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

@@ -42,6 +42,7 @@ class Organization(BaseClass):
     @classmethod
     @setup_lookup
     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)

src/submissions/backend/excel/parser.py

@@ -274,7 +274,7 @@ class SampleParser(object):
     object to pull data for samples in excel sheet and construct individual sample objects
     """
 
-    def __init__(self, xl:pd.ExcelFile, submission_type:str) -> None:
+    def __init__(self, xl:pd.ExcelFile, submission_type:str, sample_map:dict|None=None) -> None:
         """
         convert sample sub-dataframe to dictionary of records
 
@@ -286,7 +286,7 @@ class SampleParser(object):
         self.samples = []
         self.xl = xl
         self.submission_type = submission_type
-        sample_info_map = self.fetch_sample_info_map(submission_type=submission_type)
+        sample_info_map = self.fetch_sample_info_map(submission_type=submission_type, sample_map=sample_map)
         logger.debug(f"sample_info_map: {sample_info_map}")
         self.plate_map = self.construct_plate_map(plate_map_location=sample_info_map['plate_map'])
         logger.debug(f"plate_map: {self.plate_map}")
@@ -298,7 +298,7 @@ class SampleParser(object):
         if isinstance(self.lookup_table, pd.DataFrame):
             self.parse_lookup_table()
         
-    def fetch_sample_info_map(self, submission_type:str) -> dict:
+    def fetch_sample_info_map(self, submission_type:str, sample_map:dict|None=None) -> dict:
         """
         Gets info locations in excel book for submission type.
 
@@ -311,7 +311,10 @@ class SampleParser(object):
         logger.debug(f"Looking up submission type: {submission_type}")
         submission_type = SubmissionType.query(name=submission_type)
         logger.debug(f"info_map: {pformat(submission_type.info_map)}")
+        if sample_map is None:
             sample_info_map = submission_type.info_map['samples']
+        else:
+            sample_info_map = sample_map
         self.custom_sub_parser = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=submission_type.name).parse_samples
         self.custom_sample_parser = BasicSample.find_polymorphic_subclass(polymorphic_identity=f"{submission_type.name} Sample").parse_sample
         return sample_info_map

src/submissions/backend/validators/pydant.py

@@ -518,7 +518,7 @@ class PydSubmission(BaseModel, extra='allow'):
                 case "samples":
                     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(f"Sample SQL object to be added to submission: {sample.__dict__}")
                         for assoc in associations:
                             instance.submission_sample_associations.append(assoc)
                 case "equipment":
@@ -534,7 +534,6 @@ class PydSubmission(BaseModel, extra='allow'):
                             association.save()
                             logger.debug(f"Equipment association SQL object to be added to submission: {association.__dict__}")
                             instance.submission_equipment_associations.append(association)
-                
                 case _:
                     try:
                         instance.set_attribute(key=key, value=value)
@@ -548,7 +547,10 @@ class PydSubmission(BaseModel, extra='allow'):
             instance.calculate_base_cost()
         except (TypeError, AttributeError) as e:
             logger.debug(f"Looks like that kit doesn't have cost breakdown yet due to: {e}, using full plate cost.")
+            try:
                 instance.run_cost = instance.extraction_kit.cost_per_run
+            except AttributeError:
+                instance.run_cost = 0
         logger.debug(f"Calculated base run cost of: {instance.run_cost}")
         # Apply any discounts that are applicable for client and kit.
         try:

src/submissions/frontend/widgets/submission_widget.py

@@ -469,11 +469,11 @@ class SubmissionFormWidget(QWidget):
         Args:
             fname (Path | None, optional): Input filename. Defaults to None.
         """        
-        pyd = self.parse_form()
+        self.parse_form()
         if isinstance(fname, bool) or fname == None:
-            fname = select_save_file(obj=self, default_name=pyd.construct_filename(), extension="csv")
+            fname = select_save_file(obj=self, default_name=self.pyd.construct_filename(), extension="csv")
         try:
-            pyd.csv.to_csv(fname.__str__(), index=False)
+            self.pyd.csv.to_csv(fname.__str__(), index=False)
         except PermissionError:
             logger.debug(f"Could not get permissions to {fname}. Possibly the request was cancelled.")
 

src/submissions/tools.py

@@ -117,12 +117,15 @@ def check_regex_match(pattern:str, check:str) -> bool:
         return False
 
 def get_first_blank_df_row(df:pd.DataFrame) -> int:
-    #First, find NaN entries in first column
-    # blank_row_bool = df.iloc[:,2].isna()
-    # logger.debug(f"Blank row bool: {blank_row_bool}")
-    # #Next, get index of first NaN entry
-    # blank_row_index =  [i for i, x in enumerate(blank_row_bool) if x][0]
-    # return blank_row_index
+    """
+    For some reason I need a whole function for this.
+
+    Args:
+        df (pd.DataFrame): Input dataframe.
+
+    Returns:
+        int: Index of the row after the last used row.
+    """    
     return df.shape[0] + 1
 
 # Settings