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fix: Support EnVision calculated formulas without a name prefix #1246

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Merged
nathan-stender merged 3 commits into from
Jul 23, 2026
Merged

fix: Support EnVision calculated formulas without a name prefix #1246

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8b68c67
fix: Support EnVision calculated formulas without a name prefix
nathan-stender Jul 23, 2026
6f0604d
test: Minimize expected-JSON diff by preserving original key order
nathan-stender Jul 23, 2026
99c5611
Merge branch 'main' into fix-envision-calc-formula-no-name-v2
nathan-stender Jul 23, 2026
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10 changes: 6 additions & 4 deletions src/allotropy/parsers/perkin_elmer_envision/perkin_elmer_envision_structure.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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)

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17 changes: 12 additions & 5 deletions tests/parsers/perkin_elmer_envision/perkin_elmer_envision_structure_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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:
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8 changes: 4 additions & 4 deletions tests/parsers/perkin_elmer_envision/testdata/PE_Envision_fluorescence_example01.csv
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Original file line number Diff line number Diff line change
@@ -1,13 +1,13 @@
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: General = (X / Y) * Z where X = AC HTRF Laser [Eu](1) channel 1 window 1 Y = AC HTRF Laser [Eu](1) channel 2 window 1 Z = 10000,10/13/2022 3:08:06 PM,
1,1,"=""""",N/A,N/A,N/A,N/A,N/A,N/A,N/A,Calc 1: HTRF ratio value for AC HTRF Laser [Eu],10/13/2022 3:08:06 PM,

Background information
Plate,Label,Result,Signal,Flashes/Time,Meastime,MeasInfo,
1,AC HTRF Laser [Eu],0,162,50,00:00:00.000,De=1st Ex=Top Em=Top Wdw=1 (14),
1,AC HTRF Laser [Eu],0,260,50,00:00:00.000,De=2nd Ex=Top Em=Top Wdw=1 (142),

Calculated results: Calc 1: General = (X / Y) * Z where X = AC HTRF Laser [Eu](1) channel 1 window 1 Y = AC HTRF Laser [Eu](1) channel 2 window 1 Z = 10000
Calculated results: Calc 1: HTRF ratio value for AC HTRF Laser [Eu]
,01,02,03,04,05,06,07,08,09,10,11,12,
A,3912.12920565,3923.92517971,3948.45245355,,3933.03506298,4061.92827247,3996.61746992,,,,,,
B,2385.72193555,2384.42487617,2396.10683014,,2390.61028269,2396.68321027,2424.70697585,,,,,,
Expand Down Expand Up @@ -119,8 +119,8 @@ H,- ,- ,- , ,- ,- ,- , , , , ,
Calculations:
Plate,,,,1
Formula index,,,,Calc 1
Formula name,,,,General
Formula,,,,(X / Y) * Z where X = AC HTRF Laser [Eu](1) channel 1 window 1 Y = AC HTRF Laser [Eu](1) channel 2 window 1 Z = 10000
Formula name,,,,HTRF ratio value for AC HTRF Laser [Eu]
Formula,,,,HTRF ratio value for AC HTRF Laser [Eu]

Auto export parameters:
Export format,,,,Plate2
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