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feat: Molecular Devices SoftMax Pro - update adapter to plate reader schema REC 25/03 #1011

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Merged
nathan-stender merged 4 commits into from
Jun 11, 2025
Merged

feat: Molecular Devices SoftMax Pro - update adapter to plate reader schema REC 25/03 #1011

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4d75862
migrate adapter to rec schema 25/03
joshua-benchling Jun 10, 2025
2ddb94b
update instrument table
joshua-benchling Jun 11, 2025
9d94f8d
remove main file
joshua-benchling Jun 11, 2025
5f8e5d3
Merge branch 'main' into jherna-softmax-pro-migrate-to-plate-reader-2…
nathan-stender Jun 11, 2025
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2 changes: 1 addition & 1 deletion SUPPORTED_INSTRUMENT_SOFTWARE.adoc
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Expand Up @@ -40,7 +40,7 @@ The parsers follow maturation levels of: Recommended, Candidate Release, Working
|CTL ImmunoSpot|Recommended|BENCHLING/2023/09
|Mabtech Apex|Recommended|BENCHLING/2023/09
|MSD Methodical Mind|Recommended|REC/2024/06
|Molecular Devices SoftMax Pro|Recommended|REC/2024/06
|Molecular Devices SoftMax Pro|Recommended|REC/2025/03
|MSD Discovery Workbench|Recommended|REC/2024/06
|PerkinElmer Envision|Recommended|REC/2024/06
|Revvity Kaleido|Recommended|BENCHLING/2023/09
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2 changes: 1 addition & 1 deletion src/allotropy/parsers/moldev_softmax_pro/softmax_pro_data_creator.py
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Expand Up @@ -10,7 +10,7 @@
FieldComponentDatatype,
)
from allotropy.allotrope.models.shared.definitions.units import UNITLESS
from allotropy.allotrope.schema_mappers.adm.plate_reader.rec._2024._06.plate_reader import (
from allotropy.allotrope.schema_mappers.adm.plate_reader.rec._2025._03.plate_reader import (
Measurement,
MeasurementGroup,
MeasurementType,
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4 changes: 2 additions & 2 deletions src/allotropy/parsers/moldev_softmax_pro/softmax_pro_parser.py
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@@ -1,5 +1,5 @@
from allotropy.allotrope.models.adm.plate_reader.rec._2024._06.plate_reader import Model
from allotropy.allotrope.schema_mappers.adm.plate_reader.rec._2024._06.plate_reader import (
from allotropy.allotrope.models.adm.plate_reader.rec._2025._03.plate_reader import Model
from allotropy.allotrope.schema_mappers.adm.plate_reader.rec._2025._03.plate_reader import (
Data,
Mapper,
)
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2 changes: 1 addition & 1 deletion src/allotropy/parsers/moldev_softmax_pro/softmax_pro_structure.py
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Expand Up @@ -11,7 +11,7 @@

import pandas as pd

from allotropy.allotrope.schema_mappers.adm.plate_reader.rec._2024._06.plate_reader import (
from allotropy.allotrope.schema_mappers.adm.plate_reader.rec._2025._03.plate_reader import (
ErrorDocument,
MeasurementType,
ScanPositionSettingPlateReader,
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3,054 changes: 1,527 additions & 1,527 deletions tests/parsers/moldev_softmax_pro/testdata/MD_SMP_absorbance_endpoint_example01.json
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3,054 changes: 1,527 additions & 1,527 deletions tests/parsers/moldev_softmax_pro/testdata/MD_SMP_absorbance_endpoint_example02.json
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4,214 changes: 2,107 additions & 2,107 deletions tests/parsers/moldev_softmax_pro/testdata/MD_SMP_absorbance_endpoint_example04.json
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4,214 changes: 2,107 additions & 2,107 deletions tests/parsers/moldev_softmax_pro/testdata/MD_SMP_absorbance_endpoint_example05.json
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1,846 changes: 923 additions & 923 deletions ...rsers/moldev_softmax_pro/testdata/MD_SMP_absorbance_endpoint_partial_plate_example01.json
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1,214 changes: 607 additions & 607 deletions ...rsers/moldev_softmax_pro/testdata/MD_SMP_absorbance_endpoint_partial_plate_example03.json
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4,878 changes: 2,439 additions & 2,439 deletions tests/parsers/moldev_softmax_pro/testdata/MD_SMP_fluorescence_endpoint_example06.json
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4,878 changes: 2,439 additions & 2,439 deletions tests/parsers/moldev_softmax_pro/testdata/MD_SMP_fluorescence_endpoint_example07.json
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774 changes: 387 additions & 387 deletions tests/parsers/moldev_softmax_pro/testdata/MD_SMP_luminescence_endpoint_example03.json
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966 changes: 483 additions & 483 deletions tests/parsers/moldev_softmax_pro/testdata/abs_endpoint_plates.json
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318 changes: 159 additions & 159 deletions tests/parsers/moldev_softmax_pro/testdata/fl_kinetic_plates.json
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3,074 changes: 1,537 additions & 1,537 deletions tests/parsers/moldev_softmax_pro/testdata/group_with_partial_rows.json
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66 changes: 33 additions & 33 deletions tests/parsers/moldev_softmax_pro/testdata/no_measurements.json
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@@ -1,5 +1,5 @@
{
"$asm.manifest": "http://purl.allotrope.org/manifests/plate-reader/REC/2024/06/plate-reader.manifest",
"$asm.manifest": "http://purl.allotrope.org/manifests/plate-reader/REC/2025/03/plate-reader.manifest",
"plate reader aggregate document": {
"plate reader document": [
{
Expand All @@ -20,21 +20,21 @@
"value": 505.0,
"unit": "nm"
},
"wavelength filter cutoff setting": {
"value": 495,
"unit": "nm"
},
"excitation wavelength setting": {
"value": 380,
"unit": "nm"
},
"wavelength filter cutoff setting": {
"value": 495,
"unit": "nm"
}
}
]
},
"measurement identifier": "MOLDEV_SOFTMAX_PRO_TEST_ID_0",
"sample document": {
"sample identifier": "PLate1 A1",
"location identifier": "A1",
"sample identifier": "PLate1 A1",
"well plate identifier": "PLate1"
},
"error aggregate document": {
Expand Down Expand Up @@ -81,21 +81,21 @@
"value": 505.0,
"unit": "nm"
},
"wavelength filter cutoff setting": {
"value": 495,
"unit": "nm"
},
"excitation wavelength setting": {
"value": 380,
"unit": "nm"
},
"wavelength filter cutoff setting": {
"value": 495,
"unit": "nm"
}
}
]
},
"measurement identifier": "MOLDEV_SOFTMAX_PRO_TEST_ID_1",
"sample document": {
"sample identifier": "PLate1 A2",
"location identifier": "A2",
"sample identifier": "PLate1 A2",
"well plate identifier": "PLate1"
},
"error aggregate document": {
Expand Down Expand Up @@ -142,21 +142,21 @@
"value": 505.0,
"unit": "nm"
},
"wavelength filter cutoff setting": {
"value": 495,
"unit": "nm"
},
"excitation wavelength setting": {
"value": 380,
"unit": "nm"
},
"wavelength filter cutoff setting": {
"value": 495,
"unit": "nm"
}
}
]
},
"measurement identifier": "MOLDEV_SOFTMAX_PRO_TEST_ID_2",
"sample document": {
"sample identifier": "PLate1 A3",
"location identifier": "A3",
"sample identifier": "PLate1 A3",
"well plate identifier": "PLate1"
},
"error aggregate document": {
Expand Down Expand Up @@ -203,21 +203,21 @@
"value": 505.0,
"unit": "nm"
},
"wavelength filter cutoff setting": {
"value": 495,
"unit": "nm"
},
"excitation wavelength setting": {
"value": 380,
"unit": "nm"
},
"wavelength filter cutoff setting": {
"value": 495,
"unit": "nm"
}
}
]
},
"measurement identifier": "MOLDEV_SOFTMAX_PRO_TEST_ID_3",
"sample document": {
"sample identifier": "PLate1 B1",
"location identifier": "B1",
"sample identifier": "PLate1 B1",
"well plate identifier": "PLate1"
},
"error aggregate document": {
Expand Down Expand Up @@ -264,21 +264,21 @@
"value": 505.0,
"unit": "nm"
},
"wavelength filter cutoff setting": {
"value": 495,
"unit": "nm"
},
"excitation wavelength setting": {
"value": 380,
"unit": "nm"
},
"wavelength filter cutoff setting": {
"value": 495,
"unit": "nm"
}
}
]
},
"measurement identifier": "MOLDEV_SOFTMAX_PRO_TEST_ID_4",
"sample document": {
"sample identifier": "PLate1 B2",
"location identifier": "B2",
"sample identifier": "PLate1 B2",
"well plate identifier": "PLate1"
},
"error aggregate document": {
Expand Down Expand Up @@ -325,21 +325,21 @@
"value": 505.0,
"unit": "nm"
},
"wavelength filter cutoff setting": {
"value": 495,
"unit": "nm"
},
"excitation wavelength setting": {
"value": 380,
"unit": "nm"
},
"wavelength filter cutoff setting": {
"value": 495,
"unit": "nm"
}
}
]
},
"measurement identifier": "MOLDEV_SOFTMAX_PRO_TEST_ID_5",
"sample document": {
"sample identifier": "PLate1 B3",
"location identifier": "B3",
"sample identifier": "PLate1 B3",
"well plate identifier": "PLate1"
},
"error aggregate document": {
Expand Down Expand Up @@ -372,10 +372,10 @@
"data system document": {
"ASM file identifier": "N/A",
"data system instance identifier": "N/A",
"file name": "no_measurements.txt",
"UNC path": "tests/parsers/moldev_softmax_pro/testdata/no_measurements.txt",
"file name": "no_measurements.txt",
"ASM converter name": "allotropy_molecular_devices_softmax_pro",
"ASM converter version": "0.1.61",
"ASM converter version": "0.1.92",
"software name": "SoftMax Pro"
},
"device system document": {
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