_quantstudio_minimal_test03.txt",
"UNC path": "tests/parsers/appbio_quantstudio/testdata/appbio_quantstudio_minimal_test03.txt",
"ASM converter name": "allotropy_appbio_quantstudio_rt_pcr",
"ASM converter version": "0.1.84",
"ASM converter version": "0.1.105",
"software name": "Thermo QuantStudio",
"software version": "1.0"
},
Expand Down
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