feat: CTL ImmunoSpot - use proper units in data processing document (#1098)

Author: slopez-b

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

@@ -72,6 +72,7 @@
     SeimensPerMeter,
     SquareCentimetersPerGram,
     SquareCentimetersPerMole,
+    SquareMillimeter,
     SquareResponseUnit,
     TODO,
     Unitless,
@@ -821,6 +822,16 @@ 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

@@ -339,6 +339,11 @@ 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/schemas/shared/definitions/custom.json

@@ -1199,7 +1199,7 @@
       }
     ]
   },
-  "TQuantityValueResponseUnit": {
+  "tQuantityValueResponseUnit": {
     "allOf": [
       {
         "$ref": "#/$defs/tQuantityValue"
@@ -1219,7 +1219,7 @@
       }
     ]
   },
-  "TQuantityValueResponseUnitPerSecond": {
+  "tQuantityValueResponseUnitPerSecond": {
     "allOf": [
       {
         "$ref": "#/$defs/tQuantityValue"
@@ -1319,6 +1319,26 @@
       }
     ]
   },
+  "tQuantityValueSquareMillimeter": {
+    "allOf": [
+      {
+        "$ref": "#/$defs/tQuantityValue"
+      },
+      {
+        "$ref": "#/$defs/SquareMillimeter"
+      }
+    ]
+  },
+  "tNullableQuantityValueSquareMillimeter": {
+    "allOf": [
+      {
+        "$ref": "#/$defs/tNullableQuantityValue"
+      },
+      {
+        "$ref": "#/$defs/SquareMillimeter"
+      }
+    ]
+  },
   "tQuantityValueSquareResponseUnit": {
     "allOf": [
       {
@@ -1399,4 +1419,4 @@
       }
     ]
   }
-}
+}

src/allotropy/allotrope/schemas/shared/definitions/units.json

@@ -791,6 +791,18 @@
       "unit"
     ]
   },
+  "SquareMillimeter": {
+    "properties": {
+      "unit": {
+        "type": "string",
+        "const": "mm^2",
+        "$asm.unit-iri": "http://qudt.org/vocab/unit#SquareMillimeter"
+      }
+    },
+    "required": [
+      "unit"
+    ]
+  },
   "SquareResponseUnit": {
     "properties": {
       "unit": {

src/allotropy/parsers/ctl_immunospot/ctl_immunospot_structure.py

@@ -5,6 +5,10 @@
 
 import pandas as pd
 
+from allotropy.allotrope.models.shared.definitions.custom import (
+    TQuantityValueSquareMillimeter,
+    TQuantityValueUnitless,
+)
 from allotropy.allotrope.models.shared.definitions.definitions import (
     FieldComponentDatatype,
 )
@@ -24,6 +28,8 @@
 from allotropy.parsers.utils.uuids import random_uuid_str
 from allotropy.parsers.utils.values import (
     assert_not_none,
+    quantity_or_none,
+    try_float_or_none,
 )
 
 
@@ -35,11 +41,26 @@ def _create_measurement(
     histograms: dict[str, tuple[list[float], list[float]]],
     header_data: dict[str, float | str | None],
 ) -> Measurement:
+    def get_value_or_none(
+        data: dict[str, float | str | None], name: str
+    ) -> float | None:
+        value = str(data.pop(name, None)).split()[0]
+        return try_float_or_none(value)
+
     location_identifier = f"{well_row}{well_col}"
     data_processing_document = {
-        "Min. SpotSize": header_data.pop("Min. SpotSize", None),
-        "Max. SpotSize": header_data.pop("Max. SpotSize", None),
-        "Spot Separation": header_data.pop("Spot Separation", None),
+        "Min. SpotSize": quantity_or_none(
+            TQuantityValueSquareMillimeter,
+            get_value_or_none(header_data, "Min. SpotSize"),
+        ),
+        "Max. SpotSize": quantity_or_none(
+            TQuantityValueSquareMillimeter,
+            get_value_or_none(header_data, "Max. SpotSize"),
+        ),
+        "Spot Separation": quantity_or_none(
+            TQuantityValueUnitless,
+            get_value_or_none(header_data, "Spot Separation"),
+        ),
     }
     has_data = any(
         value is not None and str(value).strip() != ""
@@ -65,29 +86,31 @@ def _create_measurement(
                 for name, data in plate_data.items()
             ],
         ),
-        custom_data_cubes=[
-            DataCube(
-                label="spot count histogram",
-                structure_dimensions=[
-                    DataCubeComponent(
-                        concept="spot size",
-                        type_=FieldComponentDatatype.double,
-                        unit=UNITLESS,
-                    )
-                ],
-                structure_measures=[
-                    DataCubeComponent(
-                        concept="spot count",
-                        type_=FieldComponentDatatype.double,
-                        unit="Number",
-                    )
-                ],
-                dimensions=[histograms[location_identifier][0]],
-                measures=[histograms[location_identifier][1]],
-            )
-        ]
-        if histograms and location_identifier in histograms
-        else None,
+        custom_data_cubes=(
+            [
+                DataCube(
+                    label="spot count histogram",
+                    structure_dimensions=[
+                        DataCubeComponent(
+                            concept="spot size",
+                            type_=FieldComponentDatatype.double,
+                            unit=UNITLESS,
+                        )
+                    ],
+                    structure_measures=[
+                        DataCubeComponent(
+                            concept="spot count",
+                            type_=FieldComponentDatatype.double,
+                            unit="Number",
+                        )
+                    ],
+                    dimensions=[histograms[location_identifier][0]],
+                    measures=[histograms[location_identifier][1]],
+                )
+            ]
+            if histograms and location_identifier in histograms
+            else None
+        ),
         device_control_custom_info=header_data,
     )