From 4d02859e8b3d3b701232f18a83233644ca09fcd5 Mon Sep 17 00:00:00 2001
From: Nathan Stender <nathan.stender@benchling.com>
Date: Tue, 7 Apr 2026 03:26:00 -0400
Subject: [PATCH] fix: Use immutable copy pattern for WellItem result
 attachment

Previously, WellItem._result was mutated after construction inside
_create_measurement(), violating the intended immutability of the
private field. This was a temporary workaround added during the PR #546
refactor when Result was changed from a public mutable field to a
private field with property accessor.

The root issue: WellItem and Result data come from different file
sections and are parsed at different times, but calculated documents
need access to result data through well items.

Solution: Use dataclasses.replace() to create immutable copies of
WellItem with _result properly set at construction time. This avoids
mutation while maintaining the architectural separation between
"wells without results" and "wells with results".

Changes:
- Added enrich_wells_with_results() that returns new Well/WellItem
  instances with results attached via dataclasses.replace()
- Removed TODO and mutation from _create_measurement()
- Parser now uses enriched_wells for both calculated documents and
  measurements

All tests pass, no golden file changes.

Co-Authored-By: Claude Opus 4.1 <noreply@anthropic.com>
---
 .../appbio_quantstudio_data_creator.py        | 26 +++++++++++++++++--
 .../appbio_quantstudio_parser.py              |  8 ++++--
 2 files changed, 30 insertions(+), 4 deletions(-)

diff --git a/src/allotropy/parsers/appbio_quantstudio/appbio_quantstudio_data_creator.py b/src/allotropy/parsers/appbio_quantstudio/appbio_quantstudio_data_creator.py
index d8571c9ead..38883603c4 100644
--- a/src/allotropy/parsers/appbio_quantstudio/appbio_quantstudio_data_creator.py
+++ b/src/allotropy/parsers/appbio_quantstudio/appbio_quantstudio_data_creator.py
@@ -241,8 +241,6 @@ def _create_measurement(
 ) -> Measurement | None:
     if not result:
         return None
-    # TODO: temp workaround for cal doc result
-    well_item._result = result
 
     (
         reporter_dye_data_cube,
@@ -332,6 +330,30 @@ def get_well_item_results(
     )
 
 
+def enrich_wells_with_results(
+    wells: list[Well],
+    results_data: dict[int, dict[str, Result]],
+) -> list[Well]:
+    """Return new Wells with results attached to well items via immutable copy.
+
+    This creates new WellItem instances with _result properly set at construction time
+    (via dataclasses.replace), avoiding mutation of the private field after creation.
+    """
+    from dataclasses import replace
+
+    enriched_wells = []
+    for well in wells:
+        enriched_items = []
+        for well_item in well.items:
+            result = get_well_item_results(well_item, results_data)
+            if result:
+                enriched_items.append(replace(well_item, _result=result))
+            else:
+                enriched_items.append(well_item)
+        enriched_wells.append(replace(well, items=enriched_items))
+    return enriched_wells
+
+
 def get_well_item_amp_data(
     well_item: WellItem, amp_data: dict[int, dict[str, AmplificationData]]
 ) -> AmplificationData | None:
diff --git a/src/allotropy/parsers/appbio_quantstudio/appbio_quantstudio_parser.py b/src/allotropy/parsers/appbio_quantstudio/appbio_quantstudio_parser.py
index d0937e9e5a..12d0b6518d 100644
--- a/src/allotropy/parsers/appbio_quantstudio/appbio_quantstudio_parser.py
+++ b/src/allotropy/parsers/appbio_quantstudio/appbio_quantstudio_parser.py
@@ -8,6 +8,7 @@
     create_calculated_data,
     create_measurement_groups,
     create_metadata,
+    enrich_wells_with_results,
 )
 from allotropy.parsers.appbio_quantstudio.appbio_quantstudio_reader import (
     AppBioQuantStudioReader,
@@ -41,8 +42,11 @@ def parse_data(
         results_data, result_metadata = Result.create(reader, header.experiment_type)
         melt_data = MeltCurveRawData.create(reader)
 
+        # Create immutable copies of wells with results attached
+        enriched_wells = enrich_wells_with_results(wells, results_data)
+
         calculated_data_documents = iter_calculated_data_documents(
-            [well_item for well in wells for well_item in well.items],
+            [well_item for well in enriched_wells for well_item in well.items],
             header.experiment_type,
             result_metadata.reference_sample_description,
             result_metadata.reference_dna_description,
@@ -52,7 +56,7 @@ def parse_data(
             metadata=create_metadata(header, original_file_path),
             measurement_groups=create_measurement_groups(
                 header,
-                wells,
+                enriched_wells,
                 amp_data,
                 multi_data,
                 results_data,