feat: Bio-Rad Bio-Plex Manager - Add support for statistics dimensions

SUPPORTED_INSTRUMENT_SOFTWARE.adoc

@@ -31,7 +31,7 @@ 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
+.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

src/allotropy/parsers/biorad_bioplex_manager/biorad_bioplex_manager_parser.py

@@ -1,9 +1,9 @@
 from __future__ import annotations
 
-from allotropy.allotrope.models.adm.multi_analyte_profiling.benchling._2024._01.multi_analyte_profiling import (
+from allotropy.allotrope.models.adm.multi_analyte_profiling.benchling._2024._09.multi_analyte_profiling import (
     Model,
 )
-from allotropy.allotrope.schema_mappers.adm.multi_analyte_profiling.benchling._2024._01.multi_analyte_profiling import (
+from allotropy.allotrope.schema_mappers.adm.multi_analyte_profiling.benchling._2024._09.multi_analyte_profiling import (
     Data,
     Mapper,
 )

src/allotropy/parsers/biorad_bioplex_manager/biorad_bioplex_manager_structure.py

@@ -5,18 +5,18 @@
 import xml.etree.ElementTree as Et
 
 from allotropy.allotrope.models.shared.components.plate_reader import SampleRoleType
-from allotropy.allotrope.models.shared.definitions.definitions import (
-    TStatisticDatumRole,
-)
-from allotropy.allotrope.schema_mappers.adm.multi_analyte_profiling.benchling._2024._01.multi_analyte_profiling import (
+from allotropy.allotrope.schema_mappers.adm.multi_analyte_profiling.benchling._2024._09.multi_analyte_profiling import (
     Analyte,
     Error,
     Measurement,
     MeasurementGroup,
     Metadata,
+    StatisticDimension,
+    StatisticsDocument,
 )
 from allotropy.exceptions import get_key_or_error
 from allotropy.parsers.biorad_bioplex_manager import constants
+from allotropy.parsers.constants import NOT_APPLICABLE
 from allotropy.parsers.utils.uuids import random_uuid_str
 from allotropy.parsers.utils.values import (
     num_to_chars,
@@ -153,15 +153,32 @@ def create_analyte(
 ) -> Analyte:
     # Look up analyte name from sample
     assay_bead_identifier = bead_region_xml.attrib["RegionNumber"]
+
+    # Create statistics dimensions from available statistics in the XML
+    statistic_dimensions = []
+    for statistic_name, statistic_config in constants.STATISTIC_SECTIONS_CONF.items():
+        statistic_value = get_val_from_xml(bead_region_xml, statistic_name)
+        statistic_dimensions.append(
+            StatisticDimension(
+                value=try_float(statistic_value, f"{statistic_name} statistic"),
+                unit=statistic_config.unit,
+                statistic_datum_role=statistic_config.role,
+            )
+        )
+
     return Analyte(
         identifier=random_uuid_str(),
         name=analyte_region_dict[assay_bead_identifier],
-        value=try_float(get_val_from_xml(bead_region_xml, "Median"), "fluorescence"),
         assay_bead_identifier=assay_bead_identifier,
         assay_bead_count=try_int(
             get_val_from_xml(bead_region_xml, "RegionCount"), "assay_bead_count"
         ),
-        statistic_datum_role=TStatisticDatumRole.median_role,
+        statistics=[
+            StatisticsDocument(
+                statistical_feature="fluorescence",
+                statistic_dimensions=statistic_dimensions,
+            )
+        ],
     )
 
 
@@ -213,15 +230,18 @@ def get_well_name(well_attrib: dict[str, str]) -> str:
 def create_metadata(
     root_xml: Et.Element, system_metadata: SystemMetadata, file_path: str
 ) -> Metadata:
+    path = Path(file_path)
     return Metadata(
-        file_name=Path(file_path).name,
+        file_name=path.name,
         unc_path=file_path,
         software_name=constants.SOFTWARE_NAME,
         software_version=root_xml.attrib["BioPlexManagerVersion"],
         equipment_serial_number=system_metadata.serial_number,
         firmware_version=system_metadata.controller_version,
         product_manufacturer=constants.PRODUCT_MANUFACTURER,
         device_type=constants.DEVICE_TYPE,
+        asm_file_identifier=path.with_suffix(".json").name,
+        data_system_instance_identifier=NOT_APPLICABLE,
     )
 
 

src/allotropy/parsers/biorad_bioplex_manager/constants.py

@@ -1,6 +1,11 @@
+from dataclasses import dataclass
+
 from allotropy.allotrope.models.shared.components.plate_reader import SampleRoleType
+from allotropy.allotrope.models.shared.definitions.definitions import (
+    TStatisticDatumRole,
+)
 
-SOFTWARE_NAME = "“Bio-Plex Manager"
+SOFTWARE_NAME = "Bio-Plex Manager"
 PRODUCT_MANUFACTURER = "Bio-Rad"
 DEVICE_TYPE = "multi analyte profiling analyzer"
 CONTAINER_TYPE = "well plate"
@@ -27,3 +32,48 @@
     "PlateDimensions",
     "Wells",
 ]
+
+
+@dataclass(frozen=True)
+class StatisticSectionConfig:
+    role: TStatisticDatumRole
+    unit: str
+
+
+# Statistics mapping for Bio-Rad BioPlex XML elements
+STATISTIC_SECTIONS_CONF = {
+    "Median": StatisticSectionConfig(
+        role=TStatisticDatumRole.median_role,
+        unit="RFU",
+    ),
+    "Mean": StatisticSectionConfig(
+        role=TStatisticDatumRole.arithmetic_mean_role,
+        unit="RFU",
+    ),
+    "CV": StatisticSectionConfig(
+        role=TStatisticDatumRole.coefficient_of_variation_role,
+        unit="(unitless)",
+    ),
+    "StdDev": StatisticSectionConfig(
+        role=TStatisticDatumRole.standard_deviation_role,
+        unit="(unitless)",
+    ),
+    "TrimmedMean": StatisticSectionConfig(
+        role=TStatisticDatumRole.trimmed_arithmetic_mean_role,
+        unit="RFU",
+    ),
+    "TrimmedStdDev": StatisticSectionConfig(
+        role=TStatisticDatumRole.trimmed_standard_deviation_role,
+        unit="(unitless)",
+    ),
+    # "StdErr": StatisticSectionConfig(
+    #     role=TStatisticDatumRole.standard_error_role,
+    #     unit="RFU",
+    # ),
+    # "TrimmedCV": StatisticSectionConfig(
+    #     role=TStatisticDatumRole.trimmed_coefficient_of_variation_role,
+    #     unit="(unitless)",
+    # ),
+    # Note: StdErr (standard error) and TrimmedCV (trimmed coefficient of variation)
+    # are not supported yet
+}

tests/parsers/biorad_bioplex_manager/biorad_bioplex_manager_structure_test.py

@@ -5,9 +5,11 @@
 from allotropy.allotrope.models.shared.definitions.definitions import (
     TStatisticDatumRole,
 )
-from allotropy.allotrope.schema_mappers.adm.multi_analyte_profiling.benchling._2024._01.multi_analyte_profiling import (
+from allotropy.allotrope.schema_mappers.adm.multi_analyte_profiling.benchling._2024._09.multi_analyte_profiling import (
     Analyte,
     Error,
+    StatisticDimension,
+    StatisticsDocument,
 )
 from allotropy.parsers.biorad_bioplex_manager.biorad_bioplex_manager_structure import (
     AnalyteMetadata,
@@ -89,13 +91,52 @@ def test_create_analyte_document_data() -> None:
             bead_xml,
             analyte_region_dict=analyte_region_dict,
         )
+
+    # Expected statistics from the XML
+    expected_statistics = [
+        StatisticsDocument(
+            statistical_feature="fluorescence",
+            statistic_dimensions=[
+                StatisticDimension(
+                    value=992.5,
+                    unit="RFU",
+                    statistic_datum_role=TStatisticDatumRole.median_role,
+                ),
+                StatisticDimension(
+                    value=983.391296386718750,
+                    unit="RFU",
+                    statistic_datum_role=TStatisticDatumRole.arithmetic_mean_role,
+                ),
+                StatisticDimension(
+                    value=0.223858922719955440,
+                    unit="(unitless)",
+                    statistic_datum_role=TStatisticDatumRole.coefficient_of_variation_role,
+                ),
+                StatisticDimension(
+                    value=220.140914916992190,
+                    unit="(unitless)",
+                    statistic_datum_role=TStatisticDatumRole.standard_deviation_role,
+                ),
+                StatisticDimension(
+                    value=974.904785156250000,
+                    unit="RFU",
+                    statistic_datum_role=TStatisticDatumRole.trimmed_arithmetic_mean_role,
+                ),
+                StatisticDimension(
+                    value=181.356109619140620,
+                    unit="(unitless)",
+                    statistic_datum_role=TStatisticDatumRole.trimmed_standard_deviation_role,
+                ),
+            ],
+        )
+    ]
+
     assert analyte_document_data == Analyte(
         identifier="dummy_id",
         name="Pn4",
-        value=992.5,
         assay_bead_count=46,
         assay_bead_identifier="62",
-        statistic_datum_role=TStatisticDatumRole.median_role,
+        statistics=expected_statistics,
     )