Pydantic added for validation.

src/submissions/backend/pydant/__init__.py

@@ -0,0 +1,65 @@
+import uuid
+from pydantic import BaseModel, validator
+from datetime import date
+from typing import List, Any
+from tools import RSLNamer
+from pathlib import Path
+import re
+import logging
+
+logger = logging.getLogger(f"submissions.{__name__}")
+
+class PydSubmission(BaseModel):
+    filepath: Path
+    submission_type: str
+    submitter_plate_num: str|None
+    rsl_plate_num: str
+    submitted_date: date
+    submitting_lab: str
+    sample_count: int
+    extraction_kit: str
+    technician: str
+    reagents: List[dict]
+    samples: List[Any]
+
+    @validator("submitted_date", pre=True)
+    @classmethod
+    def strip_datetime_string(cls, value):
+        return re.sub(r"_\d$", "", value)
+
+    @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")
+    @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")
+    @classmethod
+    def remove_atcc(cls, value):
+        return_val = []
+        for reagent in value:
+            match reagent['type']:
+                case 'atcc':
+                    continue
+                case _:
+                    return_val.append(reagent)
+        return return_val