feat: Add unread keys to custom information document

src/allotropy/allotrope/converter.py

@@ -80,12 +80,14 @@
 
 
 DICT_KEY_TO_MODEL_KEY_REPLACEMENTS = {
+    ".": "_POINT_",
     "-": "_DASH_",
     "°": "_DEG_",
     "/": "_SLASH_",
     "\\": "_BSLASH_",
     "(": "_OPAREN_",
     ")": "_CPAREN_",
+    "%": "_PERCENT_",
     # NOTE: this MUST be at the end, or it will break other key replacements.
     " ": "_",
 }
@@ -108,6 +110,8 @@
 def add_custom_information_document(
     model: ModelClass, custom_info_doc: Any
 ) -> ModelClass:
+    if not custom_info_doc:
+        return model
 
     if isinstance(custom_info_doc, dict):
         custom_info_doc = structure_custom_information_document(

src/allotropy/allotrope/schema_mappers/adm/pcr/BENCHLING/_2023/_09/qpcr.py

@@ -1,6 +1,6 @@
 from collections.abc import Callable
 from dataclasses import dataclass
-from typing import TypeVar
+from typing import Any, TypeVar
 
 from allotropy.allotrope.converter import add_custom_information_document
 from allotropy.allotrope.models.adm.pcr.benchling._2023._09.qpcr import (
@@ -101,14 +101,6 @@ class ProcessedData:
     normalized_reporter_result: float | None = None
     baseline_corrected_reporter_result: float | None = None
 
-    # Metadata
-    comments: str | None = None
-    highsd: str | None = None
-    noamp: str | None = None
-    expfail: str | None = None
-    tholdfail: str | None = None
-    prfdrop: str | None = None
-
     data_cubes: list[DataCube] | None = None
 
 
@@ -138,13 +130,7 @@ class Measurement:
     processed_data: ProcessedData | None = None
     data_cubes: list[DataCube] | None = None
 
-    # Custom metadata
-    well_identifier: int | None = None
-    omit: bool | None = None
-    sample_color: str | None = None
-    biogroup_name: str | None = None
-    biogroup_color: str | None = None
-    target_color: str | None = None
+    custom_info: dict[str, Any] | None = None
 
 
 @dataclass
@@ -170,6 +156,7 @@ class Metadata:
     software_name: str | None = None
     software_version: str | None = None
     product_manufacturer: str | None = None
+    custom_info: dict[str, Any] | None = None
 
 
 @dataclass
@@ -218,17 +205,20 @@ def _get_technique_document(
     ) -> QPCRDocumentItem:
         return QPCRDocumentItem(
             analyst=measurement_group.analyst,
-            measurement_aggregate_document=MeasurementAggregateDocument(
-                experimental_data_identifier=measurement_group.experimental_data_identifier,
-                experiment_type=metadata.experiment_type,
-                container_type=metadata.container_type,
-                plate_well_count=TQuantityValueNumber(
-                    value=measurement_group.plate_well_count
+            measurement_aggregate_document=add_custom_information_document(
+                MeasurementAggregateDocument(
+                    experimental_data_identifier=measurement_group.experimental_data_identifier,
+                    experiment_type=metadata.experiment_type,
+                    container_type=metadata.container_type,
+                    plate_well_count=TQuantityValueNumber(
+                        value=measurement_group.plate_well_count
+                    ),
+                    measurement_document=[
+                        self._get_measurement_document_item(measurement, metadata)
+                        for measurement in measurement_group.measurements
+                    ],
                 ),
-                measurement_document=[
-                    self._get_measurement_document_item(measurement, metadata)
-                    for measurement in measurement_group.measurements
-                ],
+                metadata.custom_info,
             ),
         )
 
@@ -237,9 +227,6 @@ def _get_measurement_document_item(
         measurement: Measurement,
         metadata: Metadata,
     ) -> MeasurementDocumentItem:
-        custom_doc = {
-            "omit": measurement.omit,
-        }
         measurement_doc = MeasurementDocumentItem(
             measurement_identifier=measurement.identifier,
             measurement_time=self.get_date_time(measurement.timestamp),
@@ -275,82 +262,65 @@ def _get_measurement_document_item(
                 MeltingCurveDataCube, "melting curve", measurement.data_cubes
             ),
         )
-        return add_custom_information_document(measurement_doc, custom_doc)
+        return add_custom_information_document(measurement_doc, measurement.custom_info)
 
     def _get_sample_document(self, measurement: Measurement) -> SampleDocument:
-        custom_doc = {
-            "well identifier": measurement.well_identifier,
-            "sample color": measurement.sample_color,
-            "biogroup name": measurement.biogroup_name,
-            "biogroup color": measurement.biogroup_color,
-            "target color": measurement.target_color,
-        }
-        sample_doc = SampleDocument(
+        return SampleDocument(
             sample_identifier=measurement.sample_identifier,
             sample_role_type=measurement.sample_role_type,
             well_location_identifier=measurement.well_location_identifier,
             well_plate_identifier=measurement.well_plate_identifier,
         )
-        return add_custom_information_document(sample_doc, custom_doc)
 
     def _get_processed_data_aggregate_document(
         self, data: ProcessedData | None
     ) -> ProcessedDataAggregateDocument | None:
         if not data:
             return None
+
         return ProcessedDataAggregateDocument(
             processed_data_document=[
-                add_custom_information_document(
-                    ProcessedDataDocumentItem(
-                        data_processing_document=DataProcessingDocument(
-                            automatic_cycle_threshold_enabled_setting=data.automatic_cycle_threshold_enabled_setting,
-                            cycle_threshold_value_setting=TQuantityValueUnitless(
-                                value=data.cycle_threshold_value_setting,
-                            ),
-                            automatic_baseline_determination_enabled_setting=data.automatic_baseline_determination_enabled_setting,
-                            genotyping_determination_method_setting=quantity_or_none(
-                                TQuantityValueUnitless,
-                                data.genotyping_determination_method_setting,
-                            ),
-                            baseline_determination_start_cycle_setting=quantity_or_none(
-                                TQuantityValueNumber,
-                                data.baseline_determination_start_cycle_setting,
-                            ),
-                            baseline_determination_end_cycle_setting=quantity_or_none(
-                                TQuantityValueNumber,
-                                data.baseline_determination_end_cycle_setting,
-                            ),
-                        ),
-                        cycle_threshold_result=TNullableQuantityValueUnitless(
-                            value=data.cycle_threshold_result,
-                        ),
-                        normalized_reporter_result=quantity_or_none(
-                            TQuantityValueUnitless, data.normalized_reporter_result
+                ProcessedDataDocumentItem(
+                    data_processing_document=DataProcessingDocument(
+                        automatic_cycle_threshold_enabled_setting=data.automatic_cycle_threshold_enabled_setting,
+                        cycle_threshold_value_setting=TQuantityValueUnitless(
+                            value=data.cycle_threshold_value_setting,
                         ),
-                        baseline_corrected_reporter_result=quantity_or_none(
+                        automatic_baseline_determination_enabled_setting=data.automatic_baseline_determination_enabled_setting,
+                        genotyping_determination_method_setting=quantity_or_none(
                             TQuantityValueUnitless,
-                            data.baseline_corrected_reporter_result,
+                            data.genotyping_determination_method_setting,
                         ),
-                        genotyping_determination_result=data.genotyping_determination_result,
-                        normalized_reporter_data_cube=self._get_data_cube(
-                            NormalizedReporterDataCube,
-                            "normalized reporter",
-                            data.data_cubes,
+                        baseline_determination_start_cycle_setting=quantity_or_none(
+                            TQuantityValueNumber,
+                            data.baseline_determination_start_cycle_setting,
                         ),
-                        baseline_corrected_reporter_data_cube=self._get_data_cube(
-                            BaselineCorrectedReporterDataCube,
-                            "baseline corrected reporter",
-                            data.data_cubes,
+                        baseline_determination_end_cycle_setting=quantity_or_none(
+                            TQuantityValueNumber,
+                            data.baseline_determination_end_cycle_setting,
                         ),
                     ),
-                    custom_info_doc={
-                        "comments": data.comments,
-                        "highsd": data.highsd,
-                        "noamp": data.noamp,
-                        "expfail": data.expfail,
-                        "tholdfail": data.tholdfail,
-                        "prfdrop": data.prfdrop,
-                    },
+                    cycle_threshold_result=TNullableQuantityValueUnitless(
+                        value=data.cycle_threshold_result,
+                    ),
+                    normalized_reporter_result=quantity_or_none(
+                        TQuantityValueUnitless, data.normalized_reporter_result
+                    ),
+                    baseline_corrected_reporter_result=quantity_or_none(
+                        TQuantityValueUnitless,
+                        data.baseline_corrected_reporter_result,
+                    ),
+                    genotyping_determination_result=data.genotyping_determination_result,
+                    normalized_reporter_data_cube=self._get_data_cube(
+                        NormalizedReporterDataCube,
+                        "normalized reporter",
+                        data.data_cubes,
+                    ),
+                    baseline_corrected_reporter_data_cube=self._get_data_cube(
+                        BaselineCorrectedReporterDataCube,
+                        "baseline corrected reporter",
+                        data.data_cubes,
+                    ),
                 )
             ]
         )

src/allotropy/parsers/appbio_quantstudio/appbio_quantstudio_data_creator.py

@@ -81,12 +81,6 @@ def _create_processed_data(
         cycle_threshold_result=result.cycle_threshold_result,
         normalized_reporter_result=result.normalized_reporter_result,
         baseline_corrected_reporter_result=result.baseline_corrected_reporter_result,
-        comments=result.comments,
-        highsd=result.highsd,
-        noamp=result.noamp,
-        expfail=result.expfail,
-        tholdfail=result.tholdfail,
-        prfdrop=result.prfdrop,
         data_cubes=_create_processed_data_cubes(amplification_data),
     )
 
@@ -187,24 +181,23 @@ def _create_measurement(
         sample_identifier=well_item.sample_identifier,
         sample_role_type=well_item.sample_role_type,
         well_location_identifier=well_item.well_location_identifier,
-        well_identifier=well_item.identifier,
         well_plate_identifier=header.barcode,
-        omit=result.omit,
-        sample_color=well_item.sample_color,
-        biogroup_name=well_item.biogroup_name,
-        biogroup_color=well_item.biogroup_color,
-        target_color=well_item.target_color,
         total_cycle_number_setting=amplification_data.total_cycle_number_setting,
         pcr_detection_chemistry=header.pcr_detection_chemistry,
         reporter_dye_setting=well_item.reporter_dye_setting,
         quencher_dye_setting=well_item.quencher_dye_setting,
         passive_reference_dye_setting=header.passive_reference_dye_setting,
         processed_data=_create_processed_data(amplification_data, result),
+        custom_info=(well_item.extra_data or {})
+        | (result.extra_data or {})
+        | {"well identifier": well_item.identifier},
         data_cubes=data_cubes,
     )
 
 
-def create_metadata(header: Header, file_name: str) -> Metadata:
+def create_metadata(
+    header: Header, results_metadata: ResultMetadata, file_name: str
+) -> Metadata:
     return Metadata(
         device_identifier=header.device_identifier,
         device_type=constants.DEVICE_TYPE,
@@ -218,6 +211,7 @@ def create_metadata(header: Header, file_name: str) -> Metadata:
         measurement_method_identifier=header.measurement_method_identifier,
         experiment_type=header.experiment_type,
         container_type=constants.CONTAINER_TYPE,
+        custom_info=header.extra_data | results_metadata.extra_data,
     )
 
 

src/allotropy/parsers/appbio_quantstudio/appbio_quantstudio_parser.py

@@ -53,7 +53,9 @@ def create_data(self, named_file_contents: NamedFileContents) -> Data:
         )
 
         return Data(
-            metadata=create_metadata(header, named_file_contents.original_file_name),
+            metadata=create_metadata(
+                header, results_metadata, named_file_contents.original_file_name
+            ),
             measurement_groups=create_measurement_groups(
                 header, wells, amp_data, multi_data, results_data, melt_data
             ),