feat: Unchained Labs Lunatic & Stunner - Add support for Stunner files (#1054)

* Migrate Unchained Labs Lunatic adapter to plate reader 05/03 schema
* Add support for Stunner files
* Rename adapter to "Unchained Labs Lunatic & Stunner"
* Add support for error documents for fields containing "N/A" value,
report calculated data as -0.0 for errored fields.

Author: joshua-benchling

SUPPORTED_INSTRUMENT_SOFTWARE.adoc

@@ -47,7 +47,7 @@ The parsers follow maturation levels of: Recommended, Candidate Release, Working
 |Revvity Kaleido|Recommended|BENCHLING/2023/09
 |Tecan Magellan|Recommended|REC/2024/06
 |Thermo Fisher Scientific SkanIt|Recommended|REC/2025/03
-|Unchained Labs Lunatic|Recommended|REC/2024/06
+|Unchained Labs Lunatic & Stunner|Recommended|REC/2025/03
 .3+|Solution Analyzer|Beckman Coulter PharmSpec|Recommended|REC/2024/09
 |NovaBio Flex2|Recommended|BENCHLING/2024/09
 |Roche Cedex BioHT|Recommended|REC/2024/09

…unchained_labs_lunatic/images/image1.png …d_labs_lunatic_stunner/images/image1.pngdocs/parser_requirements/unchained_labs_lunatic/images/image1.png renamed to docs/parser_requirements/unchained_labs_lunatic_stunner/images/image1.png docs/parser_requirements/unchained_labs_lunatic/images/image1.png renamed to docs/parser_requirements/unchained_labs_lunatic_stunner/images/image1.png

@@ -104,6 +104,8 @@
     "~": "_TILDE_",
     "?": "_QMARK_",
     "^": "_CARET_",
+    "=": "_EQUALS_",
+    "@": "_AT_",
     # NOTE: this MUST be at the end, or it will break other key replacements.
     " ": "_",
 }

…unchained_labs_lunatic/images/image2.png …d_labs_lunatic_stunner/images/image2.pngdocs/parser_requirements/unchained_labs_lunatic/images/image2.png renamed to docs/parser_requirements/unchained_labs_lunatic_stunner/images/image2.png docs/parser_requirements/unchained_labs_lunatic/images/image2.png renamed to docs/parser_requirements/unchained_labs_lunatic_stunner/images/image2.png

@@ -17,6 +17,8 @@
     MeasurementAggregateDocument,
     MeasurementDocument,
     Model,
+    PeakItem,
+    PeakList,
     PlateReaderAggregateDocument,
     PlateReaderDocumentItem,
     ProcessedDataAggregateDocument,
@@ -27,6 +29,7 @@
 from allotropy.allotrope.models.shared.components.plate_reader import SampleRoleType
 from allotropy.allotrope.models.shared.definitions.custom import (
     TQuantityValueDegreeCelsius,
+    TQuantityValueKiloDalton,
     TQuantityValueMilliAbsorbanceUnit,
     TQuantityValueMillimeter,
     TQuantityValueMilliSecond,
@@ -120,6 +123,7 @@ class ErrorDocument:
 class ProcessedDataDocument:
     identifier: str | None = None
     concentration_factor: float | None = None
+    peak_list_custom_info: list[dict[str, Any]] | None = None
 
 
 @dataclass
@@ -164,6 +168,7 @@ class Measurement:
     wavelength_identifier: str | None = None
     analytical_method_identifier: str | None = None
     experimental_data_identifier: str | None = None
+    integration_time: float | None = None
 
     auto_focus_enabled_setting: bool | None = None
     exposure_duration_setting: float | None = None
@@ -323,6 +328,9 @@ def _get_ultraviolet_absorbance_measurement_document(
                 TQuantityValueNanometer,
                 measurement.electronic_absorbance_reference_wavelength_setting,
             ),
+            integration_time=quantity_or_none(
+                TQuantityValueSecondTime, measurement.integration_time
+            ),
             device_type=measurement.device_type,
             detection_type=measurement.detection_type,
             detector_wavelength_setting=quantity_or_none(
@@ -386,12 +394,30 @@ def _get_ultraviolet_absorbance_measurement_document(
                 processed_data_document=[
                     ProcessedDataDocumentItem(
                         processed_data_identifier=measurement.processed_data_document.identifier,
-                        data_processing_document={
-                            "concentration factor": quantity_or_none(
-                                TQuantityValueNanogramPerMicroliter,
-                                measurement.processed_data_document.concentration_factor,
-                            )
-                        },
+                        data_processing_document=(
+                            {
+                                "concentration factor": quantity_or_none(
+                                    TQuantityValueNanogramPerMicroliter,
+                                    measurement.processed_data_document.concentration_factor,
+                                )
+                            }
+                            if measurement.processed_data_document.concentration_factor
+                            is not None
+                            else None
+                        ),
+                        peak_list=PeakList(
+                            peak=[
+                                add_custom_information_document(
+                                    PeakItem(),
+                                    self._process_peak_custom_info(peak_custom_info),
+                                )
+                                for peak_custom_info in (
+                                    measurement.processed_data_document.peak_list_custom_info
+                                )
+                            ]
+                        )
+                        if measurement.processed_data_document.peak_list_custom_info
+                        else None,
                     )
                 ]
             )
@@ -834,3 +860,25 @@ def _get_error_aggregate_document(
             if error_documents
             else None
         )
+
+    def _process_peak_custom_info(
+        self, peak_custom_info: dict[str, Any]
+    ) -> dict[str, Any]:
+        """Process peak custom info by applying proper units to measured values."""
+        processed_info: dict[str, Any] = {}
+
+        for key, value in peak_custom_info.items():
+            if key == "peak mean diameter":
+                processed_info[key] = quantity_or_none(TQuantityValueNanometer, value)
+            elif key == "peak mode diameter":
+                processed_info[key] = quantity_or_none(TQuantityValueNanometer, value)
+            elif key == "peak est. MW":
+                processed_info[key] = quantity_or_none(TQuantityValueKiloDalton, value)
+            elif key == "peak intensity":
+                processed_info[key] = quantity_or_none(TQuantityValuePercent, value)
+            elif key == "peak mass":
+                processed_info[key] = quantity_or_none(TQuantityValuePercent, value)
+            else:
+                processed_info[key] = value
+
+        return processed_info

…_lunatic/unchained_labs_lunatic_req.html …_stunner/unchained_labs_lunatic_req.htmldocs/parser_requirements/unchained_labs_lunatic/unchained_labs_lunatic_req.html renamed to docs/parser_requirements/unchained_labs_lunatic_stunner/unchained_labs_lunatic_req.html docs/parser_requirements/unchained_labs_lunatic/unchained_labs_lunatic_req.html renamed to docs/parser_requirements/unchained_labs_lunatic_stunner/unchained_labs_lunatic_req.html

@@ -30,6 +30,8 @@ class CalculatedDataConfig:
     source_configs: tuple[CalculatedDataConfig | MeasurementConfig, ...]
     unit: str | None = None
     description: str | None = None
+    # Optional key to pull a dynamic description from the element data
+    description_value_key: str | None = None
     required: bool = False
 
     def iter_data_sources(
@@ -71,13 +73,23 @@ def _get_calc_doc_inner(
         if not data_sources:
             return None
 
+        if self.name == "B22 goodness of fit":
+            pass
         return CalculatedDocument(
             uuid=random_uuid_str(),
             name=self.name,
             value=value,
             data_sources=data_sources,
             unit=self.unit,
-            description=self.description,
+            description=(
+                self.description
+                if self.description is not None
+                else (
+                    elements[0].get_str_or_none(self.description_value_key)
+                    if self.description_value_key
+                    else None
+                )
+            ),
         )
 
     def get_cache_key(self, keys: Keys) -> str:

src/allotropy/allotrope/converter.py

@@ -1,4 +1,4 @@
-from allotropy.allotrope.schema_mappers.adm.plate_reader.rec._2024._06.plate_reader import (
+from allotropy.allotrope.schema_mappers.adm.plate_reader.rec._2025._03.plate_reader import (
     Measurement,
 )
 from allotropy.calcdocs.extractor import Element, Extractor
@@ -19,6 +19,7 @@ def to_element(cls, measurement: Measurement) -> Element:
                 "uuid": measurement.identifier,
                 "wavelength id": measurement.wavelength_identifier,
                 "absorbance": measurement.absorbance,
+                "detection type": measurement.detection_type,
                 **custom_info,
             },
         )

src/allotropy/allotrope/schema_mappers/adm/plate_reader/rec/_2025/_03/plate_reader.py

@@ -16,3 +16,15 @@ def sort_elements(self, elements: list[Element]) -> dict[str, list[Element]]:
             if uuid := element.get_str("uuid"):
                 items[uuid].append(element)
         return dict(items)
+
+
+class DetectionTypeView(View):
+    def __init__(self, sub_view: View | None = None):
+        super().__init__(name="detection_type", sub_view=sub_view)
+
+    def sort_elements(self, elements: list[Element]) -> dict[str, list[Element]]:
+        items = defaultdict(list)
+        for element in elements:
+            if detection_type := element.get_str("detection type"):
+                items[detection_type].append(element)
+        return dict(items)

src/allotropy/calcdocs/config.py

@@ -119,8 +119,8 @@
     ThermoFisherVisionliteParser,
 )
 from allotropy.parsers.thermo_skanit.thermo_skanit_parser import ThermoSkanItParser
-from allotropy.parsers.unchained_labs_lunatic.unchained_labs_lunatic_parser import (
-    UnchainedLabsLunaticParser,
+from allotropy.parsers.unchained_labs_lunatic_stunner.unchained_labs_lunatic_stunner_parser import (
+    UnchainedLabsLunaticStunnerParser,
 )
 from allotropy.parsers.utils.timestamp_parser import TimestampParser
 from allotropy.parsers.vendor_parser import VendorParser
@@ -273,7 +273,7 @@ def get_parser(
     Vendor.THERMO_FISHER_QUBIT_FLEX: ThermoFisherQubitFlexParser,
     Vendor.THERMO_FISHER_VISIONLITE: ThermoFisherVisionliteParser,
     Vendor.THERMO_SKANIT: ThermoSkanItParser,
-    Vendor.UNCHAINED_LABS_LUNATIC: UnchainedLabsLunaticParser,
+    Vendor.UNCHAINED_LABS_LUNATIC: UnchainedLabsLunaticStunnerParser,
 }