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refactor: Consolidate calculated data documents into shared mapping #1223

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33c7b11
refactor: Consolidate calculated data documents into shared mapping
nathan-stender Jun 8, 2026
2da3d2a
Merge branch 'main' into refactor/consolidate-calculated-data-documents
nathan-stender Jun 11, 2026
70b1ecc
refactor: Replace calcdocs helper function pyramids with declarative …
nathan-stender Jun 11, 2026
2fd392c
refactor: Replace string source references with direct object references
nathan-stender Jun 12, 2026
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35 changes: 9 additions & 26 deletions ...ma_mappers/adm/binding_affinity_analyzer/benchling/_2024/_12/binding_affinity_analyzer.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,6 @@
DataSourceDocumentItem,
DataSystemDocument,
)
from allotropy.allotrope.models.shared.definitions.definitions import TQuantityValue
from allotropy.allotrope.models.shared.definitions.quantity_values import (
TQuantityValueDegreeCelsius,
TQuantityValueMicroliterPerMinute,
Expand All @@ -46,6 +45,9 @@
from allotropy.parsers.utils.calculated_data_documents.definition import (
CalculatedDocument,
)
from allotropy.parsers.utils.calculated_data_documents.mapping import (
map_calculated_data_documents,
)
from allotropy.parsers.utils.values import assert_not_none, quantity_or_none
from allotropy.types import DictType

Expand Down Expand Up @@ -392,29 +394,10 @@ def _get_surface_plasmon_resonance_measurement_document(
def _get_calculated_data_aggregate_document(
self, calculated_data_items: list[CalculatedDocument] | None
) -> CalculatedDataAggregateDocument | None:
if not calculated_data_items:
return None

return CalculatedDataAggregateDocument(
calculated_data_document=[
CalculatedDataDocumentItem(
calculated_data_identifier=calculated_data_item.uuid,
calculated_data_name=calculated_data_item.name,
calculation_description=calculated_data_item.description,
calculated_result=TQuantityValue(
value=calculated_data_item.value,
unit=assert_not_none(calculated_data_item.unit),
),
data_source_aggregate_document=DataSourceAggregateDocument(
data_source_document=[
DataSourceDocumentItem(
data_source_identifier=item.reference.uuid,
data_source_feature=item.feature,
)
for item in calculated_data_item.data_sources
]
),
)
for calculated_data_item in calculated_data_items
]
return map_calculated_data_documents( # type: ignore[no-any-return]
calculated_data_items,
CalculatedDataAggregateDocument,
CalculatedDataDocumentItem,
DataSourceAggregateDocument,
DataSourceDocumentItem,
)
57 changes: 15 additions & 42 deletions src/allotropy/allotrope/schema_mappers/adm/cell_counting/rec/_2024/_09/cell_counting.py
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -27,10 +27,6 @@
ImageAggregateDocument,
ImageDocumentItem,
)
from allotropy.allotrope.models.shared.definitions.definitions import (
JsonFloat,
TQuantityValue,
)
from allotropy.allotrope.models.shared.definitions.quantity_values import (
TQuantityValueCell,
TQuantityValueMicroliter,
Expand All @@ -41,7 +37,12 @@
)
from allotropy.allotrope.schema_mappers.schema_mapper import SchemaMapper
from allotropy.constants import ASM_CONVERTER_VERSION
from allotropy.parsers.utils.calculated_data_documents.definition import DataSource
from allotropy.parsers.utils.calculated_data_documents.definition import (
CalculatedDocument,
)
from allotropy.parsers.utils.calculated_data_documents.mapping import (
map_calculated_data_documents,
)
from allotropy.parsers.utils.values import quantity_or_none


Expand Down Expand Up @@ -145,20 +146,10 @@ class Metadata:


@dataclass(frozen=True)
class CalculatedDataItem:
identifier: str
name: str
value: JsonFloat
unit: str
data_sources: list[DataSource]
description: str | None = None


@dataclass
class Data:
metadata: Metadata
measurement_groups: list[MeasurementGroup]
calculated_data: list[CalculatedDataItem] | None = None
calculated_data: list[CalculatedDocument] | None = None


def has_value(model: object) -> bool:
Expand Down Expand Up @@ -210,7 +201,7 @@ def _get_technique_document(
self,
measurement_group: MeasurementGroup,
metadata: Metadata,
calculated_data: list[CalculatedDataItem] | None = None,
calculated_data: list[CalculatedDocument] | None = None,
) -> CellCountingDocumentItem:
return CellCountingDocumentItem(
analyst=measurement_group.analyst,
Expand Down Expand Up @@ -418,30 +409,12 @@ def _get_error_aggregate_document(
)

def _get_calculated_data_aggregate_document(
self, calculated_data_items: list[CalculatedDataItem] | None
self, calculated_data_items: list[CalculatedDocument] | None
) -> CalculatedDataAggregateDocument | None:
if not calculated_data_items:
return None

return CalculatedDataAggregateDocument(
calculated_data_document=[
CalculatedDataDocumentItem(
calculated_data_identifier=calculated_data_item.identifier,
calculated_data_name=calculated_data_item.name,
calculated_result=TQuantityValue(
value=calculated_data_item.value,
unit=calculated_data_item.unit,
),
data_source_aggregate_document=DataSourceAggregateDocument(
data_source_document=[
DataSourceDocumentItem(
data_source_identifier=item.reference.uuid,
data_source_feature=item.feature,
)
for item in calculated_data_item.data_sources
]
),
)
for calculated_data_item in calculated_data_items
]
return map_calculated_data_documents( # type: ignore[no-any-return]
calculated_data_items,
CalculatedDataAggregateDocument,
CalculatedDataDocumentItem,
DataSourceAggregateDocument,
DataSourceDocumentItem,
)
62 changes: 16 additions & 46 deletions ...tropy/allotrope/schema_mappers/adm/electrophoresis/benchling/_2024/_09/electrophoresis.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -26,10 +26,7 @@
ProcessedDataDocumentItem,
SampleDocument,
)
from allotropy.allotrope.models.shared.definitions.definitions import (
JsonFloat,
TQuantityValue,
)
from allotropy.allotrope.models.shared.definitions.definitions import JsonFloat
from allotropy.allotrope.models.shared.definitions.quantity_values import (
TQuantityValueDegreeCelsius,
TQuantityValuePercent,
Expand All @@ -38,6 +35,12 @@
)
from allotropy.allotrope.schema_mappers.schema_mapper import SchemaMapper
from allotropy.constants import ASM_CONVERTER_VERSION
from allotropy.parsers.utils.calculated_data_documents.definition import (
CalculatedDocument,
)
from allotropy.parsers.utils.calculated_data_documents.mapping import (
map_calculated_data_documents,
)
from allotropy.parsers.utils.values import (
quantity_or_none,
quantity_or_none_from_unit,
Expand Down Expand Up @@ -67,21 +70,6 @@ class ProcessedData:
data_regions: list[ProcessedDataFeature]


@dataclass(frozen=True)
class DataSource:
identifier: str
feature: str


@dataclass(frozen=True)
class CalculatedDataItem:
identifier: str
name: str
value: float
unit: str
data_sources: list[DataSource]


@dataclass(frozen=True)
class Error:
error: str
Expand All @@ -106,7 +94,7 @@ class Measurement:
compartment_temperature: float | None = None

# Optional processed data
calculated_data: list[CalculatedDataItem] | None = None
calculated_data: list[CalculatedDocument] | None = None

# Errors
errors: list[Error] | None = None
Expand Down Expand Up @@ -146,7 +134,7 @@ class Metadata:
class Data:
metadata: Metadata
measurement_groups: list[MeasurementGroup]
calculated_data: list[CalculatedDataItem] | None = None
calculated_data: list[CalculatedDocument] | None = None


class Mapper(SchemaMapper[Data, Model]):
Expand Down Expand Up @@ -309,32 +297,14 @@ def _get_data_region_agg_document(
)

def _get_calculated_data_aggregate_document(
self, calculated_data_items: list[CalculatedDataItem] | None
self, calculated_data_items: list[CalculatedDocument] | None
) -> CalculatedDataAggregateDocument | None:
if not calculated_data_items:
return None

return CalculatedDataAggregateDocument(
calculated_data_document=[
CalculatedDataDocumentItem(
calculated_data_identifier=calculated_data_item.identifier,
calculated_data_name=calculated_data_item.name,
calculated_result=TQuantityValue(
value=calculated_data_item.value,
unit=calculated_data_item.unit,
),
data_source_aggregate_document=DataSourceAggregateDocument(
data_source_document=[
DataSourceDocumentItem(
data_source_identifier=item.identifier,
data_source_feature=item.feature,
)
for item in calculated_data_item.data_sources
]
),
)
for calculated_data_item in calculated_data_items
]
return map_calculated_data_documents( # type: ignore[no-any-return]
calculated_data_items,
CalculatedDataAggregateDocument,
CalculatedDataDocumentItem,
DataSourceAggregateDocument,
DataSourceDocumentItem,
)

def _get_error_aggregate_document(
Expand Down
35 changes: 10 additions & 25 deletions ...schema_mappers/adm/multi_analyte_profiling/benchling/_2024/_09/multi_analyte_profiling.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -47,6 +47,9 @@
from allotropy.parsers.utils.calculated_data_documents.definition import (
CalculatedDocument,
)
from allotropy.parsers.utils.calculated_data_documents.mapping import (
map_calculated_data_documents,
)
from allotropy.parsers.utils.values import quantity_or_none


Expand Down Expand Up @@ -350,29 +353,11 @@ def _get_error_aggregate_document(
def _get_calculated_data_aggregate_document(
self, calculated_data_items: list[CalculatedDocument] | None
) -> CalculatedDataAggregateDocument | None:
if not calculated_data_items:
return None

return CalculatedDataAggregateDocument(
calculated_data_document=[
CalculatedDataDocumentItem(
calculated_data_identifier=calculated_data_item.uuid,
calculated_data_name=calculated_data_item.name,
calculation_description=calculated_data_item.description,
calculated_result=TQuantityValue(
value=calculated_data_item.value,
unit=calculated_data_item.unit or Unitless.unit,
),
data_source_aggregate_document=DataSourceAggregateDocument(
data_source_document=[
DataSourceDocumentItem(
data_source_identifier=item.reference.uuid,
data_source_feature=item.feature,
)
for item in calculated_data_item.data_sources
]
),
)
for calculated_data_item in calculated_data_items
]
return map_calculated_data_documents( # type: ignore[no-any-return]
calculated_data_items,
CalculatedDataAggregateDocument,
CalculatedDataDocumentItem,
DataSourceAggregateDocument,
DataSourceDocumentItem,
unit_fallback=Unitless.unit,
)
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