Pre-refactor

src/submissions/backend/db/functions/constructions.py

@@ -2,7 +2,7 @@
 Used to construct models from input dictionaries.
 '''
 from getpass import getuser
-from tools import Settings, RSLNamer, check_regex_match
+from tools import Settings, RSLNamer, check_regex_match, check_authorization, massage_common_reagents
 from .. import models
 from .lookups import *
 import logging
@@ -190,6 +190,7 @@ def construct_samples(ctx:Settings, instance:models.BasicSubmission, samples:Lis
             continue
     return instance
 
+@check_authorization
 def construct_kit_from_yaml(ctx:Settings, kit_dict:dict) -> dict:
     """
     Create and store a new kit in the database based on a .yml file
@@ -197,16 +198,16 @@ def construct_kit_from_yaml(ctx:Settings, kit_dict:dict) -> dict:
 
     Args:
         ctx (Settings): Context object passed down from frontend
-        exp (dict): Experiment dictionary created from yaml file
+        kit_dict (dict): Experiment dictionary created from yaml file
 
     Returns:
         dict: a dictionary containing results of db addition
     """    
-    from tools import check_is_power_user, massage_common_reagents
+    # from tools import check_is_power_user, massage_common_reagents
     # Don't want just anyone adding kits
-    if not check_is_power_user(ctx=ctx):
-        logger.debug(f"{getuser()} does not have permission to add kits.")
-        return {'code':1, 'message':"This user does not have permission to add kits.", "status":"warning"}
+    # if not check_is_power_user(ctx=ctx):
+    #     logger.debug(f"{getuser()} does not have permission to add kits.")
+    #     return {'code':1, 'message':"This user does not have permission to add kits.", "status":"warning"}
     submission_type = lookup_submission_type(ctx=ctx, name=kit_dict['used_for'])
     logger.debug(f"Looked up submission type: {kit_dict['used_for']} and got {submission_type}")
     kit = models.KitType(name=kit_dict["kit_name"])

src/submissions/backend/db/functions/misc.py

@@ -258,4 +258,3 @@ def get_polymorphic_subclass(base:object, polymorphic_identity:str|None=None):
             logger.error(f"Could not get polymorph {polymorphic_identity} of {base} due to {e}")
             return base
 
-    

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

@@ -294,6 +294,19 @@ class BasicSubmission(Base):
             Workbook: updated workbook
         """        
         return input_excel
+    
+    @classmethod
+    def enforce_naming_schema(cls, input_str:str) -> str:
+        """
+        Used to ensure proper custom naming of submission.
+
+        Args:
+            input_str (str): name parsed by default parser
+
+        Returns:
+            str: custom parser output.
+        """        
+        return input_str
 
 # Below are the custom submission types
 

src/submissions/backend/pydant/__init__.py

@@ -2,7 +2,7 @@
 Contains pydantic models and accompanying validators
 '''
 import uuid
-from pydantic import BaseModel, field_validator, Extra, Field
+from pydantic import BaseModel, field_validator, Field
 from datetime import date, datetime
 from dateutil.parser import parse
 from dateutil.parser._parser import ParserError
@@ -74,7 +74,7 @@ class PydReagent(BaseModel):
 
     
 
-class PydSubmission(BaseModel, extra=Extra.allow):
+class PydSubmission(BaseModel, extra='allow'):
     ctx: Settings
     filepath: Path
     submission_type: dict|None