feat: Mass spectrometer ASM schema (#1121)

Taken from
https://gitlab.com/allotrope-public/asm/-/blob/main/json-schemas/adm/mass-spectrometry/REC/2025/06/mass-spectrometry.tabular.embed.schema.json?ref_type=heads

Co-authored-by: joshua-benchling <jherna@benchling.com>

Author: felipenarv

src/allotropy/allotrope/models/adm/mass_spectrometry/__init__.py

@@ -0,0 +1,139 @@
+# generated by datamodel-codegen:
+#   filename:  mass-spectrometry.schema.json
+#   timestamp: 2025-11-05T18:53:18+00:00
+
+from __future__ import annotations
+
+from dataclasses import dataclass
+
+from allotropy.allotrope.models.shared.definitions.custom import (
+    TQuantityValueDalton,
+    TQuantityValueHertz,
+    TQuantityValueMassPerCharge,
+    TQuantityValueMilliliterPerMinute,
+    TQuantityValuePercent,
+    TQuantityValueSecondTime,
+)
+from allotropy.allotrope.models.shared.definitions.definitions import (
+    TClass,
+    TQuantityValue,
+    TStringValue,
+)
+
+TNamed = str
+
+
+@dataclass(kw_only=True)
+class DeviceDocumentItem:
+    device_type: TClass
+    model_number: TStringValue
+    product_manufacturer: TStringValue
+
+
+@dataclass(kw_only=True)
+class DeviceSystemDocument:
+    asset_management_identifier: TStringValue
+    device_document: list[DeviceDocumentItem] | None = None
+
+
+@dataclass(kw_only=True)
+class DataProcessingDocumentItem:
+    data_processing_type: TStringValue | None = None
+
+
+@dataclass(kw_only=True)
+class DataProcessingAggregateDocument:
+    data_processing_document: list[DataProcessingDocumentItem] | None = None
+
+
+@dataclass(kw_only=True)
+class DetectorControlDocumentItem:
+    detection_type: TStringValue
+    detection_duration_setting: TQuantityValueSecondTime | None = None
+    detector_relative_offset_setting: TQuantityValueSecondTime | None = None
+    detector_sampling_rate_setting: TQuantityValueHertz | None = None
+    m_z_maximum_setting: TQuantityValueMassPerCharge | None = None
+    m_z_minimum_setting: TQuantityValueMassPerCharge | None = None
+    polarity_setting: TNamed | None = None
+    field_index: int | None = None
+
+
+@dataclass(kw_only=True)
+class DetectorControlAggregateDocument:
+    detector_control_document: list[DetectorControlDocumentItem] | None = None
+
+
+@dataclass(kw_only=True)
+class MeasurementDocument:
+    measurement_mode_setting: TStringValue
+    detector_control_aggregate_document: DetectorControlAggregateDocument | None = None
+
+
+@dataclass(kw_only=True)
+class ProcessedDataDocumentItem:
+    data_format_specification_type: TStringValue
+
+
+@dataclass(kw_only=True)
+class ProcessedDataAggregateDocument:
+    processed_data_document: list[ProcessedDataDocumentItem] | None = None
+
+
+@dataclass(kw_only=True)
+class SampleDocument:
+    sample_identifier: TStringValue
+
+
+@dataclass(kw_only=True)
+class SampleIntroductionDocument:
+    sample_introduction_medium: TStringValue
+    sample_introduction_mode_setting: TStringValue
+    flow_rate_setting: TQuantityValueMilliliterPerMinute | None = None
+    laser_firing_frequency_setting: TQuantityValueHertz | None = None
+    sample_introduction_description: TStringValue | None = None
+
+
+@dataclass(kw_only=True)
+class MassSpectrometryDocumentItem:
+    analyst: TStringValue
+    submitter: TStringValue
+    data_processing_aggregate_document: DataProcessingAggregateDocument | None = None
+    measurement_document: MeasurementDocument | None = None
+    processed_data_aggregate_document: ProcessedDataAggregateDocument | None = None
+    sample_document: SampleDocument | None = None
+    sample_introduction_document: SampleIntroductionDocument | None = None
+
+
+@dataclass(kw_only=True)
+class MassSpectrometryAggregateDocument:
+    device_system_document: DeviceSystemDocument | None = None
+    mass_spectrometry_document: list[MassSpectrometryDocumentItem] | None = None
+
+
+@dataclass(kw_only=True)
+class PeakItem:
+    identifier: TStringValue | None = None
+    m_z: TQuantityValueMassPerCharge | None = None
+    mass: TQuantityValueDalton | None = None
+    peak_area: TQuantityValue | None = None
+    peak_height: TQuantityValue | None = None
+    peak_width: TQuantityValue | None = None
+    relative_peak_area: TQuantityValuePercent | None = None
+    relative_peak_height: TQuantityValuePercent | None = None
+    written_name: TStringValue | None = None
+    field_index: int | None = None
+
+
+@dataclass(kw_only=True)
+class PeakList:
+    peak: list[PeakItem] | None = None
+
+
+@dataclass(kw_only=True)
+class Model:
+    manifest: str = "http://purl.allotrope.org/manifests/mass-spectrometry/REC/2025/06/mass-spectrometry.manifest"
+    data_processing_description: TStringValue | None = None
+    mass_spectrometry_aggregate_document: MassSpectrometryAggregateDocument | None = (
+        None
+    )
+    peak_list: PeakList | None = None

src/allotropy/allotrope/models/adm/mass_spectrometry/rec/_2025/_06/__init__.py

@@ -20,6 +20,7 @@
     Hertz,
     KiloDalton,
     KiloPascal,
+    MassPerCharge,
     MicrogramPerMicroliter,
     MicrogramPerMilliliter,
     Microliter,
@@ -227,6 +228,16 @@ class TNullableQuantityValueKiloPascal(KiloPascal, TNullableQuantityValue):
     pass
 
 
+@dataclass(frozen=True, kw_only=True)
+class TQuantityValueMassPerCharge(MassPerCharge, TQuantityValue):
+    pass
+
+
+@dataclass(frozen=True, kw_only=True)
+class TNullableQuantityValueMassPerCharge(MassPerCharge, TNullableQuantityValue):
+    pass
+
+
 @dataclass(frozen=True, kw_only=True)
 class TQuantityValueMicrogramPerMicroliter(MicrogramPerMicroliter, TQuantityValue):
     pass

src/allotropy/allotrope/models/adm/mass_spectrometry/rec/_2025/_06/mass_spectrometry.py

@@ -79,6 +79,11 @@ class KiloPascal(HasUnit):
     unit: str = "kPa"
 
 
+@dataclass(frozen=True, kw_only=True)
+class MassPerCharge(HasUnit):
+    unit: str = "m/z"
+
+
 @dataclass(frozen=True, kw_only=True)
 class MicrogramPerMicroliter(HasUnit):
     unit: str = "ug/µL"