Bug fixing for new AddEdit forms.

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

@@ -243,7 +243,10 @@ class BaseClass(Base):
     @classmethod
     def get_pydantic_model(cls):
         from backend.validators import pydant
-        model = getattr(pydant, f"Pyd{cls.__name__}")
+        try:
+            model = getattr(pydant, f"Pyd{cls.__name__}")
+        except AttributeError:
+            return None
         return model
 
 

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

@@ -286,6 +286,10 @@ class Control(BaseClass):
         """
         return None
 
+    def delete(self):
+        self.__database_session__.delete(self)
+        self.__database_session__.commit()
+
 
 class PCRControl(Control):
     """
@@ -296,7 +300,7 @@ class PCRControl(Control):
     subtype = Column(String(16))  #: PC or NC
     target = Column(String(16))  #: N1, N2, etc.
     ct = Column(FLOAT) #: PCR result
-    reagent_lot = Column(String(64), ForeignKey("_reagent.name", ondelete="SET NULL",
+    reagent_lot = Column(String(64), ForeignKey("_reagent.lot", ondelete="SET NULL",
                                                 name="fk_reagent_lot"))
     reagent = relationship("Reagent", foreign_keys=reagent_lot) #: reagent used for this control
 

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

@@ -540,6 +540,24 @@ class Reagent(BaseClass, LogMixin):
         report.add_result(Result(msg=f"Updating last used {rt} was not performed.", status="Information"))
         return report
 
+    @classmethod
+    def query_or_create(cls, **kwargs) -> Reagent:
+        from backend.validators.pydant import PydReagent
+        new = False
+        instance = cls.query(**kwargs)
+        if not instance or isinstance(instance, list):
+            if "role" not in kwargs:
+                try:
+                    kwargs['role'] = kwargs['name']
+                except KeyError:
+                    pass
+            instance = PydReagent(**kwargs)
+            new = True
+            instance, _ = instance.toSQL()
+        logger.debug(f"Instance: {instance}")
+        return instance, new
+
+
     @classmethod
     @setup_lookup
     def query(cls,

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

@@ -936,14 +936,20 @@ class BasicSubmission(BaseClass, LogMixin):
             Generator[dict, None, None]: Dictionaries of row values.
         """
         location_map = cls.get_submission_type().sample_map['pcr_controls']
+        # logger.debug(f"Location map: {location_map}")
         submission = cls.query(rsl_plate_num=rsl_plate_num)
         name_column = 1
         for item in location_map:
+            logger.debug(f"Checking {item}")
             worksheet = xl[item['sheet']]
             for iii, row in enumerate(worksheet.iter_rows(max_row=len(worksheet['A']), max_col=name_column), start=1):
+                logger.debug(f"Checking row {row}, {iii}")
                 for cell in row:
+                    logger.debug(f"Checking cell: {cell}, with value {cell.value} against {item['name']}")
                     if cell.value == item['name']:
-                        subtype, target = item['name'].split("-")
+                        subtype, _ = item['name'].split("-")
+                        target = item['target']
+                        logger.debug(f"Subtype: {subtype}, target: {target}")
                         ct = worksheet.cell(row=iii, column=item['ct_column']).value
                         # NOTE: Kind of a stop gap solution to find control reagents.
                         if subtype == "PC":
@@ -955,6 +961,9 @@ class BasicSubmission(BaseClass, LogMixin):
                             ctrl = next((assoc.reagent for assoc in submission.submission_reagent_associations
                                          if any(["molecular grade water" in item.name.lower() for item in
                                                  assoc.reagent.role])), None)
+                        else:
+                            ctrl = None
+                        logger.debug(f"Control reagent: {ctrl.__dict__}")
                         try:
                             ct = float(ct)
                         except ValueError:
@@ -963,13 +972,15 @@ class BasicSubmission(BaseClass, LogMixin):
                             ctrl = ctrl.lot
                         else:
                             ctrl = None
-                        yield dict(
-                            name=f"{rsl_plate_num}<{item['name']}>",
+                        output = dict(
+                            name=f"{rsl_plate_num}<{item['name']}-{target}>",
                             ct=ct,
                             subtype=subtype,
                             target=target,
                             reagent_lot=ctrl
                         )
+                        logger.debug(f"Control output: {pformat(output)}")
+                        yield output
 
     @classmethod
     def filename_template(cls) -> str:
@@ -1663,10 +1674,12 @@ class Wastewater(BasicSubmission):
         submitted_date = datetime.strptime(" ".join(parser.pcr['run_start_date/time'].split(" ")[:-1]),
                                            "%Y-%m-%d %I:%M:%S %p")
         for control in pcr_controls:
+            logger.debug(f"Control coming into save: {control}")
             new_control = PCRControl(**control)
             new_control.submitted_date = submitted_date
             new_control.controltype = controltype
             new_control.submission = self
+            logger.debug(f"Control coming into save: {new_control.__dict__}")
             new_control.save()
         return report