Merge branch 'main' into jnegri-additional-parser-requirements

Signed-off-by: Joe Negri <[email protected]>
Benchling-Open-Source · Jun 21, 2024 · 671be33 · 671be33
2 parents 4bfd71b + 76167d6
commit 671be33
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -14,6 +14,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Added github enforcement that CHANGELOG.md is updated
 - Added test files Agilent TapeStation Analysis
 - Added requirements for remaining parsers to /docs
+- Add Alphalisa assay support to Gen5 adapter
+- Add fluorescence point detection measurement extension to Spectrophotometry BENCHLING/2023/12 schema
 
 ### Fixed
 

diff --git a/...allotropy/allotrope/models/adm/spectrophotometry/benchling/_2023/_12/spectrophotometry.py b/...allotropy/allotrope/models/adm/spectrophotometry/benchling/_2023/_12/spectrophotometry.py
@@ -1,6 +1,6 @@
 # generated by datamodel-codegen:
 #   filename:  spectrophotometry.schema.json
-#   timestamp: 2024-06-04T03:30:29+00:00
+#   timestamp: 2024-06-20T15:46:58+00:00
 
 from __future__ import annotations
 
@@ -20,6 +20,7 @@
     TQuantityValueNanogramPerMilliliter,
     TQuantityValueNanometer,
     TQuantityValuePicogramPerMilliliter,
+    TQuantityValueRelativeFluorescenceUnit,
     TQuantityValueSecondTime,
     TQuantityValueSquareCentimetersPerGram,
 )
@@ -421,11 +422,47 @@ class UltravioletAbsorbancePointDetectionMeasurementDocumentItems:
     compartment_temperature: TQuantityValueDegreeCelsius | None = None
 
 
+@dataclass(kw_only=True)
+class FluorescencePointDetectionDeviceControlDocumentItem(DeviceControlDocument):
+    detector_wavelength_setting: TQuantityValueNanometer | None = None
+    detector_bandwidth_setting: TQuantityValueNanometer | None = None
+    wavelength_filter_cutoff_setting: TQuantityValueNanometer | None = None
+    excitation_bandwidth_setting: TQuantityValueNanometer | None = None
+    excitation_wavelength_setting: TQuantityValueNanometer | None = None
+    field_index: int | None = None
+
+
+FluorescencePointDetectionDeviceControlDocument = list[
+    FluorescencePointDetectionDeviceControlDocumentItem
+]
+
+
+@dataclass(kw_only=True)
+class FluorescencePointDetectionDeviceControlAggregateDocument:
+    device_control_document: FluorescencePointDetectionDeviceControlDocument
+
+
+@dataclass(kw_only=True)
+class FluorescencePointDetectionMeasurementDocumentItems:
+    measurement_identifier: TStringValue
+    device_control_aggregate_document: FluorescencePointDetectionDeviceControlAggregateDocument
+    sample_document: SampleDocument
+    fluorescence: TQuantityValueRelativeFluorescenceUnit
+    measurement_time: TDateTimeStampValue | None = None
+    detection_type: TStringValue | None = None
+    processed_data_aggregate_document: ProcessedDataAggregateDocument | None = None
+    calculated_data_aggregate_document: CalculatedDataAggregateDocument | None = None
+    statistics_aggregate_document: StatisticsAggregateDocument | None = None
+    compartment_temperature: TQuantityValueDegreeCelsius | None = None
+    mass_concentration: TQuantityValuePicogramPerMilliliter | None = None
+
+
 @dataclass(kw_only=True)
 class MeasurementAggregateDocument:
     measurement_time: TDateTimeStampValue
     measurement_document: list[
-        UltravioletAbsorbancePointDetectionMeasurementDocumentItems
+        FluorescencePointDetectionMeasurementDocumentItems
+        | UltravioletAbsorbancePointDetectionMeasurementDocumentItems
     ]
     experiment_type: TStringValue | None = None
     container_type: ContainerType | None = None

diff --git a/...y/allotrope/schemas/adm/spectrophotometry/BENCHLING/2023/12/spectrophotometry.schema.json b/...y/allotrope/schemas/adm/spectrophotometry/BENCHLING/2023/12/spectrophotometry.schema.json
@@ -6,7 +6,7 @@
       "properties": {
         "spectrophotometry aggregate document": {
           "type": "object",
-          "$asm.property-class": "TO DO",
+          "$asm.property-class": "http://purl.allotrope.org/ontologies/result#AFR_0002937",
           "$asm.pattern": "aggregate datum",
           "properties": {
             "device system document": {
@@ -316,9 +316,12 @@
                         "$asm.array-mixed": false,
                         "$asm.pattern": "indexed datum",
                         "items": {
-                          "anyOf": [
+                          "oneOf": [
                             {
                               "$ref": "#/$defs/ultravioletAbsorbancePointDetectionMeasurementDocumentItems"
+                            },
+                            {
+                              "$ref": "#/$defs/fluorescencePointDetectionMeasurementDocumentItems"
                             }
                           ]
                         },
@@ -1130,6 +1133,135 @@
         }
       }
     },
+    "fluorescencePointDetectionDeviceControlDocument": {
+      "type": "array",
+      "$asm.array-ordered": true,
+      "$asm.array-mixed": false,
+      "$asm.pattern": "indexed datum",
+      "items": {
+        "allOf": [
+          {
+            "type": "object",
+            "$asm.property-class": "http://purl.allotrope.org/ontologies/result#AFR_0002723",
+            "$asm.pattern": "aggregate datum",
+            "properties": {
+              "detector wavelength setting": {
+                "$asm.property-class": "http://purl.allotrope.org/ontologies/result#AFR_0002456",
+                "$asm.pattern": "quantity datum",
+                "$ref": "#/$custom/tQuantityValueNanometer"
+              },
+              "detector bandwidth setting": {
+                "$asm.property-class": "http://purl.allotrope.org/ontologies/result#AFR_0002477",
+                "$asm.pattern": "quantity datum",
+                "$ref": "#/$custom/tQuantityValueNanometer"
+              },
+              "wavelength filter cutoff setting": {
+                "$asm.property-class": "http://purl.allotrope.org/ontologies/result#AFR_0002478",
+                "$asm.pattern": "quantity datum",
+                "$ref": "#/$custom/tQuantityValueNanometer"
+              },
+              "excitation bandwidth setting": {
+                "$asm.property-class": "http://purl.allotrope.org/ontologies/result#AFR_0002548",
+                "$asm.pattern": "quantity datum",
+                "$ref": "#/$custom/tQuantityValueNanometer"
+              },
+              "excitation wavelength setting": {
+                "$asm.property-class": "http://purl.allotrope.org/ontologies/result#AFR_0002479",
+                "$asm.pattern": "quantity datum",
+                "$ref": "#/$custom/tQuantityValueNanometer"
+              }
+            }
+          },
+          {
+            "$ref": "#/$defs/deviceControlDocument"
+          },
+          {
+            "properties": {
+              "@index": {
+                "type": "integer",
+                "minimum": 1,
+                "maximum": 2147483647
+              }
+            }
+          }
+        ]
+      },
+      "minItems": 1
+    },
+    "fluorescencePointDetectionDeviceControlAggregateDocument": {
+      "type": "object",
+      "$asm.property-class": "http://purl.allotrope.org/ontologies/result#AFR_0002722",
+      "$asm.pattern": "aggregate datum",
+      "required": [
+        "device control document"
+      ],
+      "properties": {
+        "device control document": {
+          "$ref": "#/$defs/fluorescencePointDetectionDeviceControlDocument"
+        }
+      }
+    },
+    "fluorescencePointDetectionMeasurementDocumentItems": {
+      "type": "object",
+      "$asm.property-class": "http://purl.allotrope.org/ontologies/result#AFR_0002375",
+      "$asm.pattern": "aggregate datum",
+      "required": [
+        "fluorescence",
+        "sample document",
+        "device control aggregate document",
+        "measurement identifier"
+      ],
+      "properties": {
+        "measurement time": {
+          "$asm.property-class": "http://purl.allotrope.org/ontologies/result#AFR_0000952",
+          "$asm.pattern": "value datum",
+          "$asm.type": "http://www.w3.org/2001/XMLSchema#dateTimeStamp",
+          "$ref": "#/$defs/tDateTimeStampValue"
+        },
+        "measurement identifier": {
+          "$asm.property-class": "http://purl.allotrope.org/ontologies/result#AFR_0001121",
+          "$asm.pattern": "value datum",
+          "$asm.type": "http://www.w3.org/2001/XMLSchema#string",
+          "$ref": "#/$defs/tStringValue"
+        },
+        "device control aggregate document": {
+          "$ref": "#/$defs/fluorescencePointDetectionDeviceControlAggregateDocument"
+        },
+        "sample document": {
+          "$ref": "#/$defs/sampleDocument"
+        },
+        "detection type": {
+          "$asm.property-class": "http://purl.allotrope.org/ontologies/result#AFR_0002534",
+          "$asm.pattern": "value datum",
+          "$asm.type": "http://www.w3.org/2001/XMLSchema#string",
+          "$ref": "#/$defs/tStringValue"
+        },
+        "processed data aggregate document": {
+          "$ref": "#/$defs/processedDataAggregateDocument"
+        },
+        "calculated data aggregate document": {
+          "$ref": "#/$defs/calculatedDataAggregateDocument"
+        },
+        "statistics aggregate document": {
+          "$ref": "#/$defs/statisticsAggregateDocument"
+        },
+        "compartment temperature": {
+          "$asm.property-class": "http://purl.allotrope.org/ontologies/result#AFR_0002549",
+          "$asm.pattern": "quantity datum",
+          "$ref": "#/$custom/tQuantityValueDegreeCelsius"
+        },
+        "fluorescence": {
+          "$asm.property-class": "http://purl.allotrope.org/ontologies/result#AFR_0002408",
+          "$asm.pattern": "quantity datum",
+          "$ref": "#/$custom/tQuantityValueRelativeFluorescenceUnit"
+        },
+        "mass concentration": {
+          "$asm.property-class": "http://purl.allotrope.org/ontologies/result#AFR_0001661",
+          "$asm.pattern": "quantity datum",
+          "$ref": "#/$custom/tQuantityValuePicogramPerMilliliter"
+        }
+      }
+    },
     "asm": {
       "properties": {
         "$asm.manifest": {

diff --git a/src/allotropy/parsers/agilent_gen5/agilent_gen5_structure.py b/src/allotropy/parsers/agilent_gen5/agilent_gen5_structure.py
@@ -113,15 +113,15 @@ def _get_identifier_from_filename_or_none(cls, file_name: str) -> str | None:
 
 @dataclass(frozen=True)
 class FilterSet:
-    emission: str
     gain: str
+    emission: str | None = None
     excitation: str | None = None
     mirror: str | None = None
     optics: str | None = None
 
     @property
     def detector_wavelength_setting(self) -> float | None:
-        if self.emission == "Full light":
+        if self.emission == "Full light" or not self.emission:
             return None
         return try_float(self.emission.split("/")[0], "Detector wavelength")
 
@@ -218,7 +218,10 @@ def create(cls, reader: LinesReader) -> ReadData:
     def get_read_mode(procedure_details: str) -> ReadMode:
         if ReadMode.ABSORBANCE.value in procedure_details:
             return ReadMode.ABSORBANCE
-        elif ReadMode.FLUORESCENCE.value in procedure_details:
+        elif (
+            ReadMode.FLUORESCENCE.value in procedure_details
+            or ReadMode.ALPHALISA.value in procedure_details
+        ):
             return ReadMode.FLUORESCENCE
         elif ReadMode.LUMINESCENCE.value in procedure_details:
             return ReadMode.LUMINESCENCE
@@ -259,6 +262,8 @@ def _get_measurement_labels(cls, device_control_data: dict, read_mode: str) -> l
                 f"{label_prefix}{excitation},{emission}"
                 for excitation, emission in zip(excitations, emissions)
             ]
+            if not measurement_labels:
+                measurement_labels = ["Alpha"]
 
         if read_mode == ReadMode.LUMINESCENCE:
             emissions = device_control_data.get(EMISSION_KEY)
@@ -362,9 +367,8 @@ def _get_filter_sets(
             mirror = None
             if mirrors and read_mode == ReadMode.FLUORESCENCE:
                 mirror = mirrors[idx]
-
             filter_data[label] = FilterSet(
-                emission=emissions[idx],
+                emission=emissions[idx] if emissions else None,
                 gain=gains[idx],
                 excitation=excitations[idx] if excitations else None,
                 mirror=mirror,
@@ -484,6 +488,7 @@ def parse_results(
                 if well_pos not in self.wells:
                     self.wells.append(well_pos)
                 well_value = try_float_or_nan(values[col_num])
+
                 if label in read_data.measurement_labels:
                     self.measurements[well_pos].append(
                         Measurement(random_uuid_str(), well_value, label)

diff --git a/src/allotropy/parsers/agilent_gen5/constants.py b/src/allotropy/parsers/agilent_gen5/constants.py
@@ -40,6 +40,7 @@ class ReadMode(str, Enum):
     ABSORBANCE = "Absorbance"
     FLUORESCENCE = "Fluorescence"
     LUMINESCENCE = "Luminescence"
+    ALPHALISA = "Alpha"
 
 
 class ReadType(str, Enum):

diff --git a/src/allotropy/parsers/thermo_fisher_nanodrop_eight/nanodrop_eight_parser.py b/src/allotropy/parsers/thermo_fisher_nanodrop_eight/nanodrop_eight_parser.py
@@ -9,6 +9,7 @@
     DataSourceDocumentItem,
     DataSystemDocument,
     DeviceSystemDocument,
+    FluorescencePointDetectionMeasurementDocumentItems,
     MeasurementAggregateDocument,
     Model,
     ProcessedDataAggregateDocument,
@@ -242,7 +243,14 @@ def _get_spectrophotometry_document_item(
 
     def _get_measurement_document(
         self, data: pd.DataFrame, row: int
-    ) -> list[UltravioletAbsorbancePointDetectionMeasurementDocumentItems]:
+    ) -> list[
+        FluorescencePointDetectionMeasurementDocumentItems
+        | UltravioletAbsorbancePointDetectionMeasurementDocumentItems
+    ]:
+        measurement_docs: list[
+            FluorescencePointDetectionMeasurementDocumentItems
+            | UltravioletAbsorbancePointDetectionMeasurementDocumentItems
+        ]
         measurement_docs = []
         na_type = _get_str_or_none(data, row, "na type")
         concentration_col = self._get_concentration_col(data)