Merge branch 'main' of github.com:Benchling-Open-Source/allotropy into ctl_immunospot_get_unread

Author: oscar-castro-bl

src/allotropy/parsers/moldev_softmax_pro/softmax_pro_data_creator.py

@@ -249,7 +249,10 @@ def _create_measurements(plate_block: PlateBlock, position: str) -> list[Measure
 
 
 def _create_measurement_group(
-    plate_block: PlateBlock, position: str, date_last_saved: str | None
+    plate_block: PlateBlock,
+    position: str,
+    date_last_saved: str | None,
+    structure_data: StructureData,
 ) -> MeasurementGroup | None:
 
     if not (measurements := _create_measurements(plate_block, position)):
@@ -260,10 +263,41 @@ def _create_measurement_group(
         delta = datetime.timedelta(seconds=plate_block.header.read_time or 0)
         measurement_time = (parser.parse(date_last_saved) + delta).isoformat()
 
+    # Gather unread group fields for this plate/position
+    unread_rows: list[dict[str, float | str | None]] = []
+    single_plate_name: str | None = None
+    if len(structure_data.block_list.plate_blocks) == 1:
+        single_plate_name = next(iter(structure_data.block_list.plate_blocks.keys()))
+
+    for group_block in structure_data.block_list.group_blocks:
+        for group_sample_data in group_block.group_data.sample_data:
+            for (
+                plate_key,
+                positions_map,
+            ) in group_sample_data.unread_by_plate_and_position.items():
+                effective_plate = (
+                    plate_key if plate_key is not None else single_plate_name
+                )
+                # filters out unread entries that do not belong to the current plate
+                if effective_plate != plate_block.header.name:
+                    continue
+                if position in positions_map:
+                    unread_rows.extend(positions_map[position])
+
+    # Flatten unread rows into a single custom_info dict
+    custom_info = None
+    if unread_rows:
+        merged = {}
+        for row_dict in unread_rows:
+            # Only include keys with non-None values
+            merged.update({k: v for k, v in row_dict.items() if v is not None})
+        custom_info = merged
+
     return MeasurementGroup(
         measurements=measurements,
         plate_well_count=plate_block.header.num_wells,
         measurement_time=measurement_time,
+        custom_info=custom_info,
     )
 
 
@@ -274,7 +308,7 @@ def create_measurement_groups(data: StructureData) -> list[MeasurementGroup]:
         for position in plate_block.iter_wells()
         if (
             measurement_group := _create_measurement_group(
-                plate_block, position, data.date_last_saved
+                plate_block, position, data.date_last_saved, data
             )
         )
     ]

src/allotropy/parsers/moldev_softmax_pro/softmax_pro_structure.py

@@ -128,6 +128,10 @@ class GroupDataElement:
 class GroupSampleData:
     identifier: str
     data_elements: list[GroupDataElement]
+    # Capture unread fields per plate and well position. The None key is used when plate is unspecified.
+    unread_by_plate_and_position: dict[
+        str | None, dict[str, list[dict[str, float | str | None]]]
+    ]
 
     @classmethod
     def create(cls, data: pd.DataFrame, calc_data_cols: list[str]) -> GroupSampleData:
@@ -141,6 +145,9 @@ def create(cls, data: pd.DataFrame, calc_data_cols: list[str]) -> GroupSampleDat
         data_elements: dict[str, list[GroupDataElement]] = {
             column: [] for column in data_columns
         }
+        unread_by_plate_and_position: dict[
+            str | None, dict[str, list[dict[str, float | str | None]]]
+        ] = {}
         for row in row_data:
             row_results = cls._get_row_results(row, data_columns)
             position = row[str, ["Well", "Wells"]]
@@ -170,12 +177,17 @@ def create(cls, data: pd.DataFrame, calc_data_cols: list[str]) -> GroupSampleDat
                     )
                 elif data_elements[column]:
                     data_elements[column][-1].positions.append(position)
+            unread = row.get_unread(skip={"Sample"})
+            if unread:
+                by_position = unread_by_plate_and_position.setdefault(plate, {})
+                by_position.setdefault(str(position), []).append(unread)
 
         return GroupSampleData(
             identifier=identifier,
             data_elements=[
                 elem for elements in data_elements.values() for elem in elements
             ],
+            unread_by_plate_and_position=unread_by_plate_and_position,
         )
 
     @classmethod