Updating AddEdit to hopefully include ReagentAdd

src/submissions/backend/db/models/kits.py

@@ -608,7 +608,7 @@ class Reagent(BaseClass, LogMixin):
                         if isinstance(value, str):
                             field_value = datetime.strptime(value, "%Y-%m-%d")
                         elif isinstance(value, date):
-                            field_value = datetime.combine(value, datetime.min.time())
+                            field_value = datetime.combine(value, datetime.max.time())
                         else:
                             field_value = value
                         field_value.replace(tzinfo=timezone)

src/submissions/backend/db/models/submissions.py

@@ -1502,6 +1502,25 @@ class Wastewater(BasicSubmission):
                     logger.error(f"Error handling couldn't get csv due to: {e}")
         return input_dict
 
+    @classmethod
+    def parse_samples(cls, input_dict: dict) -> dict:
+        """
+        Update sample dictionary with type specific information. Extends parent
+
+        Args:
+            input_dict (dict): Input sample dictionary
+
+        Returns:
+            dict: Updated sample dictionary
+        """
+        input_dict = super().parse_samples(input_dict=input_dict)
+        # NOTE: Had to put in this section due to ENs not having rsl_number and therefore not getting PCR results.
+        check = check_key_or_attr("rsl_number", input_dict)
+        if not check:
+            input_dict['rsl_number'] = input_dict['submitter_id']
+        # logger.debug(pformat(input_dict, indent=4))
+        return input_dict
+
     @classmethod
     def parse_pcr(cls, xl: Workbook, rsl_plate_num: str) -> Generator[dict, None, None]:
         """
@@ -1633,6 +1652,7 @@ class Wastewater(BasicSubmission):
         self.save(original=False)
         for sample in self.samples:
             try:
+                # NOTE: Fix for ENs which have no rsl_number...
                 sample_dict = next(item for item in pcr_samples if item['sample'] == sample.rsl_number)
             except StopIteration:
                 continue
@@ -2539,7 +2559,7 @@ class WastewaterSample(BasicSample):
         Custom sample parser. Extends parent
 
         Args:
-            input_dict (dict): Basic parser results.
+            input_dict (dict): Basic parser results for this sample.
 
         Returns:
             dict: Updated parser results.
@@ -2554,6 +2574,8 @@ class WastewaterSample(BasicSample):
             output_dict['rsl_number'] = "RSL-WW-" + output_dict['ww_processing_num']
         if output_dict['ww_full_sample_id'] is not None and output_dict["submitter_id"] in disallowed:
             output_dict["submitter_id"] = output_dict['ww_full_sample_id']
+        check = check_key_or_attr("rsl_number", output_dict, check_none=True)
+        # logger.debug(pformat(output_dict, indent=4))
         return output_dict
 
     @classmethod

src/submissions/backend/validators/pydant.py

@@ -144,7 +144,9 @@ class PydReagent(BaseModel):
                     case "expiry":
                         if isinstance(value, str):
                             value = date(year=1970, month=1, day=1)
-                        value = datetime.combine(value, datetime.min.time())
+                        # NOTE: if min time is used, any reagent set to expire today (Bac postive control, eg) will have expired at midnight and therefore be flagged.
+                        # NOTE: Make expiry at date given, plus now time + 1 hour
+                        value = datetime.combine(value, datetime.max.time())
                         reagent.expiry = value.replace(tzinfo=timezone)
                     case _:
                         try:
@@ -826,7 +828,7 @@ class PydSubmission(BaseModel, extra='allow'):
                 case item if item in instance.timestamps():
                     logger.warning(f"Incoming timestamp key: {item}, with value: {value}")
                     if isinstance(value, date):
-                        value = datetime.combine(value, datetime.min.time())
+                        value = datetime.combine(value, datetime.max.time())
                         value = value.replace(tzinfo=timezone)
                     elif isinstance(value, str):
                         value: datetime = datetime.strptime(value, "%Y-%m-%d")
@@ -961,7 +963,7 @@ class PydSubmission(BaseModel, extra='allow'):
             if reagent not in exempt:
                 role_expiry = ReagentRole.query(name=reagent.role).eol_ext
                 try:
-                    dt = datetime.combine(reagent.expiry, datetime.min.time())
+                    dt = datetime.combine(reagent.expiry, datetime.max.time())
                 except TypeError:
                     continue
                 if datetime.now() > dt + role_expiry: