Merge branch 'main' into jherna/flowjo_migrate_get_unread

Author: nathan-stender

CHANGELOG.md

@@ -5,6 +5,47 @@ All notable changes to this packages will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.1.98] - 2025-07-08
+
+### Added
+
+- Bio-Rad Bio-Plex Manager - Add support for statistics dimensions (#1029)
+- Agilent Gen5 - Add Conc/Dil to Sample document custom fields (#1030)
+- Roche Cedex BioHT - Added support for mg/L (#1028)
+- Thermo Fisher Scientific SkanIt - Support multiplates (#1025)
+- Beckman Vi-Cell Blu - Added get_unread data to parser (#1023)
+- Molecular Devices SoftMax Pro - Enable Reduced-only file parsing (#1016)
+
+## [0.1.97] - 2025-06-24
+
+### Fixed
+
+- Agilent OpenLab CDS - use bytes to read zip file instead of file name (#1021)
+
+## [0.1.96] - 2025-06-23
+
+### Fixed
+
+- Molecular Devices SoftMax Pro - account for partial plate reads (#1013)
+
+## [0.1.95] - 2025-06-19
+
+### Added
+
+- Luminex xPONENT - migrate to BENCHLING/2024/09 schema (#1007)
+
+## [0.1.94] - 2025-06-18
+
+### Added
+
+- ChemoMetec Nucleoview - add support for tab separated files (#1015)
+- Molecular Devices SoftMax Pro - update ASM structure for spectrum data (#1012)
+- Molecular Devices SoftMax Pro - update adapter to plate reader schema REC 25/03 (#1011)
+
+### Fixed
+
+- Agilent Gen5 - fix spectrum data cube label (#1014)
+
 ## [0.1.93] - 2025-06-10
 
 ### Fixed

SUPPORTED_INSTRUMENT_SOFTWARE.adoc

@@ -31,8 +31,8 @@ The parsers follow maturation levels of: Recommended, Candidate Release, Working
 |Benchling Thermo Fisher Scientific Chromeleon|Recommended|BENCHLING/2023/09
 .2+|Liquid Handler|Beckman Coulter Biomek|Recommended|BENCHLING/2024/11
 |Beckman Echo Plate Reformat|Recommended|BENCHLING/2024/11
-.2+|Multi Analyte Profiling|Bio-Rad Bio-Plex Manager|Recommended|BENCHLING/2024/01
-|Luminex xPONENT|Recommended|BENCHLING/2024/01
+.2+|Multi Analyte Profiling|Bio-Rad Bio-Plex Manager|Recommended|BENCHLING/2024/09
+|Luminex xPONENT|Recommended|BENCHLING/2024/09
 .14+|Plate Reader|Agilent Gen5|Recommended|REC/2025/03
 |Agilent Gen5 Image|Recommended|BENCHLING/2023/09
 |BMG Labtech SMART Control|Recommended|REC/2024/06
@@ -45,7 +45,7 @@ The parsers follow maturation levels of: Recommended, Candidate Release, Working
 |PerkinElmer Envision|Recommended|REC/2024/06
 |Revvity Kaleido|Recommended|BENCHLING/2023/09
 |Tecan Magellan|Recommended|REC/2024/06
-|Thermo Fisher Scientific SkanIt|Recommended|BENCHLING/2023/09
+|Thermo Fisher Scientific SkanIt|Recommended|REC/2025/03
 |Unchained Labs Lunatic|Recommended|REC/2024/06
 .3+|Solution Analyzer|Beckman Coulter PharmSpec|Recommended|REC/2024/09
 |NovaBio Flex2|Recommended|BENCHLING/2024/09

pyproject.toml

@@ -34,6 +34,7 @@ authors = [
   { name = "Stephen Worlow", email = "stephen.worlow@benchling.com" },
   { name = "Brian Worth", email = "brian@benchling.com" },
   { name = "Alex Reis", email = "alex@manifold.bio" },
+  { name = "Jane Dance", email = "jane.dance@abcellera.com" },
 ]
 classifiers = [
   "License :: OSI Approved :: MIT License",

src/allotropy/__about__.py

@@ -1 +1 @@
-__version__ = "0.1.93"
+__version__ = "0.1.98"

src/allotropy/allotrope/models/shared/definitions/definitions.py

@@ -84,6 +84,11 @@ class TStatisticDatumRole(Enum):
     frequency_of_grandparent_role = "frequency of grandparent role"
     frequency_of_total_role = "frequency of total role"
     sum_of_squares_role = "sum of squares role"
+    mode_value_role = "mode value role"
+    trimmed_mode_value_role = "trimmed mode value role"
+    trimmed_count_role = "trimmed count role"
+    trimmed_standard_deviation_role = "trimmed standard deviation role"
+    trimmed_arithmetic_mean_role = "trimmed arithmetic mean role"
 
 
 class InvalidJsonFloat(Enum):

src/allotropy/allotrope/schema_mappers/adm/cell_counting/rec/_2024/_09/cell_counting.py

@@ -107,6 +107,12 @@ class Measurement:
     sample_custom_info: dict[str, Any] | None = None
     custom_info: dict[str, Any] | None = None
 
+    # Custom information documents
+    device_control_custom_info: dict[str, Any] | None = None
+    image_processing_custom_info: dict[str, Any] | None = None
+    data_processing_custom_info: dict[str, Any] | None = None
+    processed_data_custom_info: dict[str, Any] | None = None
+
 
 @dataclass(frozen=True)
 class MeasurementGroup:
@@ -223,21 +229,23 @@ def _get_technique_document(
     def _get_measurement_document(
         self, measurement: Measurement, metadata: Metadata
     ) -> MeasurementDocument:
+        device_control_doc = DeviceControlDocumentItem(
+            device_type=metadata.device_type,
+            detection_type=metadata.detection_type,
+            sample_volume_setting=quantity_or_none(
+                TQuantityValueMicroliter,
+                measurement.sample_volume_setting,
+            ),
+        )
+        device_control_doc = add_custom_information_document(
+            device_control_doc, measurement.device_control_custom_info or {}
+        )
         measurement_document = MeasurementDocument(
             measurement_time=self.get_date_time(measurement.timestamp),
             measurement_identifier=measurement.measurement_identifier,
             sample_document=self._get_sample_document(measurement),
             device_control_aggregate_document=DeviceControlAggregateDocument(
-                device_control_document=[
-                    DeviceControlDocumentItem(
-                        device_type=metadata.device_type,
-                        detection_type=metadata.detection_type,
-                        sample_volume_setting=quantity_or_none(
-                            TQuantityValueMicroliter,
-                            measurement.sample_volume_setting,
-                        ),
-                    )
-                ]
+                device_control_document=[device_control_doc]
             ),
             processed_data_aggregate_document=self._get_processed_data_aggregate_document(
                 measurement
@@ -247,12 +255,16 @@ def _get_measurement_document(
             ),
             image_aggregate_document=ImageAggregateDocument(
                 image_document=[
-                    ImageDocumentItem(
-                        experimental_data_identifier=measurement.experimental_data_identifier
+                    add_custom_information_document(
+                        ImageDocumentItem(
+                            experimental_data_identifier=measurement.experimental_data_identifier
+                        ),
+                        measurement.image_processing_custom_info or {},
                     )
                 ],
             )
             if measurement.experimental_data_identifier
+            or measurement.image_processing_custom_info
             else None,
         )
         return add_custom_information_document(
@@ -322,20 +334,23 @@ def _get_processed_data_aggregate_document(
                 TQuantityValueUnitless, measurement.debris_index
             ),
         }
-        data_processing_document = DataProcessingDocument(
-            cell_type_processing_method=measurement.cell_type_processing_method,
-            minimum_cell_diameter_setting=quantity_or_none(
-                TQuantityValueMicrometer,
-                measurement.minimum_cell_diameter_setting,
-            ),
-            maximum_cell_diameter_setting=quantity_or_none(
-                TQuantityValueMicrometer,
-                measurement.maximum_cell_diameter_setting,
-            ),
-            cell_density_dilution_factor=quantity_or_none(
-                TQuantityValueUnitless,
-                measurement.cell_density_dilution_factor,
+        data_processing_document = add_custom_information_document(
+            DataProcessingDocument(
+                cell_type_processing_method=measurement.cell_type_processing_method,
+                minimum_cell_diameter_setting=quantity_or_none(
+                    TQuantityValueMicrometer,
+                    measurement.minimum_cell_diameter_setting,
+                ),
+                maximum_cell_diameter_setting=quantity_or_none(
+                    TQuantityValueMicrometer,
+                    measurement.maximum_cell_diameter_setting,
+                ),
+                cell_density_dilution_factor=quantity_or_none(
+                    TQuantityValueUnitless,
+                    measurement.cell_density_dilution_factor,
+                ),
             ),
+            measurement.data_processing_custom_info or {},
         )
         processed_data_document = ProcessedDataDocumentItem(
             processed_data_identifier=measurement.processed_data_identifier,
@@ -389,7 +404,8 @@ def _get_processed_data_aggregate_document(
         return ProcessedDataAggregateDocument(
             processed_data_document=[
                 add_custom_information_document(
-                    processed_data_document, custom_document
+                    processed_data_document,
+                    custom_document | (measurement.processed_data_custom_info or {}),
                 )
             ]
         )

src/allotropy/allotrope/schema_mappers/adm/multi_analyte_profiling/benchling/_2024/_09/multi_analyte_profiling.py

@@ -3,8 +3,12 @@
 from allotropy.allotrope.models.adm.multi_analyte_profiling.benchling._2024._09.multi_analyte_profiling import (
     AnalyteAggregateDocument,
     AnalyteDocumentItem,
+    CalculatedDataAggregateDocument,
+    CalculatedDataDocumentItem,
     CalibrationAggregateDocument,
     CalibrationDocumentItem,
+    DataSourceAggregateDocument,
+    DataSourceDocumentItem,
     DataSystemDocument,
     DeviceControlAggregateDocument,
     DeviceControlDocumentItem,
@@ -17,6 +21,11 @@
     MultiAnalyteProfilingAggregateDocument,
     MultiAnalyteProfilingDocumentItem,
     SampleDocument,
+    StatisticDimensionAggregateDocument,
+    StatisticDimensionDocumentItem,
+    StatisticsAggregateDocument,
+    StatisticsDocumentItem,
+    TQuantityValueModel,
 )
 from allotropy.allotrope.models.shared.components.plate_reader import SampleRoleType
 from allotropy.allotrope.models.shared.definitions.custom import (
@@ -28,19 +37,37 @@
 from allotropy.allotrope.models.shared.definitions.definitions import (
     TStatisticDatumRole,
 )
+from allotropy.allotrope.models.shared.definitions.units import Unitless
 from allotropy.allotrope.schema_mappers.schema_mapper import SchemaMapper
 from allotropy.constants import ASM_CONVERTER_VERSION
+from allotropy.parsers.utils.calculated_data_documents.definition import (
+    CalculatedDocument,
+)
 from allotropy.parsers.utils.values import quantity_or_none
 
 
+@dataclass(frozen=True)
+class StatisticDimension:
+    value: float
+    unit: str
+    statistic_datum_role: TStatisticDatumRole
+
+
+@dataclass(frozen=True)
+class StatisticsDocument:
+    statistical_feature: str
+    statistic_dimensions: list[StatisticDimension]
+
+
 @dataclass(frozen=True)
 class Analyte:
     identifier: str
     name: str
-    value: float
     assay_bead_identifier: str
     assay_bead_count: float
-    statistic_datum_role: TStatisticDatumRole | None
+    statistics: list[StatisticsDocument] | None = None
+    statistic_datum_role: TStatisticDatumRole | None = None
+    fluorescence: float | None = None
 
 
 @dataclass(frozen=True)
@@ -115,6 +142,7 @@ class Metadata:
 class Data:
     metadata: Metadata
     measurement_groups: list[MeasurementGroup]
+    calculated_data: list[CalculatedDocument] | None = None
 
 
 class Mapper(SchemaMapper[Data, Model]):
@@ -146,6 +174,9 @@ def map_model(self, data: Data) -> Model:
                     self._get_technique_document(measurement_group, data.metadata)
                     for measurement_group in data.measurement_groups
                 ],
+                calculated_data_aggregate_document=self._get_calculated_data_aggregate_document(
+                    data.calculated_data
+                ),
             ),
             field_asm_manifest=self.MANIFEST,
         )
@@ -208,9 +239,33 @@ def _get_measurement_document(
                         ),
                         fluorescence=quantity_or_none(
                             TQuantityValueRelativeFluorescenceUnit,
-                            analyte.value,
+                            analyte.fluorescence,
                             has_statistic_datum_role=analyte.statistic_datum_role,
                         ),
+                        statistics_aggregate_document=(
+                            StatisticsAggregateDocument(
+                                statistics_document=[
+                                    StatisticsDocumentItem(
+                                        statistical_feature=statistic.statistical_feature,
+                                        statistic_dimension_aggregate_document=StatisticDimensionAggregateDocument(
+                                            statistic_dimension_document=[
+                                                StatisticDimensionDocumentItem(
+                                                    statistical_value=TQuantityValueModel(
+                                                        value=dimension.value,
+                                                        unit=dimension.unit,
+                                                        has_statistic_datum_role=dimension.statistic_datum_role,
+                                                    ),
+                                                )
+                                                for dimension in statistic.statistic_dimensions
+                                            ]
+                                        ),
+                                    )
+                                    for statistic in analyte.statistics
+                                ]
+                            )
+                            if analyte.statistics
+                            else None
+                        ),
                     )
                     for analyte in measurement.analytes
                 ]
@@ -261,3 +316,33 @@ def _get_error_aggregate_document(
                 for error in errors
             ]
         )
+
+    def _get_calculated_data_aggregate_document(
+        self, calculated_data_items: list[CalculatedDocument] | None
+    ) -> CalculatedDataAggregateDocument | None:
+        if not calculated_data_items:
+            return None
+
+        return CalculatedDataAggregateDocument(
+            calculated_data_document=[
+                CalculatedDataDocumentItem(
+                    calculated_data_identifier=calculated_data_item.uuid,
+                    calculated_data_name=calculated_data_item.name,
+                    calculation_description=calculated_data_item.description,
+                    calculated_result=TQuantityValueModel(
+                        value=calculated_data_item.value,
+                        unit=calculated_data_item.unit or Unitless.unit,
+                    ),
+                    data_source_aggregate_document=DataSourceAggregateDocument(
+                        data_source_document=[
+                            DataSourceDocumentItem(
+                                data_source_identifier=item.reference.uuid,
+                                data_source_feature=item.feature,
+                            )
+                            for item in calculated_data_item.data_sources
+                        ]
+                    ),
+                )
+                for calculated_data_item in calculated_data_items
+            ]
+        )

src/allotropy/allotrope/schemas/adm/multi-analyte-profiling/BENCHLING/2024/09/CHANGE_NOTES.md

@@ -15,6 +15,6 @@ Changes:
   * Reasoning: These should be included in REC/2024/12 core schema
   * Proposal: Add "method version" to measurement aggregate document
 
-* Add "coefficient of variation role", "trimmed mode role", "trimmed count role", "trimmed standard deviation role", "trimmed arithmetic mean role" to tStatisiticDatumRole class
+* Add "coefficient of variation role", "trimmed mode value role", "trimmed count role", "trimmed standard deviation role", "trimmed arithmetic mean role" to tStatisiticDatumRole class
   * Reasoning: Support of additional statistical terms that are exported from multi-analyte-profilers
-  * Proposal: Add "coefficient of variation role", "trimmed mode role", "trimmed count role", "trimmed standard deviation role", "trimmed arithmetic mean role" to tStatisiticDatumRole
+  * Proposal: Add "coefficient of variation role", "trimmed mode value role", "trimmed count role", "trimmed standard deviation role", "trimmed arithmetic mean role" to tStatisiticDatumRole

src/allotropy/allotrope/schemas/adm/multi-analyte-profiling/BENCHLING/2024/09/multi-analyte-profiling.schema.json

@@ -2081,7 +2081,7 @@
             "variance role",
             "mode value role",
             "maximum value role",
-            "trimmed mode role",
+            "trimmed mode value role",
             "trimmed count role",
             "trimmed standard deviation role",
             "trimmed arithmetic mean role",