allow zero values in the measures but skipping nan values

Author: joshua-benchling

src/allotropy/parsers/moldev_softmax_pro/softmax_pro_data_creator.py

@@ -78,7 +78,12 @@ def _get_data_cube(
             )
         ],
         dimensions=[data_element.elapsed_time],
-        measures=[data_element.kinetic_measures],
+        measures=[
+            [
+                value if value is not None else NEGATIVE_ZERO
+                for value in data_element.kinetic_measures
+            ]
+        ],
     )
 
 
@@ -87,7 +92,7 @@ def _get_spectrum_data_cube(
 ) -> DataCube | None:
     wavelengths = [data_element.wavelength for data_element in data_elements]
     values = [data_element.value for data_element in data_elements]
-    if NEGATIVE_ZERO in values:
+    if None in values:
         # Ignore the wells completely from the ASM if there is an nan value
         return None
 
@@ -106,7 +111,7 @@ def _get_spectrum_data_cube(
             )
         ],
         dimensions=[wavelengths],
-        measures=[values],
+        measures=[[value if value is not None else NEGATIVE_ZERO for value in values]],
     )
 
 
@@ -173,17 +178,29 @@ def _create_measurements(plate_block: PlateBlock, position: str) -> list[Measure
             type_=measurement_type,
             identifier=data_element.uuid,
             absorbance=(
-                data_element.value
+                (
+                    data_element.value
+                    if data_element.value is not None
+                    else NEGATIVE_ZERO
+                )
                 if measurement_type == MeasurementType.ULTRAVIOLET_ABSORBANCE
                 else None
             ),
             fluorescence=(
-                data_element.value
+                (
+                    data_element.value
+                    if data_element.value is not None
+                    else NEGATIVE_ZERO
+                )
                 if measurement_type == MeasurementType.FLUORESCENCE
                 else None
             ),
             luminescence=(
-                data_element.value
+                (
+                    data_element.value
+                    if data_element.value is not None
+                    else NEGATIVE_ZERO
+                )
                 if measurement_type == MeasurementType.LUMINESCENCE
                 else None
             ),

src/allotropy/parsers/moldev_softmax_pro/softmax_pro_structure.py

@@ -373,7 +373,7 @@ class DataElement:
     temperature: float | None
     wavelength: float
     position: str
-    value: float
+    value: float | None
     error_document: list[ErrorDocument]
     custom_info: dict[str, str] = field(default_factory=dict)
     elapsed_time: list[float] = field(default_factory=list)
@@ -422,7 +422,7 @@ def create(
                 temperature=temperature,
                 wavelength=wavelength,
                 position=str(position),
-                value=NEGATIVE_ZERO if value is None else value,
+                value=value,
                 error_document=(
                     [ErrorDocument(str(raw_value), header.read_mode)]
                     if value is None
@@ -702,7 +702,7 @@ def create(
                 temperature=temperature,
                 wavelength=wavelength,
                 position=str(position),
-                value=NEGATIVE_ZERO if value is None else value,
+                value=value,
                 error_document=error_document,
             )
 

src/main.py

@@ -0,0 +1,12 @@
+from allotropy.parser_factory import Vendor
+from allotropy.testing.utils import from_file
+
+file_name = "partial_plate_with_empty_values.txt"
+
+test_filepath = f"../tests/parsers/moldev_softmax_pro/testdata/{file_name}"
+test_output_file = f"{test_filepath.replace('txt', 'json')}"
+allotrope_dict = from_file(test_filepath, Vendor.MOLDEV_SOFTMAX_PRO)
+
+# print(json.dumps(allotrope_dict, indent=4, ensure_ascii=False))
+# with open(test_output_file, "w", encoding="utf-8") as output_file:
+#     output_file.write(json.dumps(allotrope_dict, indent=4, ensure_ascii=False))