Adaptations to allow for stand alone scripts.

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

@@ -339,7 +339,6 @@ class Reagent(BaseClass):
     
     submissions = association_proxy("reagent_submission_associations", "submission") #: Association proxy to SubmissionSampleAssociation.samples
 
-
     def __repr__(self):
         if self.name != None:
             return f"<Reagent({self.name}-{self.lot})>"

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

@@ -41,7 +41,8 @@ class Organization(BaseClass):
 
     @classmethod
     @setup_lookup
-    def query(cls, 
+    def query(cls,
+                id:int|None=None, 
                 name:str|None=None,
                 limit:int=0,
                 ) -> Organization|List[Organization]:
@@ -56,6 +57,12 @@ class Organization(BaseClass):
             Organization|List[Organization]: 
         """    
         query: Query = cls.__database_session__.query(cls)
+        match id:
+            case int():
+                query = query.filter(cls.id==id)
+                limit = 1
+            case _:
+                pass
         match name:
             case str():
                 # logger.debug(f"Looking up organization with name: {name}")

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

@@ -1242,9 +1242,9 @@ class Wastewater(BasicSubmission):
         outstr = super().enforce_name(instr=instr, data=data)
         try:
             outstr = re.sub(r"PCR(-|_)", "", outstr)
-        except AttributeError as e:
+        except (AttributeError, TypeError) as e:
             logger.error(f"Problem using regex: {e}")
-            outstr = RSLNamer.construct_new_plate_name(instr=outstr)
+            outstr = RSLNamer.construct_new_plate_name(data=data)
         outstr = outstr.replace("RSLWW", "RSL-WW")
         outstr = re.sub(r"WW(\d{4})", r"WW-\1", outstr, flags=re.IGNORECASE)
         outstr = re.sub(r"(\d{4})-(\d{2})-(\d{2})", r"\1\2\3", outstr)