Update to reagent parser to exclude 'not applicable'

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

@@ -32,7 +32,6 @@ from pathlib import Path
 from jinja2.exceptions import TemplateNotFound
 from jinja2 import Template
 
-
 logger = logging.getLogger(f"submissions.{__name__}")
 
 class BasicSubmission(BaseClass):
@@ -593,7 +592,7 @@ class BasicSubmission(BaseClass):
         return input_excel
     
     @classmethod
-    def enforce_name(cls, instr:str, data:dict|None=None) -> str:
+    def enforce_name(cls, instr:str, data:dict|None={}) -> str:
         """
         Custom naming method for this class.
 
@@ -604,8 +603,40 @@ class BasicSubmission(BaseClass):
         Returns:
             str: Updated name.
         """        
-        logger.info(f"Hello from {cls.__mapper_args__['polymorphic_identity']} Enforcer!")
+        # logger.info(f"Hello from {cls.__mapper_args__['polymorphic_identity']} Enforcer!")
-        return instr
+        # return instr
+        from backend.validators import RSLNamer
+        defaults = cls.get_default_info()
+        data['abbreviation'] = defaults['abbreviation']
+        if 'submission_type' not in data.keys() or data['submission_type'] in [None, ""]:
+            data['submission_type'] = defaults['submission_type']
+        # outstr = super().enforce_name(instr=instr, data=data)
+        if instr in [None, ""]:
+            outstr = RSLNamer.construct_new_plate_name(data=data)
+        else:
+            outstr = instr
+        if re.search(rf"{data['abbreviation']}", outstr, flags=re.IGNORECASE) is None:
+            outstr = re.sub(rf"RSL-?", rf"RSL-{data['abbreviation']}-", outstr, flags=re.IGNORECASE)
+        try:
+            outstr = re.sub(r"(\d{4})-(\d{2})-(\d{2})", r"\1\2\3", outstr)
+            outstr = re.sub(rf"{data['abbreviation']}(\d{6})", rf"{data['abbreviation']}-\1", outstr, flags=re.IGNORECASE).upper()
+        except (AttributeError, TypeError) as e:
+            outstr = RSLNamer.construct_new_plate_name(data=data)
+        try:
+            plate_number = re.search(r"(?:(-|_)\d)(?!\d)", outstr).group().strip("_").strip("-")
+            # logger.debug(f"Plate number is: {plate_number}")
+        except AttributeError as e:
+            plate_number = "1"
+        outstr = re.sub(r"(\d{8})(-|_)?\d?(R\d?)?", rf"\1-{plate_number}\3", outstr)
+        # logger.debug(f"After addition of plate number the plate name is: {outstr}")
+        try:
+            repeat = re.search(r"-\dR(?P<repeat>\d)?", outstr).groupdict()['repeat']
+            if repeat == None:
+                repeat = "1"
+        except AttributeError as e:
+            repeat = ""
+        return re.sub(r"(-\dR)\d?", rf"\1 {repeat}", outstr).replace(" ", "")
+        # return outstr
 
     @classmethod
     def parse_pcr(cls, xl:pd.DataFrame, rsl_number:str) -> list:
@@ -1052,42 +1083,6 @@ class BacterialCulture(BasicSubmission):
         input_excel["Sample List"].cell(row=15, column=2, value=getuser())
         return input_excel
 
-    @classmethod
-    def enforce_name(cls, instr:str, data:dict|None={}) -> str:
-        """
-        Extends parent
-        """        
-        from backend.validators import RSLNamer
-        defaults = cls.get_default_info()
-        data['abbreviation'] = defaults['abbreviation']
-        if 'submission_type' not in data.keys() or data['submission_type'] in [None, ""]:
-            data['submission_type'] = defaults['submission_type']
-        outstr = super().enforce_name(instr=instr, data=data)
-        if outstr in [None, ""]:
-            outstr = RSLNamer.construct_new_plate_name(data=data)
-        if re.search(rf"{data['abbreviation']}", outstr, flags=re.IGNORECASE) is None:
-            outstr = re.sub(rf"RSL-?", rf"RSL-{data['abbreviation']}-", outstr, flags=re.IGNORECASE)
-        try:
-            outstr = re.sub(r"(\d{4})-(\d{2})-(\d{2})", r"\1\2\3", outstr)
-            outstr = re.sub(rf"{data['abbreviation']}(\d{6})", rf"{data['abbreviation']}-\1", outstr, flags=re.IGNORECASE).upper()
-        except (AttributeError, TypeError) as e:
-            outstr = RSLNamer.construct_new_plate_name(data=data)
-        try:
-            plate_number = re.search(r"(?:(-|_)\d)(?!\d)", outstr).group().strip("_").strip("-")
-            # logger.debug(f"Plate number is: {plate_number}")
-        except AttributeError as e:
-            plate_number = "1"
-        outstr = re.sub(r"(\d{8})(-|_)?\d?(R\d?)?", rf"\1-{plate_number}\3", outstr)
-        # logger.debug(f"After addition of plate number the plate name is: {outstr}")
-        try:
-            repeat = re.search(r"-\dR(?P<repeat>\d)?", outstr).groupdict()['repeat']
-            if repeat == None:
-                repeat = "1"
-        except AttributeError as e:
-            repeat = ""
-        return re.sub(r"(-\dR)\d?", rf"\1 {repeat}", outstr).replace(" ", "")
-        # return outstr
-
     @classmethod
     def get_regex(cls) -> str:
         """
@@ -1227,37 +1222,17 @@ class Wastewater(BasicSubmission):
         return samples
     
     @classmethod
-    def enforce_name(cls, instr:str, data:dict|None=None) -> str:
+    def enforce_name(cls, instr:str, data:dict|None={}) -> str:
         """
         Extends parent
         """        
-        from backend.validators import RSLNamer
-        defaults = cls.get_default_info()
-        data['abbreviation'] = defaults['abbreviation']
-        outstr = super().enforce_name(instr=instr, data=data)
         try:
-            outstr = re.sub(r"PCR(-|_)", "", outstr)
+            # Deal with PCR file.
+            instr = re.sub(r"PCR(-|_)", "", instr)
         except (AttributeError, TypeError) as e:
             logger.error(f"Problem using regex: {e}")
-            outstr = RSLNamer.construct_new_plate_name(data=data)
+        outstr = super().enforce_name(instr=instr, data=data)
-        outstr = outstr.replace("RSLWW", "RSL-WW")
+        return outstr
-        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)
-        # logger.debug(f"Coming out of the preliminary parsing, the plate name is {outstr}")
-        try:
-            plate_number = re.search(r"(?:(-|_)\d)(?!\d)", outstr).group().strip("_").strip("-")
-            # logger.debug(f"Plate number is: {plate_number}")
-        except AttributeError as e:
-            plate_number = "1"
-        outstr = re.sub(r"(\d{8})(-|_)?\d?(R\d?)?", rf"\1-{plate_number}\3", outstr)
-        # logger.debug(f"After addition of plate number the plate name is: {outstr}")
-        try:
-            repeat = re.search(r"-\dR(?P<repeat>\d)?", outstr).groupdict()['repeat']
-            if repeat == None:
-                repeat = "1"
-        except AttributeError as e:
-            repeat = ""
-        return re.sub(r"(-\dR)\d?", rf"\1 {repeat}", outstr).replace(" ", "")
 
     @classmethod
     def get_regex(cls) -> str:
@@ -1275,8 +1250,9 @@ class Wastewater(BasicSubmission):
         Extends parent
         """
         samples = super().adjust_autofill_samples(samples)
-        return [item for item in samples if not item.submitter_id.startswith("EN")]
+        samples = [item for item in samples if not item.submitter_id.startswith("EN")]
-    
+        return samples
+
     @classmethod
     def custom_sample_autofill_row(cls, sample, worksheet: Worksheet) -> int:
         """
@@ -1325,8 +1301,8 @@ class WastewaterArtic(BasicSubmission):
         return output
 
     @classmethod
-    def get_abbreviation(cls) -> str:
+    def get_default_info(cls) -> str:
-        return "AR"
+        return dict(abbreviation="AR", submission_type="Wastewater Artic")
 
     @classmethod
     def parse_info(cls, input_dict:dict, xl:pd.ExcelFile|None=None) -> dict:
@@ -1350,6 +1326,28 @@ class WastewaterArtic(BasicSubmission):
         input_dict['source_plates'] = plates
         return input_dict
 
+    @classmethod
+    def enforce_name(cls, instr:str, data:dict|None={}) -> str:
+        """
+        Extends parent
+        """        
+        try:
+            # Deal with PCR file.
+            instr = re.sub(r"Artic", "", instr, flags=re.IGNORECASE)
+        except (AttributeError, TypeError) as e:
+            logger.error(f"Problem using regex: {e}")
+        try:
+            check = instr.startswith("RSL")
+        except AttributeError:
+            check = False
+        if not check:
+            try:
+                instr = "RSL" + instr
+            except:
+                instr = "RSL"
+        outstr = super().enforce_name(instr=instr, data=data)
+        return outstr
+
     @classmethod
     def parse_samples(cls, input_dict: dict) -> dict:
         """
@@ -1420,27 +1418,6 @@ class WastewaterArtic(BasicSubmission):
         year = f"20{year}"
         return f"EN{year}{month}{day}-{en_num}"
 
-    @classmethod
-    def enforce_name(cls, instr:str|None=None, data:dict|None=None) -> str:
-        """
-        Extends parent
-        """        
-        from backend.validators import RSLNamer
-        data['abbreviation'] = cls.get_abbreviation()
-        outstr = super().enforce_name(instr=instr, data=data)
-        try:
-            outstr = re.sub(r"(\d{4})-(\d{2})-(\d{2})", r"RSL-AR-\1\2\3", outstr, flags=re.IGNORECASE)
-        except (AttributeError, TypeError):
-            if instr != None:
-                data['rsl_plate_num'] = instr
-            # logger.debug(f"Create new plate name from submission parameters")
-            outstr = RSLNamer.construct_new_plate_name(data=data)
-        try:
-            plate_number = int(re.search(r"_|-\d?_", outstr).group().strip("_").strip("-"))
-        except (AttributeError, ValueError) as e:
-            plate_number = 1
-        return re.sub(r"(_|-\d)?_ARTIC", f"-{plate_number}", outstr)
-
     @classmethod
     def get_regex(cls) -> str:
         """
@@ -1676,10 +1653,11 @@ class WastewaterArtic(BasicSubmission):
             self.gel_info = output
             dt = datetime.strftime(datetime.now(), "%Y-%m-%d %H:%M:%S")
             com = dict(text=comment, name=getuser(), time=dt)
-            if self.comment is not None:
+            if com['text'] != None and com['text'] != "":
-                self.comment.append(com)
+                if self.comment is not None:
-            else:
+                    self.comment.append(com)
-                self.comment = [com]
+                else:
+                    self.comment = [com]
             logger.debug(pformat(self.gel_info))
             with ZipFile(self.__directory_path__.joinpath("submission_imgs.zip"), 'a') as zipf:
                 # Add a file located at the source_path to the destination within the zip

src/submissions/backend/excel/parser.py

@@ -266,7 +266,8 @@ class ReagentParser(object):
                 # logger.debug(f"Got lot for {item}-{name}: {lot} as {type(lot)}")
                 lot = str(lot)
                 logger.debug(f"Going into pydantic: name: {name}, lot: {lot}, expiry: {expiry}, type: {item.strip()}, comment: {comment}")
-                listo.append(PydReagent(type=item.strip(), lot=lot, expiry=expiry, name=name, comment=comment, missing=missing))
+                if name.lower() != "not applicable":
+                    listo.append(PydReagent(type=item.strip(), lot=lot, expiry=expiry, name=name, comment=comment, missing=missing))
         return listo
 
 class SampleParser(object):

src/submissions/backend/validators/pydant.py

@@ -138,19 +138,19 @@ class PydReagent(BaseModel):
             # NOTE: this will now be done only in the reporting phase to account for potential changes in end-of-life extensions
         return reagent, report
 
-    def toForm(self, parent:QWidget, extraction_kit:str) -> QComboBox:
+    # def toForm(self, parent:QWidget, extraction_kit:str) -> QComboBox:
-        """
+    #     """
-        Converts this instance into a form widget
+    #     Converts this instance into a form widget
 
-        Args:
+    #     Args:
-            parent (QWidget): Parent widget of the constructed object
+    #         parent (QWidget): Parent widget of the constructed object
-            extraction_kit (str): Name of extraction kit used
+    #         extraction_kit (str): Name of extraction kit used
 
-        Returns:
+    #     Returns:
-            QComboBox: Form object.
+    #         QComboBox: Form object.
-        """        
+    #     """        
-        from frontend.widgets.submission_widget import ReagentFormWidget
+    #     from frontend.widgets.submission_widget import ReagentFormWidget
-        return ReagentFormWidget(parent=parent, reagent=self, extraction_kit=extraction_kit)
+    #     return ReagentFormWidget(parent=parent, reagent=self, extraction_kit=extraction_kit)
     
 class PydSample(BaseModel, extra='allow'):
 
@@ -705,16 +705,19 @@ class PydSubmission(BaseModel, extra='allow'):
         # logger.debug("Sorting samples by row/column")
         samples = sorted(self.samples, key=attrgetter('column', 'row'))
         submission_obj = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type)
+        # custom function to adjust values for writing.
         samples = submission_obj.adjust_autofill_samples(samples=samples)
         logger.debug(f"Samples: {pformat(samples)}")
         # Fail safe against multiple instances of the same sample
         for iii, sample in enumerate(samples, start=1):
             logger.debug(f"Sample: {sample}")
+            # custom function to find the row of this sample
             row = submission_obj.custom_sample_autofill_row(sample, worksheet=worksheet)
             logger.debug(f"Writing to {row}")
             if row == None:
                 row = sample_info['lookup_table']['start_row'] + iii
             fields = [field for field in list(sample.model_fields.keys()) + list(sample.model_extra.keys()) if field in sample_info['sample_columns'].keys()]
+            logger.debug(f"Here are the fields we are going to fill:\n\t{fields}")
             for field in fields:
                 column = sample_info['sample_columns'][field]
                 value = getattr(sample, field)

src/submissions/frontend/widgets/submission_widget.py

@@ -280,7 +280,10 @@ class SubmissionFormWidget(QWidget):
         if key not in self.ignore:
             match value:
                 case PydReagent():
-                    widget = self.ReagentFormWidget(self, reagent=value, extraction_kit=extraction_kit)
+                    if value.name.lower() != "not applicable":
+                        widget = self.ReagentFormWidget(self, reagent=value, extraction_kit=extraction_kit)
+                    else:
+                        widget = None
                 case _:
                     widget = self.InfoItem(self, key=key, value=value, submission_type=submission_type)
             return widget