feat: Add electrophoresis/BENCHLING/2024/09 schema and mapper and upd…

…ate Aglient Tapestation parser to use it. (#715) - Move electrophoresis rec 09/24 as benchling 09/24 schema - Implement schema mapper for electrophoresis benchling 09/24 - Update Agilent Tapestation Analysis parser to use electrophoresis benchling 09/24 schema
Benchling-Open-Source · Oct 15, 2024 · 17481d1 · 17481d1
1 parent 0c6854e
commit 17481d1
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Showing 11 changed files with 8,158 additions and 7,464 deletions.
diff --git a/...electrophoresis/rec/_2024/_09/__init__.py → ...ophoresis/benchling/_2024/_09/__init__.py b/...electrophoresis/rec/_2024/_09/__init__.py → ...ophoresis/benchling/_2024/_09/__init__.py
diff --git a/...phoresis/rec/_2024/_09/electrophoresis.py → ...is/benchling/_2024/_09/electrophoresis.py b/...phoresis/rec/_2024/_09/electrophoresis.py → ...is/benchling/_2024/_09/electrophoresis.py
@@ -1,13 +1,15 @@
 # generated by datamodel-codegen:
 #   filename:  electrophoresis.schema.json
-#   timestamp: 2024-10-07T20:16:06+00:00
+#   timestamp: 2024-10-15T14:18:09+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,
     TQuantityValueMilliAbsorbanceUnitTimesMilliliter,
     TQuantityValueMilliAbsorbanceUnitTimesSecond,
@@ -16,8 +18,6 @@
     TQuantityValueNumber,
     TQuantityValuePercent,
     TQuantityValueRelativeFluorescenceUnit,
-    TQuantityValueRelativeFluorescenceUnitTimesMilliliter,
-    TQuantityValueRelativeFluorescenceUnitTimesSecond,
     TQuantityValueSecondTime,
     TQuantityValueUnitless,
 )
@@ -46,11 +46,6 @@ class AdmCoreREC202409ManifestSchema:
     shapes: list[str] | None = None
 
 
-@dataclass(kw_only=True)
-class OrderedItem:
-    field_index: int | None = None
-
-
 @dataclass(kw_only=True)
 class CustomInformationDocumentItem:
     scalar_double_datum: TDoubleValue | None = None
@@ -61,48 +56,13 @@ class CustomInformationDocumentItem:
     datum_label: TStringValue | None = None
 
 
-@dataclass(kw_only=True)
-class CustomInformationAggregateDocument:
-    custom_information_document: list[CustomInformationDocumentItem]
-
-
-@dataclass(kw_only=True)
-class DataSourceDocumentItem:
-    data_source_identifier: TStringValue
-    data_source_feature: TStringValue | None = None
-    field_index: int | None = None
-
-
-@dataclass(kw_only=True)
-class DataSourceAggregateDocument:
-    data_source_document: list[DataSourceDocumentItem]
-
-
 @dataclass(kw_only=True)
 class ElectronicProjectRecord:
     written_name: TStringValue
     description: Any | None = None
     start_time: TDateTimeValue | None = None
 
 
-@dataclass(kw_only=True)
-class ElectronicSignatureDocumentItem:
-    account_identifier: TStringValue
-    personal_name: TStringValue
-    signature_role_type: TStringValue
-    time: TStringValue
-    identifier: TStringValue | None = None
-    measurement_identifier: TStringValue | None = None
-    method_identifier: TStringValue | None = None
-    processed_data_identifier: TStringValue | None = None
-    field_index: int | None = None
-
-
-@dataclass(kw_only=True)
-class ElectronicSignatureAggregateDocument:
-    electronic_signature_document: list[ElectronicSignatureDocumentItem] | None = None
-
-
 @dataclass(kw_only=True)
 class ErrorDocumentItem:
     error: TStringValue
@@ -125,15 +85,6 @@ class ImageAggregateDocument:
     image_document: list[ImageDocumentItem] | None = None
 
 
-@dataclass(kw_only=True)
-class ProcessedDataAggregateDocument:
-    processed_data_document: list[ProcessedDataDocumentItem]
-    custom_information_aggregate_document: CustomInformationAggregateDocument | None = (
-        None
-    )
-    electronic_project_record: ElectronicProjectRecord | None = None
-
-
 @dataclass(kw_only=True)
 class StatisticsDocumentItem:
     statistical_feature: TClass
@@ -157,6 +108,50 @@ class AnalysisSequenceDocument:
     version_number: TStringValue | None = None
 
 
+@dataclass(kw_only=True)
+class CustomInformationAggregateDocument:
+    custom_information_document: list[CustomInformationDocumentItem]
+
+
+@dataclass(kw_only=True)
+class DataSourceDocumentItem:
+    data_source_identifier: TStringValue
+    data_source_feature: TStringValue | None = None
+    field_index: int | None = None
+
+
+@dataclass(kw_only=True)
+class DataSourceAggregateDocument:
+    data_source_document: list[DataSourceDocumentItem]
+
+
+@dataclass(kw_only=True)
+class ElectronicSignatureDocumentItem:
+    account_identifier: TStringValue
+    personal_name: TStringValue
+    signature_role_type: TStringValue
+    time: TStringValue
+    identifier: TStringValue | None = None
+    measurement_identifier: TStringValue | None = None
+    method_identifier: TStringValue | None = None
+    processed_data_identifier: TStringValue | None = None
+    field_index: int | None = None
+
+
+@dataclass(kw_only=True)
+class ElectronicSignatureAggregateDocument:
+    electronic_signature_document: list[ElectronicSignatureDocumentItem] | None = None
+
+
+@dataclass(kw_only=True)
+class ProcessedDataAggregateDocument:
+    processed_data_document: list[ProcessedDataDocumentItem] | None = None
+    custom_information_aggregate_document: CustomInformationAggregateDocument | None = (
+        None
+    )
+    electronic_project_record: ElectronicProjectRecord | None = None
+
+
 @dataclass(kw_only=True)
 class DataSystemDocument:
     ASM_file_identifier: TStringValue
@@ -258,26 +253,42 @@ class DeviceControlAggregateDocument:
     custom_information_aggregate_document: CustomInformationAggregateDocument | None = (
         None
     )
+    compartment_temperature: TQuantityValueDegreeCelsius | None = None
+    processed_data_aggregate_document: ProcessedDataAggregateDocument | None = None
 
 
 @dataclass(kw_only=True)
 class Peak:
     custom_information_aggregate_document: CustomInformationAggregateDocument | None = (
         None
     )
-    peak_end: TQuantityValueMilliliter | TQuantityValueSecondTime | None = None
+    peak_end: TQuantityValueKiloDalton | TQuantityValueMilliliter | TQuantityValueNumber | TQuantityValueSecondTime | None = (
+        None
+    )
+    peak_position: TQuantityValueKiloDalton | TQuantityValueMilliliter | TQuantityValueNumber | TQuantityValueSecondTime | None = (
+        None
+    )
+    peak_name: TStringValue | None = None
     identifier: TStringValue | None = None
-    relative_peak_height: TQuantityValuePercent | None = None
+    relative_peak_height: TQuantityValueKiloDalton | TQuantityValueNumber | TQuantityValuePercent | TQuantityValueSecondTime | None = (
+        None
+    )
     written_name: TStringValue | None = None
-    peak_height: TQuantityValue | TQuantityValueMilliAbsorbanceUnit | None = None
+    peak_height: TQuantityValue | TQuantityValueMilliAbsorbanceUnit | TQuantityValueRelativeFluorescenceUnit | None = (
+        None
+    )
     capacity_factor__chromatography_: TQuantityValueUnitless | None = None
     peak_area: TQuantityValue | TQuantityValueMilliAbsorbanceUnitTimesMilliliter | TQuantityValueMilliAbsorbanceUnitTimesSecond | None = (
         None
     )
     relative_peak_area: TQuantityValuePercent | None = None
+    relative_corrected_peak_area: TQuantityValuePercent | None = None
+    comment: TStringValue | None = None
     retention_time: TQuantityValueSecondTime | None = None
     retention_volume: TQuantityValueMilliliter | None = None
-    peak_start: TQuantityValueMilliliter | TQuantityValueSecondTime | None = None
+    peak_start: TQuantityValueKiloDalton | TQuantityValueMilliliter | TQuantityValueNumber | TQuantityValueSecondTime | None = (
+        None
+    )
     peak_selectivity__chromatography_: TQuantityValueUnitless | None = None
     chromatographic_peak_resolution: TQuantityValueUnitless | None = None
     field_index: int | None = None
@@ -339,20 +350,25 @@ class PeakList:
     custom_information_aggregate_document: CustomInformationAggregateDocument | None = (
         None
     )
-    peak: list[PeakItem] | list[Peak] | None = None
+    peak: list[Peak] | None = None
 
 
 @dataclass(kw_only=True)
 class DataRegionDocumentItem:
     custom_information_aggregate_document: CustomInformationAggregateDocument | None = (
         None
     )
-    data_region_end: TQuantityValueMilliliter | TQuantityValueSecondTime | None = None
+    data_region_end: TQuantityValueKiloDalton | TQuantityValueMilliliter | TQuantityValueNumber | TQuantityValueSecondTime | None = (
+        None
+    )
     data_region_identifier: TStringValue | None = None
     data_region_name: TStringValue | None = None
     data_region_area: TQuantityValue | None = None
     relative_data_region_area: TQuantityValuePercent | None = None
-    data_region_start: TQuantityValueMilliliter | TQuantityValueSecondTime | None = None
+    comment: TStringValue | None = None
+    data_region_start: TQuantityValueKiloDalton | TQuantityValueMilliliter | TQuantityValueNumber | TQuantityValueSecondTime | None = (
+        None
+    )
     field_index: int | None = None
 
 
@@ -369,21 +385,14 @@ class SampleDocument:
     sample_identifier: TStringValue
     batch_identifier: TStringValue | None = None
     description: Any | None = None
+    location_identifier: TStringValue | None = None
     sample_role_type: TClass | None = None
     written_name: TStringValue | None = None
     custom_information_aggregate_document: CustomInformationAggregateDocument | None = (
         None
     )
 
 
-@dataclass(kw_only=True)
-class PeakItem(OrderedItem):
-    peak_height: TQuantityValueRelativeFluorescenceUnit | None = None
-    peak_area: TQuantityValueRelativeFluorescenceUnitTimesMilliliter | TQuantityValueRelativeFluorescenceUnitTimesSecond | None = (
-        None
-    )
-
-
 @dataclass(kw_only=True)
 class CalculatedDataDocumentItem:
     calculated_data_name: TStringValue
@@ -439,26 +448,23 @@ class MeasurementDocument:
     measurement_time: TDateTimeStampValue | None = None
     processed_data_aggregate_document: ProcessedDataAggregateDocument | None = None
     statistics_aggregate_document: StatisticsAggregateDocument | None = None
+    compartment_temperature: TQuantityValueDegreeCelsius | None = None
     absorption_profile_data_cube: TDatacube | None = None
     chromatogram_data_cube: TDatacube | None = None
     three_dimensional_ultraviolet_spectrum_data_cube: TDatacube | None = None
-    processed_data_document: ProcessedDataDocument | None = None
     fluorescence_emission_profile_data_cube: TDatacube | None = None
 
 
-@dataclass(kw_only=True)
-class ProcessedDataDocument:
-    peak_list: PeakList | None = None
-    derived_electropherogram_data_cube: TDatacube | None = None
-
-
 @dataclass(kw_only=True)
 class MeasurementAggregateDocument:
     measurement_document: list[MeasurementDocument]
     calculated_data_aggregate_document: CalculatedDataAggregateDocument | None = None
     custom_information_aggregate_document: CustomInformationAggregateDocument | None = (
         None
     )
+    analytical_method_identifier: TStringValue | None = None
+    method_version: TStringValue | None = None
+    experimental_data_identifier: TStringValue | None = None
     diagnostic_trace_aggregate_document: DiagnosticTraceAggregateDocument | None = None
     error_aggregate_document: ErrorAggregateDocument | None = None
     image_aggregate_document: ImageAggregateDocument | None = None