feat: AppBio QuantStudio Design & Analysis - remove duplicates and hardcoded values from measurement custom info doc (#1088)

Co-authored-by: Nathan Stender <nathan.stender@benchling.com>

Author: joshua-benchling

src/allotropy/parsers/appbio_quantstudio/appbio_quantstudio_data_creator.py

@@ -125,10 +125,19 @@ def _create_processed_data(
     data_processing_custom_info = {
         "reference dna description": result_metadata.reference_dna_description,
         "reference sample description": result_metadata.reference_sample_description,
-        "Analysis Type": "SinglePlex",
-        "RQ Min/Max Confidence Level": 0.95,
     }
 
+    # Add Analysis Type and RQ Min/Max Confidence Level only if present in instrument file
+    if result_metadata.extra_data:
+        if "Analysis Type" in result_metadata.extra_data:
+            data_processing_custom_info["Analysis Type"] = result_metadata.extra_data[
+                "Analysis Type"
+            ]
+        if "RQ Min/Max Confidence Level" in result_metadata.extra_data:
+            data_processing_custom_info[
+                "RQ Min/Max Confidence Level"
+            ] = result_metadata.extra_data["RQ Min/Max Confidence Level"]
+
     for field in data_processing_field_names:
         if field in extra_data:
             data_processing_custom_info[field] = extra_data[field]
@@ -269,7 +278,6 @@ def _create_measurement(
         reporter_dye_data_cube=reporter_dye_data_cube,
         passive_reference_dye_data_cube=passive_reference_dye_data_cube,
         melting_curve_data_cube=_create_melt_curve_data_cube(melt_curve_raw_data),
-        custom_info=result_metadata.extra_data,
     )
 
 

src/allotropy/parsers/appbio_quantstudio_designandanalysis/appbio_quantstudio_designandanalysis_data_creator.py

@@ -110,11 +110,20 @@ def _create_processed_data(well_item: WellItem, data: Data) -> ProcessedData:
         "CQCONF": custom_info.get("CQCONF", "N"),
         "NOISE": custom_info.get("NOISE", "N"),
         "OUTLIERRG": custom_info.get("OUTLIERRG", "N"),
-        "Analysis Type": "SinglePlex",
-        "RQ Min/Max Confidence Level": 0.95,
         "Omit": custom_info.get("Omit", False),
     }
 
+    # Add Analysis Type and RQ Min/Max Confidence Level only if present in instrument file
+    if data.header.extra_data:
+        if "Analysis Type" in data.header.extra_data:
+            data_processing_custom_info["Analysis Type"] = data.header.extra_data[
+                "Analysis Type"
+            ]
+        if "RQ Min/Max Confidence Level" in data.header.extra_data:
+            data_processing_custom_info[
+                "RQ Min/Max Confidence Level"
+            ] = data.header.extra_data["RQ Min/Max Confidence Level"]
+
     return ProcessedData(
         automatic_cycle_threshold_enabled_setting=result.automatic_cycle_threshold_enabled_setting,
         cycle_threshold_value_setting=result.cycle_threshold_value_setting,