Update spectrophotometry schema for fluorescence measurements (Benchl…

…ing-Open-Source#469) Signed-off-by: james-leinas <[email protected]>
poojabalaji05 · Jul 3, 2024 · c0872b5 · c0872b5
1 parent 2261cd0
commit c0872b5
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Showing 4 changed files with 183 additions and 5 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -14,6 +14,7 @@ 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
 - 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/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)