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feat: Molecular Devices SoftMax Pro - move maximum wavelength signal to measurement document #1027

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feat: Molecular Devices SoftMax Pro - move maximum wavelength signal to measurement document #1027

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43 changes: 20 additions & 23 deletions src/allotropy/allotrope/schema_mappers/adm/plate_reader/rec/_2024/_06/plate_reader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -169,7 +169,6 @@ class MeasurementGroup:
analytical_method_identifier: str | None = None
experimental_data_identifier: str | None = None
experiment_type: str | None = None
maximum_wavelength_signal: float | None = None
custom_info: dict[str, Any] | None = None


Expand Down Expand Up @@ -251,13 +250,9 @@ def _get_technique_document(
],
),
)
custom_info_doc = {
"maximum wavelength signal": quantity_or_none(
TQuantityValueNanometer, measurement_group.maximum_wavelength_signal
)
}
custom_info_doc.update(measurement_group.custom_info or {})
return add_custom_information_document(plate_reader_doc, custom_info_doc)
return add_custom_information_document(
plate_reader_doc, measurement_group.custom_info
)

def _get_measurement_document(
self, measurement: Measurement
Expand Down Expand Up @@ -326,21 +321,23 @@ def _get_ultraviolet_absorbance_measurement_document(
error_aggregate_document=self._get_error_aggregate_document(
measurement.error_document
),
processed_data_aggregate_document=ProcessedDataAggregateDocument(
processed_data_document=[
ProcessedDataDocumentItem(
processed_data_identifier=measurement.processed_data_document.identifier,
data_processing_document={
"concentration factor": quantity_or_none(
TQuantityValueNanogramPerMicroliter,
measurement.processed_data_document.concentration_factor,
)
},
)
]
)
if measurement.processed_data_document
else None,
processed_data_aggregate_document=(
ProcessedDataAggregateDocument(
processed_data_document=[
ProcessedDataDocumentItem(
processed_data_identifier=measurement.processed_data_document.identifier,
data_processing_document={
"concentration factor": quantity_or_none(
TQuantityValueNanogramPerMicroliter,
measurement.processed_data_document.concentration_factor,
)
},
)
]
)
if measurement.processed_data_document
else None
),
)
return add_custom_information_document(
measurement_doc, measurement.measurement_custom_info
Expand Down
47 changes: 23 additions & 24 deletions src/allotropy/allotrope/schema_mappers/adm/plate_reader/rec/_2025/_03/plate_reader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -189,7 +189,6 @@ class MeasurementGroup:
measurement_time: str
analyst: str | None = None
experiment_type: str | None = None
maximum_wavelength_signal: float | None = None
custom_info: dict[str, Any] | None = None


Expand Down Expand Up @@ -269,13 +268,9 @@ def _get_technique_document(
],
),
)
custom_info_doc = {
"maximum wavelength signal": quantity_or_none(
TQuantityValueNanometer, measurement_group.maximum_wavelength_signal
)
}
custom_info_doc.update(measurement_group.custom_info or {})
return add_custom_information_document(plate_reader_doc, custom_info_doc)
return add_custom_information_document(
plate_reader_doc, measurement_group.custom_info
)

def _get_measurement_document(
self, measurement: Measurement
Expand Down Expand Up @@ -372,21 +367,23 @@ def _get_ultraviolet_absorbance_measurement_document(
error_aggregate_document=self._get_error_aggregate_document(
measurement.error_document
),
processed_data_aggregate_document=ProcessedDataAggregateDocument(
processed_data_document=[
ProcessedDataDocumentItem(
processed_data_identifier=measurement.processed_data_document.identifier,
data_processing_document={
"concentration factor": quantity_or_none(
TQuantityValueNanogramPerMicroliter,
measurement.processed_data_document.concentration_factor,
)
},
)
]
)
if measurement.processed_data_document
else None,
processed_data_aggregate_document=(
ProcessedDataAggregateDocument(
processed_data_document=[
ProcessedDataDocumentItem(
processed_data_identifier=measurement.processed_data_document.identifier,
data_processing_document={
"concentration factor": quantity_or_none(
TQuantityValueNanogramPerMicroliter,
measurement.processed_data_document.concentration_factor,
)
},
)
]
)
if measurement.processed_data_document
else None
),
)
return add_custom_information_document(
measurement_doc, measurement.measurement_custom_info
Expand Down Expand Up @@ -755,7 +752,9 @@ def _get_spectrum_data_cube_measurement_document(
spectrum_data_cube
)

return measurement_doc
return add_custom_information_document(
measurement_doc, measurement.measurement_custom_info
)

def _get_sample_document(self, measurement: Measurement) -> SampleDocument:
sample_doc = SampleDocument(
Expand Down
22 changes: 13 additions & 9 deletions src/allotropy/parsers/moldev_softmax_pro/softmax_pro_data_creator.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@

from dateutil import parser

from allotropy.allotrope.models.shared.definitions.custom import TQuantityValueNanometer
from allotropy.allotrope.models.shared.definitions.definitions import (
FieldComponentDatatype,
)
Expand Down Expand Up @@ -39,6 +40,7 @@
Referenceable,
)
from allotropy.parsers.utils.uuids import random_uuid_str
from allotropy.parsers.utils.values import quantity_or_none


def create_metadata(file_path: str) -> Metadata:
Expand Down Expand Up @@ -117,13 +119,22 @@ def _get_spectrum_data_cube(


def _create_spectrum_measurement(
plate_block: PlateBlock, data_elements: list[DataElement]
plate_block: PlateBlock, data_elements: list[DataElement], position: str
) -> Measurement | None:
measurement_type = plate_block.measurement_type
first_data_element = data_elements[0]
spectrum_data_cube = _get_spectrum_data_cube(plate_block, data_elements)
if not spectrum_data_cube:
return None
if isinstance(plate_block.block_data.raw_data, SpectrumRawPlateData):
first_data_element.custom_info.update(
{
"maximum wavelength signal": quantity_or_none(
TQuantityValueNanometer,
plate_block.block_data.raw_data.maximum_wavelength_signal[position],
)
}
)

# Collect error documents and update error_feature to include wavelength with unit
error_documents = []
Expand Down Expand Up @@ -183,7 +194,7 @@ def _create_measurements(plate_block: PlateBlock, position: str) -> list[Measure
MeasurementType.EMISSION_LUMINESCENCE_CUBE_SPECTRUM,
MeasurementType.EXCITATION_LUMINESCENCE_CUBE_SPECTRUM,
):
measurement = _create_spectrum_measurement(plate_block, data_elements)
measurement = _create_spectrum_measurement(plate_block, data_elements, position)
if not measurement:
return []
return [measurement]
Expand Down Expand Up @@ -263,12 +274,6 @@ def _create_measurement_group(
if not (measurements := _create_measurements(plate_block, position)):
return None

maximum_wavelength_signal = None
if isinstance(plate_block.block_data.raw_data, SpectrumRawPlateData):
maximum_wavelength_signal = (
plate_block.block_data.raw_data.maximum_wavelength_signal[position]
)

measurement_time = DEFAULT_EPOCH_TIMESTAMP
if date_last_saved:
delta = datetime.timedelta(seconds=plate_block.header.read_time or 0)
Expand All @@ -278,7 +283,6 @@ def _create_measurement_group(
measurements=measurements,
plate_well_count=plate_block.header.num_wells,
measurement_time=measurement_time,
maximum_wavelength_signal=maximum_wavelength_signal,
)


Expand Down
2 changes: 1 addition & 1 deletion src/allotropy/parsers/moldev_softmax_pro/softmax_pro_structure.py
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Original file line number Diff line number Diff line change
Expand Up @@ -375,7 +375,7 @@ class DataElement:
position: str
value: float | None
error_document: list[ErrorDocument]
custom_info: dict[str, str] = field(default_factory=dict)
custom_info: dict[str, Any] = field(default_factory=dict)
elapsed_time: list[float] = field(default_factory=list)
kinetic_measures: list[float | None] = field(default_factory=list)
sample_id: str | None = None
Expand Down
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