Pre code clean-up

src/submissions/backend/validators/__init__.py

@@ -49,12 +49,13 @@ class RSLNamer(object):
             str: parsed submission type
         """
         def st_from_path(filename:Path) -> str:
-            logger.debug(f"Using path method for {filename}.")
+            logger.info(f"Using path method for {filename}.")
             if filename.exists():
                 wb = load_workbook(filename)
                 try:
                     # NOTE: Gets first category in the metadata.
-                    submission_type = next(item.strip().title() for item in wb.properties.category.split(";"))
+                    categories = wb.properties.category.split(";")
+                    submission_type = next(item.strip().title() for item in categories)
                 except (StopIteration, AttributeError):
                     sts = {item.name: item.get_template_file_sheets() for item in SubmissionType.query()}
                     try:
@@ -67,12 +68,12 @@ class RSLNamer(object):
             return submission_type
         def st_from_str(filename:str) -> str:
             regex = BasicSubmission.construct_regex()
-            logger.debug(f"Using string method for {filename}.")
-            logger.debug(f"Using regex: {regex}")
+            logger.info(f"Using string method for {filename}.")
+            # logger.debug(f"Using regex: {regex}")
             m = regex.search(filename)
             try:
                 submission_type = m.lastgroup
-                logger.debug(f"Got submission type: {submission_type}")
+                # logger.debug(f"Got submission type: {submission_type}")
             except AttributeError as e:
                 submission_type = None
                 logger.critical(f"No submission type found or submission type found!: {e}")
@@ -118,7 +119,7 @@ class RSLNamer(object):
                 regex = re.compile(rf'{regex}', re.IGNORECASE | re.VERBOSE)
             except re.error as e:
                 regex = BasicSubmission.construct_regex()
-        logger.debug(f"Using regex: {regex}")
+        logger.info(f"Using regex: {regex}")
         match filename:
             case Path():
                 m = regex.search(filename.stem)

src/submissions/backend/validators/pydant.py

@@ -57,14 +57,14 @@ class PydReagent(BaseModel):
     @classmethod
     def rescue_lot_string(cls, value):
         if value is not None:
-            return convert_nans_to_nones(str(value))
+            return convert_nans_to_nones(str(value).strip())
         return value
 
     @field_validator("lot")
     @classmethod
     def enforce_lot_string(cls, value):
         if value is not None:
-            return value.upper()
+            return value.upper().strip()
         return value
 
     @field_validator("expiry", mode="before")
@@ -97,9 +97,9 @@ class PydReagent(BaseModel):
     @classmethod
     def enforce_name(cls, value, values):
         if value is not None:
-            return convert_nans_to_nones(str(value))
+            return convert_nans_to_nones(str(value).strip())
         else:
-            return values.data['role']
+            return values.data['role'].strip()
 
     def improved_dict(self) -> dict:
         """
@@ -210,6 +210,18 @@ class PydSample(BaseModel, extra='allow'):
     def int_to_str(cls, value):
         return str(value)
 
+    @field_validator("submitter_id")
+    @classmethod
+    def strip_sub_id(cls, value):
+        match value:
+            case dict():
+                value['value'] = value['value'].strip().upper()
+            case str():
+                value = value.strip().upper()
+            case _:
+                pass
+        return value
+
     def improved_dict(self) -> dict:
         """
         Constructs a dictionary consisting of model.fields and model.extras
@@ -439,6 +451,7 @@ class PydSubmission(BaseModel, extra='allow'):
         if value['value'] in [None, "None"]:
             return dict(value=uuid.uuid4().hex.upper(), missing=True)
         else:
+            value['value'] = value['value'].strip()
             return value
 
     @field_validator("submitted_date", mode="before")
@@ -523,6 +536,7 @@ class PydSubmission(BaseModel, extra='allow'):
         # logger.debug(f"RSL-plate initial value: {value['value']} and other values: {values.data}")
         sub_type = values.data['submission_type']['value']
         if check_not_nan(value['value']):
+            value['value'] = value['value'].strip()
             return value
         else:
             # logger.debug("Constructing plate sub_type.")
@@ -808,6 +822,7 @@ class PydSubmission(BaseModel, extra='allow'):
                     for sample in self.samples:
                         sample, associations, _ = sample.toSQL(submission=instance)
                         # logger.debug(f"Sample SQL object to be added to submission: {sample.__dict__}")
+                        logger.debug(associations)
                         for assoc in associations:
                             if assoc is not None and assoc not in instance.submission_sample_associations:
                                 instance.submission_sample_associations.append(assoc)