change level of custom info fields, skip fields already mapped

Author: joshua-benchling

src/allotropy/parsers/cytiva_biacore_t200_evaluation/cytiva_biacore_t200_evaluation_data_creator.py

@@ -47,7 +47,6 @@
 from allotropy.parsers.utils.pandas import map_rows, SeriesData
 from allotropy.parsers.utils.uuids import random_uuid_str
 from allotropy.parsers.utils.values import quantity_or_none, try_float_or_none
-from allotropy.types import DictType
 
 
 def _get_sensorgram_datacube(
@@ -109,7 +108,6 @@ def create_metadata(data: Data, named_file_contents: NamedFileContents) -> Metad
             "account identifier": sys.user_name,
             "operating system type": sys.os_type,
             "operating system version": sys.os_version,
-            **sys.unread_system_data,
             **sys.unread_application_properties,
         },
     )
@@ -471,8 +469,8 @@ def create_measurement_groups(data: Data) -> list[MeasurementGroup]:
             os_type=sys.os_type,
             os_version=sys.os_version,
             measurement_time=data.run_metadata.timestamp,
-            unread_system_data=sys.unread_system_data,
             unread_application_properties=sys.unread_application_properties,
+            measurement_aggregate_fields=sys.measurement_aggregate_fields,
         )
     # As a final fallback, look directly in application_template_details.properties
     if not sys.measurement_time and data.application_template_details:
@@ -487,8 +485,8 @@ def create_measurement_groups(data: Data) -> list[MeasurementGroup]:
                 os_type=sys.os_type,
                 os_version=sys.os_version,
                 measurement_time=ts,
-                unread_system_data=sys.unread_system_data,
                 unread_application_properties=sys.unread_application_properties,
+                measurement_aggregate_fields=sys.measurement_aggregate_fields,
             )
     if not sys.measurement_time:
         msg = "Missing measurement time. Expected application_template_details.properties.Timestamp."
@@ -497,10 +495,11 @@ def create_measurement_groups(data: Data) -> list[MeasurementGroup]:
     # Process all cycles to create one measurement document per cycle
     for cycle in data.cycle_data:
         measurements = _create_measurements_for_cycle(data, cycle)
-        custom_info: DictType = {
+        custom_info: dict[str, Any] = {
             "data collection rate": quantity_or_none(
                 TQuantityValueHertz, data.run_metadata.data_collection_rate
             ),
+            **sys.measurement_aggregate_fields,
         }
         # Add aggregate-level experimental data identifier for convenience (first measurement's FC)
         if measurements:

src/allotropy/parsers/cytiva_biacore_t200_evaluation/cytiva_biacore_t200_evaluation_structure.py

@@ -172,19 +172,16 @@ def create(chip_data: DictType) -> ChipData:
 
 @dataclass(frozen=True)
 class DetectionConfig:
+    unread_detection_data: dict[str, Any]
     detection: str | None = None
     detection_dual: str | None = None
     detection_multi: str | None = None
     flow_cell_single: str | None = None
     flow_cell_dual: str | None = None
     flow_cell_multi: str | None = None
-    unread_detection_data: dict[str, Any] = field(default_factory=dict)
 
     @staticmethod
-    def create(detection: DictType | None) -> DetectionConfig:
-        if detection is None:
-            return DetectionConfig()
-
+    def create(detection: DictType) -> DetectionConfig:
         json_data = JsonData(dict(detection))
 
         return DetectionConfig(
@@ -240,7 +237,7 @@ def create(application_template_details: DictType | None) -> RunMetadata:
                 application_template_details.get("MoleculeWeightUnit", {})
             ),
             detection_config=DetectionConfig.create(
-                application_template_details.get("detection")
+                application_template_details.get("detection", {})
             ),
             buffer_volume=try_float_or_none(
                 (application_template_details.get("prepare_run", {}) or {}).get(
@@ -283,8 +280,8 @@ class SystemInformation:
     os_type: str | None
     os_version: str | None
     measurement_time: str | None
-    unread_system_data: dict[str, Any] = field(default_factory=dict)
-    unread_application_properties: dict[str, Any] = field(default_factory=dict)
+    unread_application_properties: dict[str, Any]
+    measurement_aggregate_fields: dict[str, Any]
 
     @staticmethod
     def create(
@@ -298,6 +295,35 @@ def create(
             str, "Timestamp"
         )
 
+        # Extract specific fields for measurement aggregate custom info before skipping them
+        measurement_aggregate_fields = {}
+        target_fields = [
+            "TemplateExtension",
+            "EvaluationMethodIsOptional",
+            "TypeName",
+            "AllowPublish",
+        ]
+
+        for _field in target_fields:
+            # Check both sources, preferring application properties
+            value = app_props_data.get(str, _field) or system_info_data.get(str, _field)
+            if value is not None:
+                measurement_aggregate_fields[_field] = value
+
+        # Read other fields that we want to skip to avoid JsonData warnings
+        system_info_data.get(str, "SoftwareVersion")
+        system_info_data.get(str, "Software")
+        system_info_data.get(str, "User")
+        system_info_data.get(
+            str, "Timestamp"
+        )  # Already read above but ensure both sources are marked
+        app_props_data.get(str, "SoftwareVersion")
+        app_props_data.get(str, "Software")
+        app_props_data.get(str, "User")
+        app_props_data.get(
+            str, "Timestamp"
+        )  # Already read above but ensure both sources are marked
+
         return SystemInformation(
             application_name=system_info_data.get(str, "Application"),
             application_version=system_info_data.get(str, "Version"),
@@ -308,10 +334,10 @@ def create(
             os_type=system_info_data.get(str, "OSType"),
             os_version=system_info_data.get(str, "OSVersion"),
             measurement_time=measurement_time,
-            unread_system_data=system_info_data.get_unread(skip={"HtmlPreview"}),
             unread_application_properties=app_props_data.get_unread(
-                skip={"HtmlPreview"}
+                skip={"HtmlPreview", "Timestamp"}
             ),
+            measurement_aggregate_fields=measurement_aggregate_fields,
         )
 
 

tests/parsers/cytiva_biacore_t200_evaluation/testdata/biacore_evaluation_module_example.json

@@ -741,6 +741,10 @@
                             "value": 10.0,
                             "unit": "Hz"
                         },
+                        "TemplateExtension": "Method",
+                        "EvaluationMethodIsOptional": "false",
+                        "TypeName": "Method Builder",
+                        "AllowPublish": "true",
                         "experimental data identifier": "MASKED_EXPERIMENTAL_DATA_ID"
                     }
                 },
@@ -1485,6 +1489,10 @@
                             "value": 10.0,
                             "unit": "Hz"
                         },
+                        "TemplateExtension": "Method",
+                        "EvaluationMethodIsOptional": "false",
+                        "TypeName": "Method Builder",
+                        "AllowPublish": "true",
                         "experimental data identifier": "MASKED_EXPERIMENTAL_DATA_ID"
                     }
                 },
@@ -2229,6 +2237,10 @@
                             "value": 10.0,
                             "unit": "Hz"
                         },
+                        "TemplateExtension": "Method",
+                        "EvaluationMethodIsOptional": "false",
+                        "TypeName": "Method Builder",
+                        "AllowPublish": "true",
                         "experimental data identifier": "MASKED_EXPERIMENTAL_DATA_ID"
                     }
                 },
@@ -2973,6 +2985,10 @@
                             "value": 10.0,
                             "unit": "Hz"
                         },
+                        "TemplateExtension": "Method",
+                        "EvaluationMethodIsOptional": "false",
+                        "TypeName": "Method Builder",
+                        "AllowPublish": "true",
                         "experimental data identifier": "MASKED_EXPERIMENTAL_DATA_ID"
                     }
                 },
@@ -2991,15 +3007,7 @@
             "custom information document": {
                 "account identifier": "BiacoreT200",
                 "operating system type": "Win32NT",
-                "operating system version": "6.2.9200.0",
-                "Timestamp": "06/11/2025 12:38:26",
-                "TemplateExtension": "Method",
-                "SoftwareVersion": "3.2.1",
-                "Software": "Biacore T200 Control Software",
-                "EvaluationMethodIsOptional": "false",
-                "TypeName": "Method Builder",
-                "User": "BiacoreT200",
-                "AllowPublish": "true"
+                "operating system version": "6.2.9200.0"
             }
         },
         "device system document": {