feat: Migrate example_weyland_yutani to REC/2025/03 plate reader schema (#1177)

## Summary

- Migrate `example_weyland_yutani` tutorial parser from
BENCHLING/2023/09 to REC/2025/03 plate reader schema mapper
- First step in upgrading plate reader parsers off vendor-specific
BENCHLING schemas

## Code Changes

**Parser file**: Updated model and mapper imports from
`benchling._2023._09` → `rec._2025._03`

**Structure file**:
- Updated schema mapper imports
- Added two new required `Metadata` fields: `asm_file_identifier` and
`data_system_instance_id`
- Moved `analytical_method_identifier` and
`experimental_data_identifier` from `MeasurementGroup` to individual
`Measurement` instances (per REC/2025/03 schema structure)

## JSON Output Changes

All measurement data values are preserved identically. Structural
changes:

| Change | Details |
|--------|---------|
| Manifest URL | `BENCHLING/2023/09` → `REC/2025/03` |
| New fields | `ASM file identifier`, `data system instance identifier`
(N/A) |
| Field moves | `analytical method identifier` and `experimental data
identifier` moved from `measurement aggregate document` to each
`measurement document` item |
| Field ordering | Some fields reordered within objects (cosmetic,
different model field order) |

**Fields deleted in test data:**
- `root['plate reader aggregate document']['plate reader
document'][0]['measurement aggregate document']['analytical method
identifier']`
- `root['plate reader aggregate document']['plate reader
document'][0]['measurement aggregate document']['experimental data
identifier']`

(These fields moved to individual measurement documents, not actually
lost)

## Migration Status (Plate Reader BENCHLING Parsers)

| Parser | Status | Reason |
|--------|--------|--------|
| example_weyland_yutani | **This PR** | FLUORESCENCE only — clean
migration |
| mabtech_apex | Blocked | OPTICAL_IMAGING only — type removed from REC
|
| agilent_gen5_image | Blocked | OPTICAL_IMAGING only — type removed
from REC |
| ctl_immunospot | Blocked | OPTICAL_IMAGING only — type removed from
REC |
| revvity_kaleido | Blocked | Mixed types including OPTICAL_IMAGING |

## Test plan

- [x] `pytest tests/parsers/example_weyland_yutani/ --force-overwrite` —
2/2 pass
- [x] Full lint (ruff + black + mypy) — clean
- [x] Pre-push hook — 547/547 tests pass

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>

Author: nathan-stender

src/allotropy/parsers/example_weyland_yutani/example_weyland_yutani_parser.py

@@ -1,7 +1,7 @@
-from allotropy.allotrope.models.adm.plate_reader.benchling._2023._09.plate_reader import (
+from allotropy.allotrope.models.adm.plate_reader.rec._2025._03.plate_reader import (
     Model,
 )
-from allotropy.allotrope.schema_mappers.adm.plate_reader.benchling._2023._09.plate_reader import (
+from allotropy.allotrope.schema_mappers.adm.plate_reader.rec._2025._03.plate_reader import (
     Data,
     Mapper,
 )

src/allotropy/parsers/example_weyland_yutani/example_weyland_yutani_structure.py

@@ -5,13 +5,14 @@
 
 import pandas as pd
 
-from allotropy.allotrope.schema_mappers.adm.plate_reader.benchling._2023._09.plate_reader import (
+from allotropy.allotrope.schema_mappers.adm.plate_reader.rec._2025._03.plate_reader import (
     Measurement,
     MeasurementGroup,
     MeasurementType,
     Metadata,
 )
 from allotropy.exceptions import AllotropeConversionError
+from allotropy.parsers.constants import NOT_APPLICABLE
 from allotropy.parsers.example_weyland_yutani import constants
 from allotropy.parsers.utils.uuids import random_uuid_str
 
@@ -88,8 +89,11 @@ def create(df: pd.DataFrame | None) -> list[Plate]:
 
 
 def create_metadata(instrument: Instrument, file_path: str) -> Metadata:
+    path = Path(file_path)
     return Metadata(
-        file_name=Path(file_path).name,
+        asm_file_identifier=path.with_suffix(".json").name,
+        data_system_instance_id=NOT_APPLICABLE,
+        file_name=path.name,
         unc_path=file_path,
         model_number=instrument.serial_number,
         device_identifier=instrument.nickname,
@@ -101,8 +105,6 @@ def create_measurement_group(
 ) -> MeasurementGroup:
     return MeasurementGroup(
         plate_well_count=plate.number_of_wells,
-        analytical_method_identifier=basic_assay_info.protocol_id,
-        experimental_data_identifier=basic_assay_info.assay_id,
         # TODO(tutorial): extract and return actual measurement time
         measurement_time="2022-12-31",
         measurements=[
@@ -114,6 +116,8 @@ def create_measurement_group(
                 sample_identifier=f"Plate {plate.number}",
                 location_identifier=f"{result.col}{result.row}",
                 fluorescence=result.value,
+                analytical_method_identifier=basic_assay_info.protocol_id,
+                experimental_data_identifier=basic_assay_info.assay_id,
             )
             for result in plate.results
         ],