Addition of autofilling excel forms. Improved pydantic validation.

src/submissions/backend/pydant/__init__.py

@@ -1,65 +1,153 @@
 import uuid
-from pydantic import BaseModel, validator
-from datetime import date
+from pydantic import BaseModel, field_validator, model_validator, Extra
+from datetime import date, datetime
 from typing import List, Any
 from tools import RSLNamer
 from pathlib import Path
 import re
 import logging
+from tools import check_not_nan, convert_nans_to_nones
+import numpy as np
+
+
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
-class PydSubmission(BaseModel):
+class PydReagent(BaseModel):
+    type: str|None
+    lot: str|None
+    exp: date|None
+
+    @field_validator("type", mode='before')
+    @classmethod
+    def remove_undesired_types(cls, value):
+        match value:
+            case "atcc":
+                return None
+            case _:
+                return value
+
+    @field_validator("lot", mode='before')
+    @classmethod
+    def enforce_lot_string(cls, value):
+        if value != None:
+            return convert_nans_to_nones(str(value))
+        return value
+            
+    @field_validator("exp", mode="before")
+    @classmethod
+    def enforce_date(cls, value):
+        if isinstance(value, float) or value == np.nan:
+            raise ValueError(f"Date cannot be a float: {value}")
+        else:
+            return value
+
+    
+
+class PydSubmission(BaseModel, extra=Extra.allow):
+    ctx: dict
     filepath: Path
     submission_type: str
     submitter_plate_num: str|None
-    rsl_plate_num: str
+    rsl_plate_num: str|dict|None
     submitted_date: date
-    submitting_lab: str
+    submitting_lab: str|None
     sample_count: int
-    extraction_kit: str
-    technician: str
-    reagents: List[dict]
+    extraction_kit: str|dict|None
+    technician: str|None
+    reagents: List[PydReagent] = []
     samples: List[Any]
-
-    @validator("submitted_date", pre=True)
+    # missing_fields: List[str] = []
+    
+    @field_validator("submitted_date", mode="before")
     @classmethod
     def strip_datetime_string(cls, value):
+        if isinstance(value, datetime):
+            return value
+        if isinstance(value, date):
+            return value
         return re.sub(r"_\d$", "", value)
 
-    @validator("submitter_plate_num")
+    @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()
-
-    @validator("rsl_plate_num", pre=True)
-    @classmethod
-    def rsl_from_file(cls, value, values):
-        if value == None:
-            logger.debug(f"Pydant values:\n{values}")
-            return RSLNamer(values['filepath'].__str__()).parsed_name
         else:
             return value
         
-    @validator("technician")
+    @field_validator("submitting_lab", mode="before")
+    @classmethod
+    def transform_nan(cls, value):
+        return convert_nans_to_nones(value)
+
+    @field_validator("rsl_plate_num", mode='before')
+    @classmethod
+    def rsl_from_file(cls, value, values):
+        logger.debug(f"RSL-plate initial value: {value}")
+        if check_not_nan(value):
+            if isinstance(value, str):
+                return dict(value=value, parsed=True)
+            else:
+                return value
+        else:
+            logger.debug(f"Pydant values:{type(values)}\n{values}")
+            return dict(value=RSLNamer(values.data['filepath'].__str__()).parsed_name, parsed=False)
+
+    @field_validator("technician")
     @classmethod
     def enforce_tech(cls, value):
         if value == "nan" or value == "None":
             value = "Unknown"
-        # elif len(value.split(",")) > 1:
-        #     tech_reg = re.compile(r"\b[A-Z]{2}\b")
-        #     value = ", ".join(tech_reg.findall(value))
         return value
     
-    @validator("reagents")
+    @field_validator("reagents")
     @classmethod
     def remove_atcc(cls, value):
         return_val = []
         for reagent in value:
-            match reagent['type']:
-                case 'atcc':
-                    continue
-                case _:
-                    return_val.append(reagent)
+            logger.debug(f"Pydantic reagent: {reagent}")
+            # match reagent.type.lower():
+            #     case 'atcc':
+            #         continue
+            #     case _:
+            #         return_val.append(reagent)
+            if reagent.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:
+            # raise ValueError(f"{value} could not be used to create an integer.")
+            return convert_nans_to_nones(value)
+        
+    @field_validator("extraction_kit", mode='before')
+    @classmethod
+    def get_kit_if_none(cls, value, values):
+        from frontend.custom_widgets.pop_ups import KitSelector
+        if check_not_nan(value):
+            return dict(value=value, parsed=True)
+        else:
+            # logger.debug(values.data)
+            dlg = KitSelector(ctx=values.data['ctx'], title="Kit Needed", message="At minimum a kit is needed. Please select one.")
+            if dlg.exec():
+                return dict(value=dlg.getValues(), parsed=False)
+            else:
+                raise ValueError("Extraction kit needed.") 
+
+    # @model_validator(mode="after")
+    # def ensure_kit(cls, values):
+    #     logger.debug(f"Model values: {values}")
+    #     missing_fields = [k for k,v in values if v == None]
+    #     if len(missing_fields) > 0:
+    #         logger.debug(f"Missing fields: {missing_fields}")
+    #         values['missing_fields'] = missing_fields
+    #     return values
+
+