Big update, semi-functional

src/submissions/backend/pydant/__init__.py

@@ -48,34 +48,65 @@ class PydReagent(BaseModel):
         if value != None:
             return convert_nans_to_nones(str(value))
         return value
+    
+    @field_validator("name", mode="before")
+    @classmethod
+    def enforce_name(cls, value, values):
+        if value != None:
+            return convert_nans_to_nones(str(value))
+        else:
+            return values.data['type']
 
     
 
 class PydSubmission(BaseModel, extra=Extra.allow):
     ctx: Settings
     filepath: Path
-    submission_type: str|dict|None
-    submitter_plate_num: str|None
-    rsl_plate_num: str|dict|None
-    submitted_date: date|dict
-    submitting_lab: str|None
-    sample_count: int
-    extraction_kit: str|dict|None
-    technician: str|dict|None
-    reagents: List[PydReagent] = []
+    submission_type: dict|None
+    submitter_plate_num: dict|None
+    rsl_plate_num: dict|None
+    submitted_date: dict|None
+    submitting_lab: dict|None
+    sample_count: dict|None
+    extraction_kit: dict|None
+    technician: dict|None
+    reagents: List[dict] = []
     samples: List[Any]
     # missing_fields: List[str] = []
     
+    @field_validator("submitter_plate_num")
+    @classmethod
+    def rescue_submitter_id(cls, value):
+        if value == None:
+            return dict(value=None, parsed=False)
+        return value
+
+    @field_validator("submitter_plate_num")
+    @classmethod
+    def enforce_with_uuid(cls, value):
+        logger.debug(f"submitter plate id: {value}")
+        if value['value'] == None:
+            return dict(value=uuid.uuid4().hex.upper(), parsed=False)
+        else:
+            return value
+    
     @field_validator("submitted_date", mode="before")
     @classmethod
+    def rescue_date(cls, value):
+        if value == None:
+            return dict(value=date.today(), parsed=False)
+        return value
+
+    @field_validator("submitted_date")
+    @classmethod
     def strip_datetime_string(cls, value):
-        if not check_not_nan(value):
-            value = date.today()
-        if isinstance(value, datetime):
-            return dict(value=value, parsed=True)
-        if isinstance(value, date):
+        if isinstance(value['value'], datetime):
             return value
-        string = re.sub(r"(_|-)\d$", "", value)
+        if isinstance(value['value'], date):
+            return value
+        if isinstance(value['value'], int):
+            return dict(value=datetime.fromordinal(datetime(1900, 1, 1).toordinal() + value['value'] - 2).date(), parsed=False)
+        string = re.sub(r"(_|-)\d$", "", value['value'])
         try:
             output = dict(value=parse(string).date(), parsed=False)
         except ParserError as e:
@@ -85,31 +116,32 @@ class PydSubmission(BaseModel, extra=Extra.allow):
             except Exception as e:
                 logger.error(f"Problem with parse fallback: {e}")
         return output
-
-    @field_validator("submitter_plate_num")
-    @classmethod
-    def enforce_with_uuid(cls, value):
-        if value == None or value == "" or value == "None":
-            return uuid.uuid4().hex.upper()
-        else:
-            return value
         
     @field_validator("submitting_lab", mode="before")
     @classmethod
-    def transform_nan(cls, value):
-        return convert_nans_to_nones(value)
+    def rescue_submitting_lab(cls, value):
+        if value == None:
+            return dict(value=None, parsed=False)
+        return value
 
     @field_validator("rsl_plate_num", mode='before')
     @classmethod
+    def rescue_rsl_number(cls, value):
+        if value == None:
+            return dict(value=None, parsed=False)
+        return value
+
+    @field_validator("rsl_plate_num")
+    @classmethod
     def rsl_from_file(cls, value, values):
-        logger.debug(f"RSL-plate initial value: {value}")
-        if isinstance(values.data['submission_type'], dict):
-            sub_type = values.data['submission_type']['value']
-        elif isinstance(values.data['submission_type'], str):
-            sub_type = values.data['submission_type']
-        if check_not_nan(value):
-            if lookup_submission_by_rsl_num(ctx=values.data['ctx'], rsl_num=value) == None:
-                return dict(value=value, parsed=True)
+        logger.debug(f"RSL-plate initial value: {value['value']}")
+        # if isinstance(values.data['submission_type'], dict):
+        #     sub_type = values.data['submission_type']['value']
+        # elif isinstance(values.data['submission_type'], str):
+        sub_type = values.data['submission_type']['value']
+        if check_not_nan(value['value']):
+            if lookup_submission_by_rsl_num(ctx=values.data['ctx'], rsl_num=value['value']) == None:
+                return dict(value=value['value'], parsed=True)
             else:
                 logger.warning(f"Submission number {value} already exists in DB, attempting salvage with filepath")
                 output = RSLNamer(ctx=values.data['ctx'], instr=values.data['filepath'].__str__(), sub_type=sub_type).parsed_name
@@ -120,58 +152,60 @@ class PydSubmission(BaseModel, extra=Extra.allow):
 
     @field_validator("technician", mode="before")
     @classmethod
+    def rescue_tech(cls, value):
+        if value == None:
+            return dict(value=None, parsed=False)
+        return value
+
+    @field_validator("technician")
+    @classmethod
     def enforce_tech(cls, value):
-        if check_not_nan(value):
-            if isinstance(value, dict):
-                value['value'] = re.sub(r"\: \d", "", value['value'])
-                return value
-            else:
-                return dict(value=re.sub(r"\: \d", "", value), parsed=True)
+        if check_not_nan(value['value']):
+            value['value'] = re.sub(r"\: \d", "", value['value'])
+            return value
         else:
-            return dict(value="Unnamed", parsed=False)
+            return dict(value=convert_nans_to_nones(value['value']), parsed=False)
         return value
     
-    @field_validator("reagents")
-    @classmethod
-    def remove_atcc(cls, value):
-        return_val = []
-        for reagent in value:
-            logger.debug(f"Pydantic reagent: {reagent}")
-            if reagent.type == None:
-                continue
-            else:
-                return_val.append(reagent)
-        return return_val
+    # @field_validator("reagents")
+    # @classmethod
+    # def remove_atcc(cls, value):
+    #     return_val = []
+    #     for reagent in value:
+    #         logger.debug(f"Pydantic reagent: {reagent}")
+    #         if reagent['value'].type == None:
+    #             continue
+    #         else:
+    #             return_val.append(reagent)
+    #     return return_val
         
     @field_validator("sample_count", mode='before')
     @classmethod
-    def enforce_sample_count(cls, value):
-        if check_not_nan(value):
-            return int(value)
-        else:
-            return convert_nans_to_nones(value)
+    def rescue_sample_count(cls, value):
+        if value == None:
+            return dict(value=None, parsed=False)
+        return value
         
     @field_validator("extraction_kit", mode='before')
     @classmethod
-    def get_kit_if_none(cls, value):
+    def rescue_kit(cls, value):
         # from frontend.custom_widgets.pop_ups import KitSelector
-        if check_not_nan(value):
-            if isinstance(value, str):
-                return dict(value=value, parsed=True)
-            elif isinstance(value, dict):
-                return value
-        else:
-            raise ValueError(f"No extraction kit found.")
+        # if check_not_nan(value):
+        #     if isinstance(value, str):
+        #         return dict(value=value, parsed=True)
+        #     elif isinstance(value, dict):
+        #         return value
+        # else:
+        #     raise ValueError(f"No extraction kit found.")
+        if value == None:
+            return dict(value=None, parsed=False)
+        return value
             
-    
     @field_validator("submission_type", mode='before')
     @classmethod
     def make_submission_type(cls, value, values):
-        if check_not_nan(value):
-            if isinstance(value, dict):
-                value['value'] = value['value'].title()
-                return value
-            elif isinstance(value, str):
-                return dict(value=value.title(), parsed=False)
+        if check_not_nan(value['value']):
+            value = value['value'].title()
+            return dict(value=value, parsed=True)
         else:
             return dict(value=RSLNamer(ctx=values.data['ctx'], instr=values.data['filepath'].__str__()).submission_type.title(), parsed=False)