refactor: ThermoFisher Qubit Flex - refactor parser to use schema map…

…per design pattern (#699)

src/allotropy/allotrope/converter.py

@@ -111,18 +111,32 @@ def add_custom_information_document(
     if not custom_info_doc:
         return model
 
-    if isinstance(custom_info_doc, dict):
-        custom_info_doc = structure_custom_information_document(
-            custom_info_doc, "custom information document"
-        )
-    if not is_dataclass(custom_info_doc):
+    # Convert to a dictionary first, so we can clean up values.
+    if is_dataclass(custom_info_doc):
+        custom_info_dict = asdict(custom_info_doc)
+    elif isinstance(custom_info_doc, dict):
+        custom_info_dict = custom_info_doc
+    else:
         msg = f"Invalid custom_info_doc: {custom_info_doc}"
         raise ValueError(msg)
 
-    # Do not add custom info doc if all values are None
-    if all(value is None for value in asdict(custom_info_doc).values()):
+    # Remove None and {"value": None, "unit"...} values
+    cleaned_dict = {}
+    for key, value in custom_info_dict.items():
+        if value is None:
+            continue
+        if isinstance(value, dict) and "value" in value and value["value"] is None:
+            continue
+        cleaned_dict[key] = value
+
+    # If dict is empty after cleaning, do not attach.
+    if not cleaned_dict:
         return model
 
+    custom_info_doc = structure_custom_information_document(
+        cleaned_dict, "custom information document"
+    )
+
     model.custom_information_document = custom_info_doc  # type: ignore
     return model
 

src/allotropy/allotrope/schema_mappers/adm/spectrophotometry/benchling/_2023/_12/spectrophotometry.py

@@ -406,6 +406,16 @@ def _get_sample_document(self, measurement: Measurement) -> SampleDocument:
                 measurement.original_sample_concentration,
             )
         }
+        # TODO: this is a temporary work around until we implement the new REC custom info doc logic, at which
+        # time we will detect and convert timestamps generically.
+        if (
+            measurement.sample_custom_info
+            and "last read standards" in measurement.sample_custom_info
+        ):
+            measurement.sample_custom_info["last read standards"] = self.get_date_time(
+                measurement.sample_custom_info["last read standards"]
+            )
+
         return add_custom_information_document(
             SampleDocument(
                 sample_identifier=measurement.sample_identifier,

src/allotropy/parsers/thermo_fisher_qubit4/thermo_fisher_qubit4_reader.py

@@ -1,5 +1,6 @@
 """Reader file for ThermoFisher Qubit 4 Adapter"""
 
+import numpy as np
 import pandas as pd
 
 from allotropy.constants import DEFAULT_ENCODING
@@ -35,18 +36,17 @@ def read(cls, named_file_contents: NamedFileContents) -> pd.DataFrame:
         AllotropeConversionError: If the file format is not supported.
         """
         if named_file_contents.extension == "xlsx":
-            dataframe = read_excel(named_file_contents.contents)
+            df = read_excel(named_file_contents.contents)
         else:
-            dataframe = read_csv(
-                named_file_contents.contents,
-                index_col=False,
-                encoding=DEFAULT_ENCODING,
+            df = read_csv(
+                named_file_contents.contents, index_col=False, encoding=DEFAULT_ENCODING
             )
 
-        columns = dataframe.columns.tolist()
+        columns = df.columns.tolist()
         new_columns = [
             f"Units_{columns[i - 1]}" if "Units" in col else col
             for i, col in enumerate(columns)
         ]
-        set_columns(dataframe, new_columns)
-        return dataframe
+        set_columns(df, new_columns)
+        df = df.replace(np.nan, None)
+        return df