feat: Cytiva Biacore T200 Evaluation Module - initial implementation (#1075)

Author: joshua-benchling

.gitattributes

@@ -0,0 +1 @@
+*.bme filter=lfs diff=lfs merge=lfs -text

.github/workflows/test.yml

@@ -18,6 +18,8 @@ jobs:
 
     steps:
     - uses: actions/checkout@v3
+      with:
+        lfs: true
     - uses: actions/setup-python@v4
       with:
         python-version: "3.10"
@@ -34,6 +36,8 @@ jobs:
 
     steps:
     - uses: actions/checkout@v3
+      with:
+        lfs: true
     - uses: actions/setup-python@v4
       with:
         python-version: "3.11.9"
@@ -51,6 +55,8 @@ jobs:
 
     steps:
     - uses: actions/checkout@v3
+      with:
+        lfs: true
     - uses: actions/setup-python@v4
       with:
         python-version: "3.12"
@@ -67,6 +73,8 @@ jobs:
 
     steps:
     - uses: actions/checkout@v3
+      with:
+        lfs: true
     - uses: actions/setup-python@v4
       with:
         python-version: "3.11.9"
@@ -83,6 +91,8 @@ jobs:
 
     steps:
     - uses: actions/checkout@v3
+      with:
+        lfs: true
     - name: Check PR title
       run: ./scripts/check_title
       env:

SUPPORTED_INSTRUMENT_SOFTWARE.adoc

@@ -15,8 +15,9 @@ The parsers follow maturation levels of: Recommended, Candidate Release, Working
 [cols="4*^.^"]
 |===
 |Instrument Category|Instrument Software|Release Status|Exported ASM Schema
-.2+|Binding Affinity Analyzer|Cytiva Biacore Insight|Recommended|WD/2024/12
+.3+|Binding Affinity Analyzer|Cytiva Biacore Insight|Recommended|WD/2024/12
 |Cytiva Biacore T200 Control|Recommended|WD/2024/12
+|Cytiva Biacore T200 Evaluation|Recommended|WD/2024/12
 .6+|Cell Counting|Beckman Coulter Vi-Cell BLU|Recommended|REC/2024/09
 |Beckman Coulter Vi-Cell XR|Recommended|REC/2024/09
 |ChemoMetec NC View|Recommended|REC/2024/09

src/allotropy/allotrope/schema_mappers/adm/binding_affinity_analyzer/benchling/_2024/_12/binding_affinity_analyzer.py

@@ -78,6 +78,7 @@ class Metadata:
     sensor_chip_type: str | None = None
     lot_number: str | None = None
     sensor_chip_custom_info: DictType | None = None
+    data_system_custom_info: DictType | None = None
 
 
 @dataclass(frozen=True)
@@ -98,6 +99,7 @@ class DeviceControlDocument:
     flow_rate: float | None = None
     contact_time: float | None = None
     dilution: float | None = None
+    detection_type: str | None = None
     sample_temperature_setting: float | None = None
     device_control_custom_info: DictType | None = None
 
@@ -157,15 +159,18 @@ class Mapper(SchemaMapper[Data, Model]):
     def map_model(self, data: Data) -> Model:
         return Model(
             binding_affinity_analyzer_aggregate_document=BindingAffinityAnalyzerAggregateDocument(
-                data_system_document=DataSystemDocument(
-                    ASM_file_identifier=data.metadata.asm_file_identifier,
-                    data_system_instance_identifier=data.metadata.data_system_instance_identifier,
-                    ASM_converter_name=self.converter_name,
-                    ASM_converter_version=ASM_CONVERTER_VERSION,
-                    file_name=data.metadata.file_name,
-                    UNC_path=data.metadata.unc_path,
-                    software_version=data.metadata.software_version,
-                    software_name=data.metadata.software_name,
+                data_system_document=add_custom_information_document(
+                    DataSystemDocument(
+                        ASM_file_identifier=data.metadata.asm_file_identifier,
+                        data_system_instance_identifier=data.metadata.data_system_instance_identifier,
+                        ASM_converter_name=self.converter_name,
+                        ASM_converter_version=ASM_CONVERTER_VERSION,
+                        file_name=data.metadata.file_name,
+                        UNC_path=data.metadata.unc_path,
+                        software_version=data.metadata.software_version,
+                        software_name=data.metadata.software_name,
+                    ),
+                    data.metadata.data_system_custom_info,
                 ),
                 device_system_document=DeviceSystemDocument(
                     device_identifier=data.metadata.device_identifier,
@@ -294,6 +299,7 @@ def _get_surface_plasmon_resonance_measurement_document(
                     sample_identifier=measurement.sample_identifier,
                     sample_role_type=measurement.sample_role_type,
                     location_identifier=measurement.location_identifier,
+                    well_plate_identifier=measurement.well_plate_identifier,
                     concentration=quantity_or_none(
                         TQuantityValueNanomolar, measurement.concentration
                     ),

src/allotropy/parser_factory.py

@@ -63,6 +63,9 @@
 from allotropy.parsers.cytiva_biacore_t200_control.cytiva_biacore_t200_control_parser import (
     CytivaBiacoreT200ControlParser,
 )
+from allotropy.parsers.cytiva_biacore_t200_evaluation.cytiva_biacore_t200_evaluation_parser import (
+    CytivaBiacoreT200EvaluationParser,
+)
 from allotropy.parsers.cytiva_unicorn.cytiva_unicorn_parser import CytivaUnicornParser
 from allotropy.parsers.example_weyland_yutani.example_weyland_yutani_parser import (
     ExampleWeylandYutaniParser,
@@ -153,6 +156,7 @@ class Vendor(Enum):
     CTL_IMMUNOSPOT = "CTL_IMMUNOSPOT"
     CYTIVA_BIACORE_INSIGHT = "CYTIVA_BIACORE_INSIGHT"
     CYTIVA_BIACORE_T200_CONTROL = "CYTIVA_BIACORE_T200_CONTROL"
+    CYTIVA_BIACORE_T200_EVALUATION = "CYTIVA_BIACORE_T200_EVALUATION"
     CYTIVA_UNICORN = "CYTIVA_UNICORN"
     EXAMPLE_WEYLAND_YUTANI = "EXAMPLE_WEYLAND_YUTANI"
     FLOWJO = "FLOWJO"
@@ -250,6 +254,7 @@ def get_parser(
     Vendor.CTL_IMMUNOSPOT: CtlImmunospotParser,
     Vendor.CYTIVA_BIACORE_INSIGHT: CytivaBiacoreInsightParser,
     Vendor.CYTIVA_BIACORE_T200_CONTROL: CytivaBiacoreT200ControlParser,
+    Vendor.CYTIVA_BIACORE_T200_EVALUATION: CytivaBiacoreT200EvaluationParser,
     Vendor.CYTIVA_UNICORN: CytivaUnicornParser,
     Vendor.EXAMPLE_WEYLAND_YUTANI: ExampleWeylandYutaniParser,
     Vendor.FLOWJO: FlowjoParser,

src/allotropy/parsers/cytiva_biacore_t200_evaluation/__init__.py

@@ -0,0 +1,13 @@
+from allotropy.allotrope.models.shared.components.plate_reader import SampleRoleType
+
+DEVICE_IDENTIFIER = "Biacore"
+PRODUCT_MANUFACTURER = "Cytiva"
+MODEL_NUMBER = "T200"
+DISPLAY_NAME = "Cytiva Biacore T200 Evaluation"
+SURFACE_PLASMON_RESONANCE = "surface plasmon resonance"
+DEVICE_TYPE = "binding affinity analyzer"
+
+SAMPLE_ROLE_TYPE = {
+    "blank role": SampleRoleType.blank_role.value,
+    "sample role": SampleRoleType.sample_role.value,
+}