Merge branch 'main' into alpha_gen5

.github/workflows/test.yml

@@ -47,5 +47,5 @@ jobs:
     steps:
     - uses: actions/checkout@v3
     - name: Check CHANGELOG
-      if: ${{ !startsWith(github.event.pull_request.title, 'internal:') }}
+      if: ${{ !startsWith(github.event.pull_request.title, 'internal:') && !startsWith(github.event.pull_request.title, 'chore:') }}
       run: ./scripts/check_changelog

CHANGELOG.md

@@ -8,8 +8,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ## [Unreleased]
 
 ### Added
-
+- Add Mabtech Apex adapter
+- Added support for parsing Vi-Cell XR txt files
+- Add Electrophoresis BENCHLING/2024/06 schema.
 - Added github enforcement that CHANGELOG.md is updated
+- Added test files Agilent TapeStation Analysis
 
 ### Fixed
 

README.md

@@ -23,6 +23,7 @@ We currently have parser support for the following instruments (* asterisk indic
   - ChemoMetec Nucleoview
   - CTL ImmunoSpot
   - Luminex xPONENT
+  - *Mabtech Apex
   - Methodical Mind
   - Molecular Devices SoftMax Pro
   - NovaBio Flex2

src/allotropy/allotrope/models/adm/electrophoresis/benchling/_2024/_06/electrophoresis.py

@@ -0,0 +1,331 @@
+# generated by datamodel-codegen:
+#   filename:  electrophoresis.schema.json
+#   timestamp: 2024-06-13T15:59:35+00:00
+
+from __future__ import annotations
+
+from dataclasses import dataclass
+from typing import Any
+
+from allotropy.allotrope.models.shared.definitions.custom import (
+    TQuantityValueDegreeCelsius,
+    TQuantityValueKiloDalton,
+    TQuantityValueMilliAbsorbanceUnit,
+    TQuantityValueNanometer,
+    TQuantityValueNumber,
+    TQuantityValuePercent,
+    TQuantityValueRelativeFluorescenceUnit,
+    TQuantityValueSecondTime,
+    TQuantityValueUnitless,
+)
+from allotropy.allotrope.models.shared.definitions.definitions import (
+    TClass,
+    TDatacube,
+    TDateTimeStampValue,
+    TStatisticDatumRole,
+    TStringValue,
+    TUnit,
+)
+
+
+@dataclass(kw_only=True)
+class DiagnosticTraceDocumentItem:
+    description: Any
+
+
+@dataclass(kw_only=True)
+class DiagnosticTraceAggregateDocument:
+    diagnostic_trace_document: list[DiagnosticTraceDocumentItem] | None = None
+
+
+@dataclass(kw_only=True)
+class AdmCoreREC202403ManifestSchema:
+    vocabulary: list[str]
+    json_schemas: list[str]
+    field_id: str | None = None
+    field_type: str | None = None
+    shapes: list[str] | None = None
+
+
+@dataclass(kw_only=True)
+class OrderedItem:
+    field_index: int | None = None
+
+
+@dataclass(kw_only=True)
+class DataSourceDocumentItem:
+    data_source_identifier: TStringValue
+    data_source_feature: TStringValue
+    field_index: int | None = None
+
+
+@dataclass(kw_only=True)
+class DataSourceAggregateDocument:
+    data_source_document: list[DataSourceDocumentItem]
+
+
+@dataclass(kw_only=True)
+class ErrorDocumentItem:
+    error: TStringValue
+    error_feature: TStringValue | None = None
+
+
+@dataclass(kw_only=True)
+class ErrorAggregateDocument:
+    error_document: list[ErrorDocumentItem] | None = None
+
+
+@dataclass(kw_only=True)
+class ProcessedDataDocumentItem1(OrderedItem):
+    data_processing_document: dict[str, Any] | None = None
+    data_source_aggregate_document: DataSourceAggregateDocument | None = None
+    processed_data_identifier: TStringValue | None = None
+
+
+@dataclass(kw_only=True)
+class ProcessedDataAggregateDocument:
+    processed_data_document: list[ProcessedDataDocumentItem1]
+
+
+@dataclass(kw_only=True)
+class StatisticsDocumentItem:
+    statistical_feature: TClass
+
+
+@dataclass(kw_only=True)
+class StatisticsAggregateDocument:
+    statistics_document: list[StatisticsDocumentItem] | None = None
+
+
+@dataclass(kw_only=True)
+class TIntegerValue1:
+    field_type: TClass
+    value: int
+
+
+TIntegerValue = int | TIntegerValue1
+
+
+@dataclass(kw_only=True)
+class TQuantityValueModel:
+    value: float
+    unit: TUnit
+    has_statistic_datum_role: TStatisticDatumRole | None = None
+    field_type: TClass | None = None
+
+
+@dataclass(kw_only=True)
+class DeviceDocumentItem:
+    device_type: TStringValue
+    device_identifier: TStringValue | None = None
+    model_number: TStringValue | None = None
+    product_manufacturer: TStringValue | None = None
+    brand_name: TStringValue | None = None
+    equipment_serial_number: TStringValue | None = None
+    firmware_version: TStringValue | None = None
+    field_index: int | None = None
+
+
+@dataclass(kw_only=True)
+class DeviceSystemDocument:
+    asset_management_identifier: TStringValue | None = None
+    description: Any | None = None
+    brand_name: TStringValue | None = None
+    product_manufacturer: TStringValue | None = None
+    device_identifier: TStringValue | None = None
+    model_number: TStringValue | None = None
+    equipment_serial_number: TStringValue | None = None
+    firmware_version: TStringValue | None = None
+    device_document: list[DeviceDocumentItem] | None = None
+
+
+@dataclass(kw_only=True)
+class DataSystemDocument:
+    data_system_instance_identifier: TStringValue | None = None
+    file_name: TStringValue | None = None
+    UNC_path: TStringValue | None = None
+    software_name: TStringValue | None = None
+    software_version: TStringValue | None = None
+    ASM_converter_name: TStringValue | None = None
+    ASM_converter_version: TStringValue | None = None
+
+
+@dataclass(kw_only=True)
+class DeviceControlDocumentItem:
+    device_type: TStringValue
+    device_identifier: TStringValue | None = None
+    detection_type: TStringValue | None = None
+    product_manufacturer: TStringValue | None = None
+    brand_name: TStringValue | None = None
+    equipment_serial_number: TStringValue | None = None
+    model_number: TStringValue | None = None
+    firmware_version: TStringValue | None = None
+    field_index: int | None = None
+    detector_wavelength_setting: TQuantityValueNanometer | None = None
+    detector_bandwidth_setting: TQuantityValueNanometer | None = None
+    excitation_wavelength_setting: TQuantityValueNanometer | None = None
+    excitation_bandwidth_setting: TQuantityValueNanometer | None = None
+
+
+@dataclass(kw_only=True)
+class DeviceControlAggregateDocument:
+    device_control_document: list[DeviceControlDocumentItem]
+
+
+@dataclass(kw_only=True)
+class SampleDocument:
+    sample_identifier: TStringValue
+    description: Any | None = None
+    batch_identifier: TStringValue | None = None
+    sample_role_type: TClass | None = None
+    written_name: TStringValue | None = None
+    location_identifier: TStringValue | None = None
+
+
+@dataclass(kw_only=True)
+class PeakItem:
+    peak_identifier: TStringValue
+    peak_name: TStringValue | None = None
+    written_name: TStringValue | None = None
+    peak_height: TQuantityValueMilliAbsorbanceUnit | TQuantityValueRelativeFluorescenceUnit | None = (
+        None
+    )
+    relative_peak_height: TQuantityValueKiloDalton | TQuantityValueNumber | TQuantityValueSecondTime | None = (
+        None
+    )
+    peak_start: TQuantityValueKiloDalton | TQuantityValueNumber | TQuantityValueSecondTime | None = (
+        None
+    )
+    peak_end: TQuantityValueKiloDalton | TQuantityValueNumber | TQuantityValueSecondTime | None = (
+        None
+    )
+    peak_position: TQuantityValueKiloDalton | TQuantityValueNumber | TQuantityValueSecondTime | None = (
+        None
+    )
+    peak_area: TQuantityValueUnitless | None = None
+    relative_peak_area: TQuantityValuePercent | None = None
+    relative_corrected_peak_area: TQuantityValuePercent | None = None
+    comment: TStringValue | None = None
+    field_index: int | None = None
+
+
+@dataclass(kw_only=True)
+class PeakList:
+    peak: list[PeakItem]
+
+
+@dataclass(kw_only=True)
+class DataRegionDocumentItem:
+    region_identifier: TStringValue
+    region_name: TStringValue | None = None
+    written_name: TStringValue | None = None
+    region_start: TQuantityValueKiloDalton | TQuantityValueNumber | TQuantityValueSecondTime | None = (
+        None
+    )
+    region_end: TQuantityValueKiloDalton | TQuantityValueNumber | TQuantityValueSecondTime | None = (
+        None
+    )
+    region_area: TQuantityValueUnitless | None = None
+    relative_region_area: TQuantityValuePercent | None = None
+    comment: TStringValue | None = None
+
+
+@dataclass(kw_only=True)
+class DataRegionAggregateDocument:
+    data_region_document: list[DataRegionDocumentItem]
+
+
+@dataclass(kw_only=True)
+class CalculatedDataDocumentItem:
+    calculated_data_name: TStringValue
+    calculated_result: TQuantityValueModel
+    data_source_aggregate_document: DataSourceAggregateDocument | None = None
+    calculated_data_identifier: TStringValue | None = None
+    calculation_description: TStringValue | None = None
+    field_index: int | None = None
+
+
+@dataclass(kw_only=True)
+class CalculatedDataAggregateDocument:
+    calculated_data_document: list[CalculatedDataDocumentItem]
+
+
+@dataclass(kw_only=True)
+class ImageDocumentItem:
+    index: TIntegerValue | None = None
+    experimental_data_identifier: TStringValue | None = None
+
+
+@dataclass(kw_only=True)
+class ImageAggregateDocument:
+    image_document: list[ImageDocumentItem] | None = None
+
+
+@dataclass(kw_only=True)
+class ProcessedDataDocumentItem:
+    peak_list: PeakList
+    data_processing_document: dict[str, Any] | None = None
+    data_source_aggregate_document: DataSourceAggregateDocument | None = None
+    processed_data_identifier: TStringValue | None = None
+    field_index: int | None = None
+    derived_electropherogram_data_cube: TDatacube | None = None
+    data_region_aggregate_document: DataRegionAggregateDocument | None = None
+
+
+@dataclass(kw_only=True)
+class ProcessedDataAggregateDocument1:
+    processed_data_document: list[ProcessedDataDocumentItem]
+
+
+@dataclass(kw_only=True)
+class MeasurementDocumentItem:
+    measurement_time: TDateTimeStampValue
+    measurement_identifier: TStringValue
+    device_control_aggregate_document: DeviceControlAggregateDocument
+    sample_document: SampleDocument
+    processed_data_aggregate_document: ProcessedDataAggregateDocument1
+    detection_type: TStringValue | None = None
+    calculated_data_aggregate_document: CalculatedDataAggregateDocument | None = None
+    statistics_aggregate_document: StatisticsAggregateDocument | None = None
+    image_aggregate_document: ImageAggregateDocument | None = None
+    error_aggregate_document: ErrorAggregateDocument | None = None
+    compartment_temperature: TQuantityValueDegreeCelsius | None = None
+    electropherogram_data_cube: TDatacube | None = None
+
+
+@dataclass(kw_only=True)
+class MeasurementAggregateDocument:
+    measurement_document: list[MeasurementDocumentItem]
+    diagnostic_trace_aggregate_document: DiagnosticTraceAggregateDocument | None = None
+    processed_data_aggregate_document: ProcessedDataAggregateDocument | None = None
+    calculated_data_aggregate_document: CalculatedDataAggregateDocument | None = None
+    statistics_aggregate_document: StatisticsAggregateDocument | None = None
+    image_aggregate_document: ImageAggregateDocument | None = None
+    error_aggregate_document: ErrorAggregateDocument | None = None
+
+
+@dataclass(kw_only=True)
+class ElectrophoresisDocumentItem:
+    measurement_aggregate_document: MeasurementAggregateDocument
+    analyst: TStringValue | None = None
+    submitter: TStringValue | None = None
+    analytical_method_identifier: TStringValue | None = None
+    method_version: TStringValue | None = None
+    experimental_data_identifier: TStringValue | None = None
+    experiment_type: TStringValue | None = None
+
+
+@dataclass(kw_only=True)
+class ElectrophoresisAggregateDocument:
+    data_system_document: DataSystemDocument
+    electrophoresis_document: list[ElectrophoresisDocumentItem]
+    device_system_document: DeviceSystemDocument | None = None
+    processed_data_aggregate_document: ProcessedDataAggregateDocument | None = None
+    calculated_data_aggregate_document: CalculatedDataAggregateDocument | None = None
+    statistics_aggregate_document: StatisticsAggregateDocument | None = None
+
+
+@dataclass(kw_only=True)
+class Model:
+    electrophoresis_aggregate_document: ElectrophoresisAggregateDocument
+    field_asm_manifest: AdmCoreREC202403ManifestSchema | str

src/allotropy/allotrope/models/shared/definitions/custom.py

@@ -15,6 +15,7 @@
     DegreeCelsius,
     GramPerLiter,
     Hertz,
+    KiloDalton,
     MicrogramPerMicroliter,
     MicrogramPerMilliliter,
     Microliter,
@@ -149,6 +150,16 @@ class TNullableQuantityValueHertz(Hertz, TNullableQuantityValue):
     pass
 
 
+@dataclass(frozen=True, kw_only=True)
+class TQuantityValueKiloDalton(KiloDalton, TQuantityValue):
+    pass
+
+
+@dataclass(frozen=True, kw_only=True)
+class TNullableQuantityValueKiloDalton(KiloDalton, TNullableQuantityValue):
+    pass
+
+
 @dataclass(frozen=True, kw_only=True)
 class TQuantityValueMicrogramPerMicroliter(MicrogramPerMicroliter, TQuantityValue):
     pass

src/allotropy/allotrope/models/shared/definitions/units.py

@@ -54,6 +54,11 @@ class Hertz(HasUnit):
     unit: str = "Hz"
 
 
+@dataclass(frozen=True, kw_only=True)
+class KiloDalton(HasUnit):
+    unit: str = "kDa"
+
+
 @dataclass(frozen=True, kw_only=True)
 class MicrogramPerMicroliter(HasUnit):
     unit: str = "ug/uL"