diff --git a/src/allotropy/parsers/perkin_elmer_envision/perkin_elmer_envision_structure.py b/src/allotropy/parsers/perkin_elmer_envision/perkin_elmer_envision_structure.py index dbf89b5f9..535a76e96 100644 --- a/src/allotropy/parsers/perkin_elmer_envision/perkin_elmer_envision_structure.py +++ b/src/allotropy/parsers/perkin_elmer_envision/perkin_elmer_envision_structure.py @@ -119,10 +119,12 @@ class CalculatedPlateInfo(PlateInfo): def create(data: SeriesData) -> CalculatedPlateInfo: formula = data[str, "Formula"] - name = assert_not_none( - search(r"^([^=]*)=", formula), - msg="Unable to find expected formula name for calculated results section.", - ).group(1) + # Standard formulas embed the name before an '=' (e.g. + # "Calc 1: General = (X / Y) * Z where ..."). Some formulas are a plain + # description with no '=' (e.g. "Calc 1: OD450 direct absorbance value at + # 450 nm"), in which case the whole formula string is the name. + formula_name_match = search(r"^([^=]*)=", formula) + name = formula_name_match.group(1) if formula_name_match else formula plate_number, barcode = PlateInfo.get_plate_number_and_barcode(data) diff --git a/tests/parsers/perkin_elmer_envision/perkin_elmer_envision_structure_test.py b/tests/parsers/perkin_elmer_envision/perkin_elmer_envision_structure_test.py index 26582358c..7c3865838 100644 --- a/tests/parsers/perkin_elmer_envision/perkin_elmer_envision_structure_test.py +++ b/tests/parsers/perkin_elmer_envision/perkin_elmer_envision_structure_test.py @@ -345,20 +345,27 @@ def test_create_calculated_plate_info_with_no_formula() -> None: CalculatedPlateInfo.create(data) -def test_create_calculated_plate_info_with_invalid_formula() -> None: +def test_create_calculated_plate_info_with_formula_without_name() -> None: + # Some formulas are a plain description with no "name =" prefix; the whole + # formula string is used as the name. data = SeriesData( pd.Series( { "Plate": "dummy", "Measured height": "0", - "Formula": "invalid formula", + "Formula": "Calc 1: OD450 direct absorbance value at 450 nm", "Measurement date": "10/13/2022 3:08:06 PM", } ) ) - msg = "Unable to find expected formula name for calculated results section." - with pytest.raises(AllotropeConversionError, match=msg): - CalculatedPlateInfo.create(data) + calculated_plate_info = CalculatedPlateInfo.create(data) + assert ( + calculated_plate_info.name == "Calc 1: OD450 direct absorbance value at 450 nm" + ) + assert ( + calculated_plate_info.formula + == "Calc 1: OD450 direct absorbance value at 450 nm" + ) def test_create_basic_assay_info() -> None: diff --git a/tests/parsers/perkin_elmer_envision/testdata/PE_Envision_absorbance_OD450_384_calc_no_name.csv b/tests/parsers/perkin_elmer_envision/testdata/PE_Envision_absorbance_OD450_384_calc_no_name.csv new file mode 100644 index 000000000..48d71a644 --- /dev/null +++ b/tests/parsers/perkin_elmer_envision/testdata/PE_Envision_absorbance_OD450_384_calc_no_name.csv @@ -0,0 +1,173 @@ +Plate information +Plate,Repeat,Barcode,Measured height,Chamber temperature at start,Chamber temperature at end,Humidity at start,Humidity at end,Ambient temperature at start,Ambient temperature at end,Formula,Measurement date, +1,1,,N/A,N/A,N/A,N/A,N/A,N/A,N/A,Calc 1: OD450 direct absorbance value at 450 nm,7/17/2026 8:15:00 PM, + +Background information +Plate,Label,Result,Signal,Flashes/Time,Meastime,MeasInfo, +1,Copy of OD450 Abs 384,0,0,0.1,00:00:00.000,De=Abs Ex=N/A Em=450 nm Wdw=N/A, + +0.054,0.058,2.430,2.325,1.709,1.573,1.218,0.924,0.317,0.403,0.581,0.595,0.467,0.401,0.708,0.692,0.971,0.901,1.230,1.099,0.947,0.779,0.936,1.241, 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+0.067,0.031,2.354,2.472,1.703,1.631,0.861,0.969,0.333,0.570,0.941,0.862,0.875,0.321,0.878,0.822,1.270,1.289,1.598,1.482,1.493,1.356,1.369,1.256, +0.070,0.071,2.377,2.308,1.718,1.546,1.064,1.211,0.244,0.418,1.188,1.079,1.118,0.988,1.043,1.244,1.322,1.562,1.931,1.627,1.366,1.491,1.394,1.503, +0.076,0.086,2.438,2.378,1.683,1.695,1.029,1.019,0.370,0.483,1.352,1.395,1.093,0.904,1.266,1.506,1.352,1.480,1.783,1.790,1.721,1.439,1.503,1.518, + +Plate information +Plate,Repeat,Barcode,Measured height,Chamber temperature at start,Chamber temperature at end,Humidity at start,Humidity at end,Ambient temperature at start,Ambient temperature at end,Group,Label,ScanX,ScanY,Measinfo,Kinetics,Measurement date, +1,1,,14.44,22.51,22.41,36.5,35.5,22.41,22.41,1,Copy of OD450 Abs 384(1),0,0,De=Abs Ex=N/A Em=450 nm Wdw=N/A,0,7/17/2026 8:15:00 PM, + +Background information +Plate,Label,Result,Signal,Flashes/Time,Meastime,MeasInfo, +1,Copy of OD450 Abs 384,0,0,0.1,00:00:00.000,De=Abs Ex=N/A Em=450 nm Wdw=N/A, 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+0.051,0.064,2.453,2.352,1.788,1.668,0.908,0.865,0.595,0.409,0.490,0.684,0.587,0.494,0.680,0.771,0.920,0.949,1.280,1.261,1.348,1.100,1.243,1.256, +0.067,0.031,2.354,2.472,1.703,1.631,0.861,0.969,0.333,0.570,0.941,0.862,0.875,0.321,0.878,0.822,1.270,1.289,1.598,1.482,1.493,1.356,1.369,1.256, +0.070,0.071,2.377,2.308,1.718,1.546,1.064,1.211,0.244,0.418,1.188,1.079,1.118,0.988,1.043,1.244,1.322,1.562,1.931,1.627,1.366,1.491,1.394,1.503, +0.076,0.086,2.438,2.378,1.683,1.695,1.029,1.019,0.370,0.483,1.352,1.395,1.093,0.904,1.266,1.506,1.352,1.480,1.783,1.790,1.721,1.439,1.503,1.518, + + +Basic assay information +Assay ID: ,,,,OD450-DUMMY-001 +Assay Started: ,,,,7/17/2026 8:14:00 PM +Assay Finished: ,,,,N/A +Assay Exported: ,,,,7/17/2026 8:15:30 PM +Protocol ID: ,,,,DUMMY-OD450 +Protocol Name: ,,,,OD450 Dummy 384 +Serial#: ,,,,="1041468" + + + +Protocol information +Protocol: +Protocol name,,,,OD450 Dummy 384 +Number of assay repeats,,,,1 +Start assay repeat each,,,,N/A +Number of plate repeats,,,,1 +Start plate repeat each,,,,N/A +Is label meas. height used,,,,Yes +Height of measurement,,,,Defined in label +Is gripper height used,,,,No +Mode of measurement,,,,By Rows bi-directional +Rotated plate,,,,No +Soft move,,,,No +Protocol notes,,,, + +Plate type: +Name of the plate type,,,,Copy of 384 General miura Greiner 781086 +Number of rows,,,,16 +Number of columns,,,,24 +Number of the wells in the plate,,,,384 +Height of the plate,,,,14.35 mm + +Coordinates of corners: +Copy of 384 General miura Greiner 781086 + Copy of OD450 Abs 384 +11.66 mm x------------------------------------------------------ x 115.01 mm +8.85 mm 8.93 mm + +11.68 mm x------------------------------------------------------ x 115.04 mm +76.26 mm 76.28 mm + +Platemap: +Plate,,,,1 +Group,,,,1 + +,01,02,03,04,05,06,07,08,09,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24, +A,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- +B,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- +C,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- +D,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- +E,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- +F,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- +G,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- +H,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- +I,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- +J,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- +K,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- +L,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- +M,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- +N,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- +O,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- +P,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- + + - - Undefined + +Calculations: +Plate,,,,1 + Formula index,,,,Calc 1 + Formula name,,,,OD450 + Formula,,,,OD450 direct absorbance value at 450 nm + +Auto export parameters: +Export format,,,,Plate +Include basic assay information,,,,Yes +Place assay information at,,,,End of file +Include basic plate information,,,,Yes +Place plate information at,,,,Beginning of plate +Include protocol information,,,,Yes +Protocol info level,,,,Large +Include error and warning information,,,,Yes +Include background information,,,,Yes +Add plate number to the file name,,,,Yes +Each plate to separate file,,,,Yes +Field separator to use,,,,System +File name format,,,,\\_.csv + +Operations: +Plate 1 + Group 1 + Measurement + Label,,,,Copy of OD450 Abs 384(1) + +Labels: +Copy of OD450 Abs 384,,,,7000008 +Measurement height,,,,N/A +Measurement time,,,,0.1 s +CT,,,,0 +Aperture,,,,384 Plate Absorbance aperture +Last edited,,,,7/15/2015 10:58:42 AM +Last edited by,,,,EnVision +Factory preset,,,,No + +Aperture: +384 Plate Absorbance aperture,,,,9 +Height,,,,4.2 mm +Diameter,,,,3.7 mm +Description,,,,Dummy OD450 absorbance data; 384-well plate format +Last edited,,,,3/5/2014 12:24:05 PM +Last edited by,,,,Installation +Factory preset,,,,Yes + +Instrument: +Serial number,,,,1041468 +Nickname,,,,EnVision + +Normalization: + + + + + +Exported with EnVision Workstation version 1.13.3009.1409 diff --git a/tests/parsers/perkin_elmer_envision/testdata/PE_Envision_absorbance_OD450_384_calc_no_name.json b/tests/parsers/perkin_elmer_envision/testdata/PE_Envision_absorbance_OD450_384_calc_no_name.json new file mode 100644 index 000000000..a6a1125b1 --- /dev/null +++ b/tests/parsers/perkin_elmer_envision/testdata/PE_Envision_absorbance_OD450_384_calc_no_name.json @@ -0,0 +1,36891 @@ +{ + "$asm.manifest": "http://purl.allotrope.org/manifests/plate-reader/REC/2024/06/plate-reader.manifest", + "plate reader aggregate document": { + "calculated data aggregate document": { + "calculated data document": [ + { + "calculated data name": "Calc 1: OD450 direct absorbance value at 450 nm", + "calculated result": { + "value": 0.054, + "unit": "(unitless)" + }, + "calculated data identifier": "PERKIN_ELMER_ENVISION_TEST_ID_384", + "calculation description": "Calc 1: OD450 direct absorbance value at 450 nm", + "data source aggregate document": { + "data source document": [ + { + "data source identifier": "PERKIN_ELMER_ENVISION_TEST_ID_0", + "data source feature": "Fluorescence" + } + ] + } + }, + { + "calculated data name": "Calc 1: OD450 direct absorbance value at 450 nm", + "calculated result": { + "value": 0.058, + "unit": "(unitless)" + }, + "calculated data identifier": "PERKIN_ELMER_ENVISION_TEST_ID_385", + "calculation description": "Calc 1: OD450 direct absorbance value at 450 nm", + "data source aggregate document": { + "data source document": [ + { + "data source identifier": "PERKIN_ELMER_ENVISION_TEST_ID_1", + "data source feature": "Fluorescence" + } + ] + } + }, + { + "calculated data name": "Calc 1: OD450 direct absorbance value at 450 nm", + "calculated result": { + "value": 2.43, + "unit": "(unitless)" + }, + "calculated data identifier": "PERKIN_ELMER_ENVISION_TEST_ID_386", + "calculation description": "Calc 1: OD450 direct absorbance value at 450 nm", + "data source aggregate document": { + "data source document": [ + { + "data source identifier": "PERKIN_ELMER_ENVISION_TEST_ID_2", + "data source feature": "Fluorescence" + } + ] + } + }, + { + "calculated data name": "Calc 1: OD450 direct absorbance value at 450 nm", + "calculated result": { + "value": 2.325, + "unit": "(unitless)" + }, + "calculated data identifier": "PERKIN_ELMER_ENVISION_TEST_ID_387", + "calculation description": "Calc 1: OD450 direct absorbance value at 450 nm", + "data source aggregate document": { + "data source document": [ + { + "data source identifier": "PERKIN_ELMER_ENVISION_TEST_ID_3", + "data source feature": "Fluorescence" + } + ] + } + }, + { + "calculated data name": "Calc 1: OD450 direct absorbance value at 450 nm", + "calculated result": { + "value": 1.709, + "unit": "(unitless)" + }, + "calculated data identifier": "PERKIN_ELMER_ENVISION_TEST_ID_388", + "calculation description": "Calc 1: OD450 direct absorbance value at 450 nm", + "data source aggregate document": { + "data source document": [ + { + "data source identifier": "PERKIN_ELMER_ENVISION_TEST_ID_4", + "data source feature": "Fluorescence" + } + ] + } + }, + { + "calculated data name": "Calc 1: OD450 direct absorbance value at 450 nm", + "calculated result": { + "value": 1.573, + "unit": "(unitless)" + }, + "calculated data identifier": "PERKIN_ELMER_ENVISION_TEST_ID_389", + "calculation description": "Calc 1: OD450 direct absorbance value at 450 nm", + "data source aggregate document": { + "data source document": [ + { + "data source identifier": "PERKIN_ELMER_ENVISION_TEST_ID_5", + "data source feature": "Fluorescence" + } + ] + } + }, + { + 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