merge main

Author: oscar-castro-bl

CHANGELOG.md

@@ -5,6 +5,50 @@ 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).
 
+## [0.1.110] - 2025-11-03
+
+### Added
+
+- Thermo Fisher Scientific NanoDrop 8000 - add unread data to asm (#1094)
+- Thermo Fisher Scientific NanoDrop Eight - add unread data to asm (#1096)
+
+### Fixed
+
+- Thermo Fisher Scientific SkanIt - error detecing plate word matching (#1113)
+
+## [0.1.109] - 2025-10-28
+
+### Added
+
+- Thermo Fisher Scientific VISIONlite - add get unread data (#1097)
+- Flowjo - Added new example (#1108)
+- Beckman Coulter Biomek - clear unread data warnings (#1092)
+- Cytiva Biacore T200 - Refactor to use JsonData (#1095)
+- CTL ImmunoSpot - use proper units in data processing document (#1098)
+- Thermo Fisher Scientific SkanIt - add unread data (#1104)
+
+### Fixed
+
+- Molecular Devices SoftMax Pro - handle reduced data blocks with empty rows correctly (#1110)
+
+## [0.1.108] - 2025-10-23
+
+### Added
+
+- BMG Labtech MARS - Support for CSVs generated by Mars V3.40 R2 (#1105)
+
+## [0.1.107] - 2025-10-09
+
+### Added
+
+- Thermo Fisher Scientific Genesys30 - add unread data (#1093)
+- Mabtech Apex - support files with different plate info (#1099)
+- Cytiva Biacore T200 Evaluation Module - initial implementation (#1075)
+
+### Fixed
+
+- Thermo Fisher Scientific Qubit Flex - added handling for sep header (#1101)
+
 ## [0.1.106] - 2025-09-30
 
 ### Added

src/allotropy/__about__.py

@@ -1 +1 @@
-__version__ = "0.1.106"
+__version__ = "0.1.110"

src/allotropy/allotrope/converter.py

@@ -112,6 +112,9 @@
     "=": "_EQUALS_",
     "@": "_AT_",
     "'": "_QUOTE_",
+    "*": "_ASTERISK_",
+    ",": "_COMMA_",
+    "&": "_AMPERSAND_",
     # NOTE: this MUST be at the end, or it will break other key replacements.
     " ": "_",
 }

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

@@ -54,6 +54,7 @@
     PartsPerBillion,
     PartsPerMillion,
     Percent,
+    PerMolarPerCentimeter,
     PerMolarPerSecond,
     PerSecond,
     PH,
@@ -72,6 +73,7 @@
     SeimensPerMeter,
     SquareCentimetersPerGram,
     SquareCentimetersPerMole,
+    SquareMillimeter,
     SquareResponseUnit,
     TODO,
     Unitless,
@@ -609,6 +611,18 @@ class TNullableQuantityValuePartsPerMillion(PartsPerMillion, TNullableQuantityVa
     pass
 
 
+@dataclass(frozen=True, kw_only=True)
+class TQuantityValuePerMolarPerCentimeter(PerMolarPerCentimeter, TQuantityValue):
+    pass
+
+
+@dataclass(frozen=True, kw_only=True)
+class TNullableQuantityValuePerMolarPerCentimeter(
+    PerMolarPerCentimeter, TNullableQuantityValue
+):
+    pass
+
+
 @dataclass(frozen=True, kw_only=True)
 class TQuantityValuePerMolarPerSecond(PerMolarPerSecond, TQuantityValue):
     pass
@@ -821,6 +835,16 @@ class TNullableQuantityValueSquareCentimetersPerMole(
     pass
 
 
+@dataclass(frozen=True, kw_only=True)
+class TQuantityValueSquareMillimeter(SquareMillimeter, TQuantityValue):
+    pass
+
+
+@dataclass(frozen=True, kw_only=True)
+class TNullableQuantityValueSquareMillimeter(SquareMillimeter, TNullableQuantityValue):
+    pass
+
+
 @dataclass(frozen=True, kw_only=True)
 class TQuantityValueSquareResponseUnit(SquareResponseUnit, TQuantityValue):
     pass

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

@@ -249,6 +249,11 @@ class PartsPerMillion(HasUnit):
     unit: str = "ppm"
 
 
+@dataclass(frozen=True, kw_only=True)
+class PerMolarPerCentimeter(HasUnit):
+    unit: str = "M-1cm-1"
+
+
 @dataclass(frozen=True, kw_only=True)
 class PerMolarPerSecond(HasUnit):
     unit: str = "M-1s-1"
@@ -339,6 +344,11 @@ class SquareCentimetersPerMole(HasUnit):
     unit: str = "cm^2/mol"
 
 
+@dataclass(frozen=True, kw_only=True)
+class SquareMillimeter(HasUnit):
+    unit: str = "mm^2"
+
+
 @dataclass(frozen=True, kw_only=True)
 class SquareResponseUnit(HasUnit):
     unit: str = "RU^2"

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

@@ -220,7 +220,8 @@ class Metadata:
     equipment_serial_number: str | None = None
     product_manufacturer: str | None = None
     file_name: str | None = None
-    custom_info_doc: dict[str, Any] | None = None
+    metadata_custom_info: dict[str, Any] | None = None
+    device_control_custom_info: dict[str, Any] | None = None
 
 
 @dataclass(frozen=True)
@@ -253,7 +254,7 @@ def map_model(self, data: Data) -> Model:
                         ASM_converter_name=self.converter_name,
                         ASM_converter_version=ASM_CONVERTER_VERSION,
                     ),
-                    data.metadata.custom_info_doc,
+                    data.metadata.metadata_custom_info,
                 ),
                 plate_reader_document=[
                     self._get_technique_document(measurement_group)

src/allotropy/allotrope/schema_mappers/adm/spectrophotometry/benchling/_2023/_12/spectrophotometry.py

@@ -29,9 +29,12 @@
     UltravioletAbsorbanceSpectrumDetectionMeasurementDocumentItems,
 )
 from allotropy.allotrope.models.shared.definitions.custom import (
+    TQuantityValueKiloDalton,
     TQuantityValueMicroliter,
     TQuantityValueMilliAbsorbanceUnit,
+    TQuantityValueNanogramPerMicroliter,
     TQuantityValueNanometer,
+    TQuantityValuePerMolarPerCentimeter,
     TQuantityValueRelativeFluorescenceUnit,
     TQuantityValueUnitless,
 )
@@ -77,6 +80,7 @@ class ProcessedDataFeature:
 class ProcessedData:
     features: list[ProcessedDataFeature]
     identifier: str | None = None
+    custom_info: dict[str, Any] | None = None
 
 
 @dataclass
@@ -102,6 +106,8 @@ class Measurement:
     original_sample_concentration_unit: str | None = None
     baseline_absorbance: float | None = None
     electronic_absorbance_reference_wavelength_setting: float | None = None
+    cursor_position: float | None = None
+    cursor_absorbance: float | None = None
 
     # Measurements
     absorbance: JsonFloat | None = None
@@ -127,6 +133,7 @@ class MeasurementGroup:
     container_type: str | None = None
 
     processed_data: ProcessedData | None = None
+    custom_info: dict[str, Any] | None = None
 
 
 @dataclass(frozen=True)
@@ -194,16 +201,19 @@ def _get_technique_document(
     ) -> SpectrophotometryDocumentItem:
         return SpectrophotometryDocumentItem(
             analyst=measurement_group.analyst,
-            measurement_aggregate_document=MeasurementAggregateDocument(
-                measurement_time=self.get_date_time(
-                    assert_not_none(measurement_group.measurement_time)
+            measurement_aggregate_document=add_custom_information_document(
+                MeasurementAggregateDocument(
+                    measurement_time=self.get_date_time(
+                        assert_not_none(measurement_group.measurement_time)
+                    ),
+                    experiment_type=measurement_group.experiment_type,
+                    container_type=metadata.container_type,
+                    measurement_document=[
+                        self._get_measurement_document_item(measurement, metadata)
+                        for measurement in measurement_group.measurements
+                    ],
                 ),
-                experiment_type=measurement_group.experiment_type,
-                container_type=metadata.container_type,
-                measurement_document=[
-                    self._get_measurement_document_item(measurement, metadata)
-                    for measurement in measurement_group.measurements
-                ],
+                measurement_group.custom_info,
             ),
         )
 
@@ -265,6 +275,14 @@ def _get_ultraviolet_absorbance_measurement_document(
                 TQuantityValueMilliAbsorbanceUnit,
                 measurement.baseline_absorbance,
             ),
+            "340 raw": quantity_or_none(
+                TQuantityValueMilliAbsorbanceUnit,
+                (measurement.custom_info or {}).get("340 raw"),
+            ),
+            "Cursor Abs.": quantity_or_none(
+                TQuantityValueMilliAbsorbanceUnit,
+                measurement.cursor_absorbance,
+            ),
         }
         return add_custom_information_document(doc, custom_info_doc)
 
@@ -337,6 +355,9 @@ def _get_device_control_custom_document(
             "dilution factor": quantity_or_none(
                 TQuantityValueUnitless, measurement.dilution_factor_setting
             ),
+            "Cursor Pos.": quantity_or_none(
+                TQuantityValueNanometer, measurement.cursor_position
+            ),
         }
         return (measurement.device_control_custom_info or {}) | custom_info
 
@@ -359,14 +380,19 @@ def _get_sample_document(self, measurement: Measurement) -> SampleDocument:
                 measurement.sample_custom_info["last read standards"]
             )
 
+        sample_custom_info = measurement.sample_custom_info or {}
+        sample_custom_info["Mol. Wt. kda"] = quantity_or_none(
+            TQuantityValueKiloDalton, sample_custom_info.get("Mol. Wt. kda")
+        )
+
         return add_custom_information_document(
             SampleDocument(
                 sample_identifier=measurement.sample_identifier,
                 batch_identifier=measurement.batch_identifier,
                 location_identifier=measurement.location_identifier,
                 well_plate_identifier=measurement.well_plate_identifier,
             ),
-            (measurement.sample_custom_info or {}) | custom_info_doc,
+            sample_custom_info | custom_info_doc,
         )
 
     def _get_processed_data_aggregate_document(
@@ -375,14 +401,38 @@ def _get_processed_data_aggregate_document(
         if not data:
             return None
 
+        # Build custom info for processed data with proper TQuantityValue wrappers
+        processed_data_custom_info = {}
+        if data.custom_info:
+            processed_data_custom_info = {
+                "E1%": quantity_or_none(
+                    TQuantityValueUnitless, data.custom_info.get("E1%")
+                ),
+                "ext. coeff x10e3": quantity_or_none(
+                    TQuantityValuePerMolarPerCentimeter,
+                    data.custom_info.get("ext. coeff x10e3"),
+                ),
+                "ext.c.": quantity_or_none(
+                    TQuantityValuePerMolarPerCentimeter,
+                    data.custom_info.get("ext.c. (l/(mol*cm))"),
+                ),
+                "conc. factor": quantity_or_none(
+                    TQuantityValueNanogramPerMicroliter,
+                    data.custom_info.get("conc. factor (ng/ul)"),
+                ),
+            }
+
         return ProcessedDataAggregateDocument(
             processed_data_document=[
-                ProcessedDataDocumentItem(
-                    # TODO(nstender): figure out how to limit possible classes from get_quantity_class for typing.
-                    mass_concentration=quantity_or_none(
-                        get_quantity_class(feature.unit), feature.result  # type: ignore[arg-type]
+                add_custom_information_document(
+                    ProcessedDataDocumentItem(
+                        # TODO(nstender): figure out how to limit possible classes from get_quantity_class for typing.
+                        mass_concentration=quantity_or_none(
+                            get_quantity_class(feature.unit), feature.result  # type: ignore[arg-type]
+                        ),
+                        processed_data_identifier=data.identifier,
                     ),
-                    processed_data_identifier=data.identifier,
+                    processed_data_custom_info,
                 )
                 for feature in data.features
             ]

src/allotropy/allotrope/schema_parser/model_class_editor.py

@@ -577,7 +577,7 @@ def _get_class_lines(
     ) -> ClassLines | None:
         # Reads lines for the next class and returns as a ClassLines object.
         lines: list[str] = existing_lines or []
-        started = False
+        started = bool(lines)
         while True:
             line = file.readline()
             # Skip empty lines at the start, return when we hit a newline after the class.