Pre-refactor

TODO.md

@@ -1,3 +1,4 @@
+- [x] Change 'check_is_power_user' to decorator.
 - [x] Drag and drop files into submission form area?
 - [ ] Get info for controls into their sample hitpicks.
 - [x] Move submission-type specific parser functions into class methods in their respective models.

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

src/submissions/tools/__init__.py

@@ -6,7 +6,6 @@ import re
 import numpy as np
 import logging
 import pandas as pd
-from datetime import datetime
 from jinja2 import Environment, FileSystemLoader
 import yaml
 import sys, os, stat, platform, getpass
@@ -18,6 +17,7 @@ from sqlalchemy import create_engine
 from pydantic import field_validator
 from pydantic_settings import BaseSettings, SettingsConfigDict
 from typing import Any, Tuple
+from datetime import datetime
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -133,18 +133,21 @@ def massage_common_reagents(reagent_name:str):
         reagent_name = "molecular_grade_water"
     reagent_name = reagent_name.replace("µ", "u")
     return reagent_name
-        
+
 class RSLNamer(object):
     """
     Object that will enforce proper formatting on RSL plate names.
     """
     def __init__(self, ctx, instr:str, sub_type:str|None=None):
+        from backend.db.functions import get_polymorphic_subclass
+        from backend.db.models import BasicSubmission
         self.ctx = ctx
         self.submission_type = sub_type
         self.retrieve_rsl_number(in_str=instr)
         if self.submission_type != None:
-            parser = getattr(self, f"enforce_{self.submission_type.replace(' ', '_').lower()}")
-            parser()
+            custom_enforcer = get_polymorphic_subclass(BasicSubmission, self.submission_type).enforce_naming_schema
+            # parser = getattr(self, f"enforce_{self.submission_type.replace(' ', '_').lower()}")
+            # parser()
             self.parsed_name = self.parsed_name.replace("_", "-")
         
     def retrieve_rsl_number(self, in_str:str|Path):
@@ -220,8 +223,6 @@ class RSLNamer(object):
             repeat = ""
         self.parsed_name = re.sub(r"(-\dR)\d?", rf"\1 {repeat}", self.parsed_name).replace(" ", "")
         
-    
-
     def enforce_bacterial_culture(self):
         """
         Uses regex to enforce proper formatting of bacterial culture samples
@@ -588,6 +589,7 @@ def jinja_template_loading():
 def check_is_power_user(ctx:Settings) -> bool:
     """
     Check to ensure current user is in power users list.
+    NOTE: Depreciated in favour of 'check_authorization' below.
 
     Args:
         ctx (dict): settings passed down from gui.
@@ -604,6 +606,16 @@ def check_is_power_user(ctx:Settings) -> bool:
         check = False
     return check
 
+def check_authorization(func):
+    def wrapper(*args, **kwargs):
+        logger.debug(f"Checking authorization")
+        if getpass.getuser() in kwargs['ctx'].power_users:
+            return func(*args, **kwargs)
+        else:
+            logger.error(f"User {getpass.getuser()} is not authorized for this function.")
+            return dict(code=1, message="This user does not have permission for this function.", status="warning")
+    return wrapper
+
 def check_if_app(ctx:Settings=None) -> bool:
     """
     Checks if the program is running from pyinstaller compiled
@@ -636,4 +648,3 @@ def convert_well_to_row_column(input_str:str) -> Tuple[int, int]:
     except IndexError:
         return None, None
     return row, column
-