Moments before disaster

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

@@ -168,7 +168,7 @@ class BaseClass(Base):
             logger.error(f"Error message: {type(e)}")
             self.__database_session__.rollback()
             report.add_result(Result(msg=e, status="Critical"))
-        return report
+            return report
 
 
 class ConfigItem(BaseClass):

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

@@ -245,7 +245,6 @@ class BasicSubmission(BaseClass):
             case _:
                 return SubmissionType.query(cls.__mapper_args__['polymorphic_identity'])
 
-
     @classmethod
     def construct_info_map(cls, submission_type: SubmissionType | None = None,
                            mode: Literal["read", "write"] = "read") -> dict:
@@ -424,8 +423,9 @@ class BasicSubmission(BaseClass):
         except Exception as e:
             logger.error(f"Column count error: {e}")
         # NOTE: Get kit associated with this submission
-        assoc = next((item for item in self.extraction_kit.kit_submissiontype_associations if item.submission_type == self.submission_type),
-                      None)
+        assoc = next((item for item in self.extraction_kit.kit_submissiontype_associations if
+                      item.submission_type == self.submission_type),
+                     None)
         # logger.debug(f"Came up with association: {assoc}")
         # NOTE: If every individual cost is 0 this is probably an old plate.
         if all(item == 0.0 for item in [assoc.constant_cost, assoc.mutable_cost_column, assoc.mutable_cost_sample]):
@@ -464,15 +464,23 @@ class BasicSubmission(BaseClass):
         Returns:
             str: html output string.
         """
-        output_samples = []
+        # output_samples = []
         # logger.debug("Setting locations.")
-        for column in range(1, plate_columns + 1):
-            for row in range(1, plate_rows + 1):
-                try:
-                    well = next((item for item in sample_list if item['row'] == row and item['column'] == column), dict(name="", row=row, column=column, background_color="#ffffff"))
-                except StopIteration:
-                    well = dict(name="", row=row, column=column, background_color="#ffffff")
-                output_samples.append(well)
+        # for column in range(1, plate_columns + 1):
+        #     for row in range(1, plate_rows + 1):
+        #         try:
+        #             well = next((item for item in sample_list if item['row'] == row and item['column'] == column), dict(name="", row=row, column=column, background_color="#ffffff"))
+        #         except StopIteration:
+        #             well = dict(name="", row=row, column=column, background_color="#ffffff")
+        #         output_samples.append(well)
+        rows = range(1, plate_rows + 1)
+        columns = range(1, plate_columns + 1)
+        # NOTE: An overly complicated list comprehension create a list of sample locations
+        # NOTE: next will return a blank cell if no value found for row/column
+        output_samples = [next((item for item in sample_list if item['row'] == row and item['column'] == column),
+                               dict(name="", row=row, column=column, background_color="#ffffff"))
+                          for row in rows
+                          for column in columns]
         env = jinja_template_loading()
         template = env.get_template("plate_map.html")
         html = template.render(samples=output_samples, PLATE_ROWS=plate_rows, PLATE_COLUMNS=plate_columns)
@@ -510,16 +518,17 @@ class BasicSubmission(BaseClass):
         df = pd.DataFrame.from_records(subs)
         # logger.debug(f"Column names: {df.columns}")
         # NOTE: Exclude sub information
-        excluded = ['controls', 'extraction_info', 'pcr_info', 'comment', 'comments', 'samples', 'reagents',
+        exclude = ['controls', 'extraction_info', 'pcr_info', 'comment', 'comments', 'samples', 'reagents',
                     'equipment', 'gel_info', 'gel_image', 'dna_core_submission_number', 'gel_controls',
                     'source_plates', 'pcr_technician', 'ext_technician', 'artic_technician', 'cost_centre',
                     'signed_by', 'artic_date', 'gel_barcode', 'gel_date', 'ngs_date', 'contact_phone', 'contact',
                     'tips', 'gel_image_path', 'custom']
-        for item in excluded:
-            try:
-                df = df.drop(item, axis=1)
-            except:
-                logger.warning(f"Couldn't drop '{item}' column from submissionsheet df.")
+        df = df.loc[:, ~df.columns.isin(exclude)]
+        # for item in excluded:
+        #     try:
+        #         df = df.drop(item, axis=1)
+        #     except:
+        #         logger.warning(f"Couldn't drop '{item}' column from submissionsheet df.")
         if chronologic:
             try:
                 df.sort_values(by="id", axis=0, inplace=True, ascending=False)
@@ -599,7 +608,7 @@ class BasicSubmission(BaseClass):
                     field_value = value.strip()
                 except AttributeError:
                     field_value = value
-        # insert into field
+        # NOTE: insert into field
         try:
             self.__setattr__(key, field_value)
         except AttributeError as e:
@@ -616,16 +625,17 @@ class BasicSubmission(BaseClass):
         Returns:
             Result: _description_
         """
-        # assoc = [item for item in self.submission_sample_associations if item.sample == sample][0]
         try:
             assoc = next(item for item in self.submission_sample_associations if item.sample == sample)
         except StopIteration:
             report = Report()
-            report.add_result(Result(msg=f"Couldn't find submission sample association for {sample.submitter_id}", status="Warning"))
+            report.add_result(
+                Result(msg=f"Couldn't find submission sample association for {sample.submitter_id}", status="Warning"))
             return report
         for k, v in input_dict.items():
             try:
                 setattr(assoc, k, v)
+                # NOTE: for some reason I don't think assoc.__setattr__(k, v) doesn't work here.
             except AttributeError:
                 logger.error(f"Can't set {k} to {v}")
         result = assoc.save()
@@ -702,15 +712,7 @@ class BasicSubmission(BaseClass):
         Returns:
             re.Pattern: Regular expression pattern to discriminate between submission types.
         """
-        # rstring = rf'{"|".join([item.get_regex() for item in cls.__subclasses__()])}'
-        # rstring = rf'{"|".join([item.defaults["regex"] for item in SubmissionType.query()])}'
-        res = []
-        for item in SubmissionType.query():
-            try:
-                res.append(item.defaults['regex'])
-            except TypeError:
-                logger.error(f"Problem: {item.__dict__}")
-                continue
+        res = [st.defaults['regex'] for st in SubmissionType.query() if st.defaults]
         rstring = rf'{"|".join(res)}'
         regex = re.compile(rstring, flags=re.IGNORECASE | re.VERBOSE)
         return regex
@@ -737,21 +739,21 @@ class BasicSubmission(BaseClass):
         match polymorphic_identity:
             case str():
                 try:
-                    logger.info(f"Recruiting: {cls}")
                     model = cls.__mapper__.polymorphic_map[polymorphic_identity].class_
                 except Exception as e:
                     logger.error(
                         f"Could not get polymorph {polymorphic_identity} of {cls} due to {e}, falling back to BasicSubmission")
             case _:
                 pass
-        if attrs is None or len(attrs) == 0:
-            return model
-        if any([not hasattr(cls, attr) for attr in attrs.keys()]):
+        # if attrs is None or len(attrs) == 0:
+        #     logger.info(f"Recruiting: {cls}")
+        #     return model
+        if attrs and any([not hasattr(cls, attr) for attr in attrs.keys()]):
             # looks for first model that has all included kwargs
             try:
-                model = [subclass for subclass in cls.__subclasses__() if
-                         all([hasattr(subclass, attr) for attr in attrs.keys()])][0]
-            except IndexError as e:
+                model = next(subclass for subclass in cls.__subclasses__() if
+                             all([hasattr(subclass, attr) for attr in attrs.keys()]))
+            except StopIteration as e:
                 raise AttributeError(
                     f"Couldn't find existing class/subclass of {cls} with all attributes:\n{pformat(attrs.keys())}")
         logger.info(f"Recruiting model: {model}")
@@ -785,15 +787,19 @@ class BasicSubmission(BaseClass):
                     input_dict['custom'][k] = ws.cell(row=v['read']['row'], column=v['read']['column']).value
                 case "range":
                     ws = xl[v['sheet']]
-                    input_dict['custom'][k] = []
+                    # input_dict['custom'][k] = []
                     if v['start_row'] != v['end_row']:
                         v['end_row'] = v['end_row'] + 1
+                    rows = range(v['start_row'], v['end_row'])
                     if v['start_column'] != v['end_column']:
                         v['end_column'] = v['end_column'] + 1
-                    for ii in range(v['start_row'], v['end_row']):
-                        for jj in range(v['start_column'], v['end_column'] + 1):
-                            input_dict['custom'][k].append(
-                                dict(value=ws.cell(row=ii, column=jj).value, row=ii, column=jj))
+                    columns = range(v['start_column'], v['end_column'])
+                    input_dict['custom'][k] = [dict(value=ws.cell(row=row, column=column).value, row=row, column=column)
+                                               for row in rows for column in columns]
+                    # for ii in range(v['start_row'], v['end_row']):
+                    #     for jj in range(v['start_column'], v['end_column'] + 1):
+                    #         input_dict['custom'][k].append(
+                    #             dict(value=ws.cell(row=ii, column=jj).value, row=ii, column=jj))
         return input_dict
 
     @classmethod
@@ -907,38 +913,43 @@ class BasicSubmission(BaseClass):
         else:
             outstr = instr
         if re.search(rf"{data['abbreviation']}", outstr, flags=re.IGNORECASE) is None:
+            # NOTE: replace RSL- with RSL-abbreviation-
             outstr = re.sub(rf"RSL-?", rf"RSL-{data['abbreviation']}-", outstr, flags=re.IGNORECASE)
         try:
+            # NOTE: remove dashes from date
             outstr = re.sub(r"(\d{4})-(\d{2})-(\d{2})", r"\1\2\3", outstr)
+            # NOTE: insert dash between abbreviation and date
             outstr = re.sub(rf"{data['abbreviation']}(\d{6})", rf"{data['abbreviation']}-\1", outstr,
                             flags=re.IGNORECASE).upper()
         except (AttributeError, TypeError) as e:
             logger.error(f"Error making outstr: {e}, sending to RSLNamer to make new plate name.")
             outstr = RSLNamer.construct_new_plate_name(data=data)
         try:
+            # NOTE: Grab plate number
             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"
+        # NOTE: insert dash between date and plate number
         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:
+            # NOTE: grab repeat number
             repeat = re.search(r"-\dR(?P<repeat>\d)?", outstr).groupdict()['repeat']
             if repeat is None:
                 repeat = "1"
         except AttributeError as e:
             repeat = ""
+        # NOTE: Insert repeat number?
         outstr = re.sub(r"(-\dR)\d?", rf"\1 {repeat}", outstr).replace(" ", "")
-        # abb = cls.get_default_info('abbreviation')
-        # outstr = re.sub(rf"RSL{abb}", rf"RSL-{abb}", outstr)
-        # return re.sub(rf"{abb}(\d)", rf"{abb}-\1", outstr)
+        # NOTE: This should already have been done. Do I dare remove it?
         outstr = re.sub(rf"RSL{data['abbreviation']}", rf"RSL-{data['abbreviation']}", outstr)
         return re.sub(rf"{data['abbreviation']}(\d)", rf"{data['abbreviation']}-\1", outstr)
 
     @classmethod
     def parse_pcr(cls, xl: Workbook, rsl_plate_num: str) -> list:
         """
-        Perform custom parsing of pcr info.
+        Perform parsing of pcr info. Since most of our PC outputs are the same format, this should work for most.
 
         Args:
             xl (pd.DataFrame): pcr info form
@@ -959,7 +970,6 @@ class BasicSubmission(BaseClass):
             for k, v in fields.items():
                 sheet = xl[v['sheet']]
                 sample[k] = sheet.cell(row=idx, column=v['column']).value
-            # yield sample
             samples.append(sample)
         return samples
 
@@ -974,19 +984,20 @@ class BasicSubmission(BaseClass):
         """
         return "{{ rsl_plate_num }}"
 
-    @classmethod
-    def custom_sample_autofill_row(cls, sample, worksheet: Worksheet) -> int:
-        """
-        Updates row information
-
-        Args:
-            sample (_type_): _description_
-            worksheet (Workbook): _description_
-
-        Returns:
-            int: New row number
-        """
-        return None
+    # @classmethod
+    # def custom_sample_autofill_row(cls, sample, worksheet: Worksheet) -> int:
+    #     """
+    #     Updates row information
+    #
+    #     Args:
+    #         sample (_type_): _description_
+    #         worksheet (Workbook): _description_
+    #
+    #     Returns:
+    #         int: New row number
+    #     """
+    #     logger.debug(f"Sample from args: {sample}")
+    #     return None
 
     @classmethod
     def adjust_autofill_samples(cls, samples: List[Any]) -> List[Any]:
@@ -1232,7 +1243,10 @@ class BasicSubmission(BaseClass):
             except (SQLIntegrityError, SQLOperationalError, AlcIntegrityError, AlcOperationalError) as e:
                 self.__database_session__.rollback()
                 raise e
-            obj.setData()
+            try:
+                obj.setData()
+            except AttributeError:
+                logger.debug("App will not refresh data at this time.")
 
     def show_details(self, obj):
         """
@@ -1408,29 +1422,29 @@ class BacterialCulture(BasicSubmission):
                 pos_control_reg['missing'] = False
         return input_dict
 
-    @classmethod
-    def custom_sample_autofill_row(cls, sample, worksheet: Worksheet) -> int:
-        """
-        Extends parent
-        """
-        # logger.debug(f"Checking {sample.well}")
-        # logger.debug(f"here's the worksheet: {worksheet}")
-        row = super().custom_sample_autofill_row(sample, worksheet)
-        df = pd.DataFrame(list(worksheet.values))
-        # logger.debug(f"Here's the dataframe: {df}")
-        idx = df[df[0] == sample.well]
-        if idx.empty:
-            new = f"{sample.well[0]}{sample.well[1:].zfill(2)}"
-            # logger.debug(f"Checking: {new}")
-            idx = df[df[0] == new]
-        # logger.debug(f"Here is the row: {idx}")
-        row = idx.index.to_list()[0]
-        return row + 1
+    # @classmethod
+    # def custom_sample_autofill_row(cls, sample, worksheet: Worksheet) -> int:
+    #     """
+    #     Extends parent
+    #     """
+    #     # logger.debug(f"Checking {sample.well}")
+    #     # logger.debug(f"here's the worksheet: {worksheet}")
+    #     row = super().custom_sample_autofill_row(sample, worksheet)
+    #     df = pd.DataFrame(list(worksheet.values))
+    #     # logger.debug(f"Here's the dataframe: {df}")
+    #     idx = df[df[0] == sample.well]
+    #     if idx.empty:
+    #         new = f"{sample.well[0]}{sample.well[1:].zfill(2)}"
+    #         # logger.debug(f"Checking: {new}")
+    #         idx = df[df[0] == new]
+    #     # logger.debug(f"Here is the row: {idx}")
+    #     row = idx.index.to_list()[0]
+    #     return row + 1
 
     @classmethod
     def custom_info_parser(cls, input_dict: dict, xl: Workbook | None = None, custom_fields: dict = {}) -> dict:
         input_dict = super().custom_info_parser(input_dict=input_dict, xl=xl, custom_fields=custom_fields)
-        logger.debug(f"\n\nInfo dictionary:\n\n{pformat(input_dict)}\n\n")
+        # logger.debug(f"\n\nInfo dictionary:\n\n{pformat(input_dict)}\n\n")
         return input_dict
 
 
@@ -1561,20 +1575,20 @@ class Wastewater(BasicSubmission):
         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:
-        """
-        Extends parent
-        """
-        # logger.debug(f"Checking {sample.well}")
-        # logger.debug(f"here's the worksheet: {worksheet}")
-        row = super().custom_sample_autofill_row(sample, worksheet)
-        df = pd.DataFrame(list(worksheet.values))
-        # logger.debug(f"Here's the dataframe: {df}")
-        idx = df[df[1] == sample.sample_location]
-        # logger.debug(f"Here is the row: {idx}")
-        row = idx.index.to_list()[0]
-        return row + 1
+    # @classmethod
+    # def custom_sample_autofill_row(cls, sample, worksheet: Worksheet) -> int:
+    #     """
+    #     Extends parent
+    #     """
+    #     # logger.debug(f"Checking {sample.well}")
+    #     # logger.debug(f"here's the worksheet: {worksheet}")
+    #     row = super().custom_sample_autofill_row(sample, worksheet)
+    #     df = pd.DataFrame(list(worksheet.values))
+    #     # logger.debug(f"Here's the dataframe: {df}")
+    #     idx = df[df[1] == sample.sample_location]
+    #     # logger.debug(f"Here is the row: {idx}")
+    #     row = idx.index.to_list()[0]
+    #     return row + 1
 
     @classmethod
     def get_details_template(cls, base_dict: dict) -> Tuple[dict, Template]:
@@ -1816,7 +1830,7 @@ class WastewaterArtic(BasicSubmission):
                     datum['values'].append(d)
             data.append(datum)
         input_dict['gel_info'] = data
-        logger.debug(f"Wastewater Artic custom info:\n\n{pformat(input_dict)}")
+        # logger.debug(f"Wastewater Artic custom info:\n\n{pformat(input_dict)}")
         egel_image_section = custom_fields['image_range']
         img: Image = scrape_image(wb=xl, info_dict=egel_image_section)
         if img is not None:
@@ -2259,18 +2273,19 @@ class BasicSample(BaseClass):
 
     def to_sub_dict(self, full_data: bool = False) -> dict:
         """
-        gui friendly dictionary, extends parent method.
+        gui friendly dictionary
 
         Args:
             full_data (bool): Whether to use full object or truncated. Defaults to False
 
         Returns:
-            dict: well location and name (sample id, organism) NOTE: keys must sync with WWSample to_sub_dict above
+            dict: submitter id and sample type and linked submissions if full data
         """
         # logger.debug(f"Converting {self} to dict.")
-        sample = {}
-        sample['submitter_id'] = self.submitter_id
-        sample['sample_type'] = self.sample_type
+        sample = dict(
+            submitter_id=self.submitter_id,
+            sample_type=self.sample_type
+        )
         if full_data:
             sample['submissions'] = sorted([item.to_sub_dict() for item in self.sample_submission_associations],
                                            key=itemgetter('submitted_date'))
@@ -2307,22 +2322,22 @@ class BasicSample(BaseClass):
             polymorphic_identity = polymorphic_identity['value']
         if polymorphic_identity is not None:
             try:
-                # return [item for item in cls.__subclasses__() if
-                #         item.__mapper_args__['polymorphic_identity'] == polymorphic_identity][0]
                 model = cls.__mapper__.polymorphic_map[polymorphic_identity].class_
             except Exception as e:
                 logger.error(f"Could not get polymorph {polymorphic_identity} of {cls} due to {e}")
                 model = cls
+            logger.info(f"Recruiting model: {model}")
+            return model
         else:
             model = cls
         if attrs is None or len(attrs) == 0:
             return model
         if any([not hasattr(cls, attr) for attr in attrs.keys()]):
-            # looks for first model that has all included kwargs
+            # NOTE: looks for first model that has all included kwargs
             try:
-                model = [subclass for subclass in cls.__subclasses__() if
-                         all([hasattr(subclass, attr) for attr in attrs.keys()])][0]
-            except IndexError as e:
+                model = next(subclass for subclass in cls.__subclasses__() if
+                             all([hasattr(subclass, attr) for attr in attrs.keys()]))
+            except StopIteration as e:
                 raise AttributeError(
                     f"Couldn't find existing class/subclass of {cls} with all attributes:\n{pformat(attrs.keys())}")
         logger.info(f"Recruiting model: {model}")
@@ -2343,7 +2358,7 @@ class BasicSample(BaseClass):
         return input_dict
 
     @classmethod
-    def get_details_template(cls, base_dict: dict) -> Tuple[dict, Template]:
+    def get_details_template(cls) -> Template:
         """
         Get the details jinja template for the correct class
 
@@ -2353,7 +2368,6 @@ class BasicSample(BaseClass):
         Returns:
             Tuple(dict, Template): (Updated dictionary, Template to be rendered)
         """
-        base_dict['excluded'] = ['submissions', 'excluded', 'colour', 'tooltip']
         env = jinja_template_loading()
         temp_name = f"{cls.__name__.lower()}_details.html"
         # logger.debug(f"Returning template: {temp_name}")
@@ -2362,7 +2376,7 @@ class BasicSample(BaseClass):
         except TemplateNotFound as e:
             logger.error(f"Couldn't find template {e}")
             template = env.get_template("basicsample_details.html")
-        return base_dict, template
+        return template
 
     @classmethod
     @setup_lookup
@@ -2459,6 +2473,7 @@ class BasicSample(BaseClass):
             search = f"%{v}%"
             try:
                 attr = getattr(model, k)
+                # NOTE: the secret sauce is in attr.like
                 query = query.filter(attr.like(search))
             except (ArgumentError, AttributeError) as e:
                 logger.error(f"Attribute {k} unavailable due to:\n\t{e}\nSkipping.")
@@ -2488,8 +2503,6 @@ class BasicSample(BaseClass):
         Returns:
             pd.DataFrame: Dataframe all samples
         """
-        if not isinstance(sample_list, list):
-            sample_list = [sample_list]
         try:
             samples = [sample.to_sub_dict() for sample in sample_list]
         except TypeError as e:
@@ -2497,12 +2510,9 @@ class BasicSample(BaseClass):
             return None
         df = pd.DataFrame.from_records(samples)
         # NOTE: Exclude sub information
-        for item in ['concentration', 'organism', 'colour', 'tooltip', 'comments', 'samples', 'reagents',
-                     'equipment', 'gel_info', 'gel_image', 'dna_core_submission_number', 'gel_controls']:
-            try:
-                df = df.drop(item, axis=1)
-            except KeyError as e:
-                logger.warning(f"Couldn't drop '{item}' column from submissionsheet df due to {e}.")
+        exclude = ['concentration', 'organism', 'colour', 'tooltip', 'comments', 'samples', 'reagents',
+                     'equipment', 'gel_info', 'gel_image', 'dna_core_submission_number', 'gel_controls']
+        df = df.loc[:, ~df.columns.isin(exclude)]
         return df
 
     def show_details(self, obj):
@@ -2570,7 +2580,7 @@ class WastewaterSample(BasicSample):
         gui friendly dictionary, extends parent method.
 
         Returns:
-            dict: well location and name (sample id, organism) NOTE: keys must sync with WWSample to_sub_dict above
+            dict: sample id, type, received date, collection date
         """
         sample = super().to_sub_dict(full_data=full_data)
         sample['ww_processing_num'] = self.ww_processing_num
@@ -2713,7 +2723,7 @@ class SubmissionSampleAssociation(BaseClass):
         Returns:
             dict: Updated dictionary with row, column and well updated
         """
-        # Get sample info
+        # NOTE: Get associated sample info
         # logger.debug(f"Running {self.__repr__()}")
         sample = self.sample.to_sub_dict()
         # logger.debug("Sample conversion complete.")
@@ -2791,8 +2801,6 @@ class SubmissionSampleAssociation(BaseClass):
             model = cls
         else:
             try:
-                # output = [item for item in cls.__subclasses__() if
-                #           item.__mapper_args__['polymorphic_identity'] == polymorphic_identity][0]
                 model = cls.__mapper__.polymorphic_map[polymorphic_identity].class_
             except Exception as e:
                 logger.error(f"Could not get polymorph {polymorphic_identity} of {cls} due to {e}")
@@ -2974,11 +2982,10 @@ class WastewaterAssociation(SubmissionSampleAssociation):
         if scaler == 0.0:
             scaler = 45
         bg = (45 - scaler) * 17
-        red = min([128 + bg, 255])
+        red = min([64 + bg, 255])
         grn = max([255 - bg, 0])
         blu = 128
-        rgb = f"rgb({red}, {grn}, {blu})"
-        sample['background_color'] = rgb
+        sample['background_color'] = f"rgb({red}, {grn}, {blu})"
         try:
             sample[
                 'tooltip'] += f"<br>- ct N1: {'{:.2f}'.format(self.ct_n1)} ({self.n1_status})<br>- ct N2: {'{:.2f}'.format(self.ct_n2)} ({self.n2_status})"
@@ -2995,13 +3002,13 @@ class WastewaterAssociation(SubmissionSampleAssociation):
             int: incremented id
         """
         try:
-            parent = next((base for base in cls.__bases__ if base.__name__=="SubmissionSampleAssociation"),
+            parent = next((base for base in cls.__bases__ if base.__name__ == "SubmissionSampleAssociation"),
                           SubmissionSampleAssociation)
             return max([item.id for item in parent.query()]) + 1
         except StopIteration as e:
             logger.error(f"Problem incrementing id: {e}")
             return 1
-        
+
     @classmethod
     def autoincrement_id(cls) -> int:
         return super().autoincrement_id()

src/submissions/backend/excel/parser.py

@@ -1,7 +1,6 @@
 '''
 contains parser objects for pulling values from client generated submission sheets.
 '''
-import sys
 from copy import copy
 from getpass import getuser
 from pprint import pformat
@@ -12,9 +11,7 @@ from backend.db.models import *
 from backend.validators import PydSubmission, PydReagent, RSLNamer, PydSample, PydEquipment, PydTips
 import logging, re
 from collections import OrderedDict
-from datetime import date
-from dateutil.parser import parse, ParserError
-from tools import check_not_nan, convert_nans_to_nones, is_missing, remove_key_from_list_of_dicts, check_key_or_attr
+from tools import check_not_nan, convert_nans_to_nones, is_missing, check_key_or_attr
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -70,34 +67,24 @@ class SheetParser(object):
             check = info['submission_type']['value'] not in [None, "None", "", " "]
         except KeyError:
             return
-        logger.debug(f"Checking old submission type: {self.submission_type.name} against new: {info['submission_type']['value']}")
+        logger.info(
+            f"Checking for updated submission type: {self.submission_type.name} against new: {info['submission_type']['value']}")
         if self.submission_type.name != info['submission_type']['value']:
             # logger.debug(f"info submission type: {info}")
             if check:
                 self.submission_type = SubmissionType.query(name=info['submission_type']['value'])
-                logger.debug(f"Updated self.submission_type to {self.submission_type}. Rerunning parse.")
+                logger.info(f"Updated self.submission_type to {self.submission_type}. Rerunning parse.")
                 self.parse_info()
-
             else:
                 self.submission_type = RSLNamer.retrieve_submission_type(filename=self.filepath)
                 self.parse_info()
-
-
         for k, v in info.items():
             match k:
                 # NOTE: exclude samples.
                 case "sample":
                     continue
-                # case "submission_type":
-                #     self.sub[k] = v
-                #     # NOTE: Rescue submission type using scraped values to be used in Sample, Reagents, etc.
-                #     if v not in [None, "None", "", " "]:
-                #         self.submission_type = SubmissionType.query(name=v)
-                #         logger.debug(f"Updated self.submission_type to {self.submission_type}")
                 case _:
                     self.sub[k] = v
-        # print(f"\n\n {self.sub} \n\n")
-
 
     def parse_reagents(self, extraction_kit: str | None = None):
         """
@@ -110,8 +97,8 @@ class SheetParser(object):
             extraction_kit = self.sub['extraction_kit']
         # logger.debug(f"Parsing reagents for {extraction_kit}")
         parser = ReagentParser(xl=self.xl, submission_type=self.submission_type,
-                                             extraction_kit=extraction_kit)
-        self.sub['reagents'] = [item for item in parser.parse_reagents()]
+                               extraction_kit=extraction_kit)
+        self.sub['reagents'] = [reagent for reagent in parser.parse_reagents()]
 
     def parse_samples(self):
         """
@@ -125,14 +112,14 @@ class SheetParser(object):
         Calls equipment parser to pull info from the excel sheet
         """
         parser = EquipmentParser(xl=self.xl, submission_type=self.submission_type)
-        self.sub['equipment'] = parser.parse_equipment()
+        self.sub['equipment'] = [equipment for equipment in parser.parse_equipment()]
 
     def parse_tips(self):
         """
         Calls tips parser to pull info from the excel sheet
         """
         parser = TipParser(xl=self.xl, submission_type=self.submission_type)
-        self.sub['tips'] = parser.parse_tips()
+        self.sub['tips'] = [tip for tip in parser.parse_tips()]
 
     def import_kit_validation_check(self):
         """
@@ -297,16 +284,18 @@ class ReagentParser(object):
     Object to pull reagents from excel sheet.
     """
 
-    def __init__(self, xl: Workbook, submission_type: str, extraction_kit: str,
+    def __init__(self, xl: Workbook, submission_type: str | SubmissionType, extraction_kit: str,
                  sub_object: BasicSubmission | None = None):
         """
         Args:
             xl (Workbook): Openpyxl workbook from submitted excel file.
-            submission_type (str): Type of submission expected (Wastewater, Bacterial Culture, etc.)
+            submission_type (str|SubmissionType): Type of submission expected (Wastewater, Bacterial Culture, etc.)
             extraction_kit (str): Extraction kit used.
             sub_object (BasicSubmission | None, optional): Submission object holding methods. Defaults to None.
         """
         # logger.debug("\n\nHello from ReagentParser!\n\n")
+        if isinstance(submission_type, str):
+            submission_type = SubmissionType.query(name=submission_type)
         self.submission_type_obj = submission_type
         self.sub_object = sub_object
         if isinstance(extraction_kit, dict):
@@ -381,7 +370,7 @@ class ReagentParser(object):
                     check = True
                 if check:
                     yield dict(role=item.strip(), lot=lot, expiry=expiry, name=name, comment=comment,
-                                      missing=missing)
+                               missing=missing)
         # return listo
 
 
@@ -408,7 +397,8 @@ class SampleParser(object):
         self.submission_type = submission_type.name
         self.submission_type_obj = submission_type
         if sub_object is None:
-            logger.warning(f"Sample parser attempting to fetch submission class with polymorphic identity: {self.submission_type}")
+            logger.warning(
+                f"Sample parser attempting to fetch submission class with polymorphic identity: {self.submission_type}")
             sub_object = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type)
         self.sub_object = sub_object
         self.sample_info_map = self.fetch_sample_info_map(submission_type=submission_type, sample_map=sample_map)
@@ -521,18 +511,16 @@ class SampleParser(object):
             new_samples.append(PydSample(**translated_dict))
         return result, new_samples
 
-    def reconcile_samples(self) -> List[dict]:
+    def reconcile_samples(self) -> Generator[dict, None, None]:
         """
         Merges sample info from lookup table and plate map.
 
         Returns:
             List[dict]: Reconciled samples
         """
-        # TODO: Move to pydantic validator?
         if self.plate_map_samples is None or self.lookup_samples is None:
             self.samples = self.lookup_samples or self.plate_map_samples
             return
-        samples = []
         merge_on_id = self.sample_info_map['lookup_table']['merge_on_id']
         plate_map_samples = sorted(copy(self.plate_map_samples), key=lambda d: d['id'])
         lookup_samples = sorted(copy(self.lookup_samples), key=lambda d: d[merge_on_id])
@@ -561,9 +549,11 @@ class SampleParser(object):
             if not check_key_or_attr(key='submitter_id', interest=new, check_none=True):
                 new['submitter_id'] = psample['id']
             new = self.sub_object.parse_samples(new)
-            samples.append(new)
-        samples = remove_key_from_list_of_dicts(samples, "id")
-        return sorted(samples, key=lambda k: (k['row'], k['column']))
+            del new['id']
+            yield new
+            # samples.append(new)
+        # samples = remove_key_from_list_of_dicts(samples, "id")
+        # return sorted(samples, key=lambda k: (k['row'], k['column']))
 
 
 class EquipmentParser(object):
@@ -643,13 +633,13 @@ class EquipmentParser(object):
                     eq = Equipment.query(name=asset)
                 process = ws.cell(row=v['process']['row'], column=v['process']['column']).value
                 try:
-                    output.append(
-                        dict(name=eq.name, processes=[process], role=k, asset_number=eq.asset_number,
-                             nickname=eq.nickname))
+                    # output.append(
+                    yield dict(name=eq.name, processes=[process], role=k, asset_number=eq.asset_number,
+                               nickname=eq.nickname)
                 except AttributeError:
                     logger.error(f"Unable to add {eq} to list.")
                 # logger.debug(f"Here is the output so far: {pformat(output)}")
-        return output
+        # return output
 
 
 class TipParser(object):
@@ -676,7 +666,7 @@ class TipParser(object):
         Returns:
             List[dict]: List of locations
         """
-        return {k:v for k,v in self.submission_type.construct_tips_map()}
+        return {k: v for k, v in self.submission_type.construct_tips_map()}
 
     def parse_tips(self) -> List[dict]:
         """
@@ -710,12 +700,12 @@ class TipParser(object):
                 # logger.debug(f"asset: {asset}")
                 eq = Tips.query(lot=lot, name=asset, limit=1)
                 try:
-                    output.append(
-                        dict(name=eq.name, role=k, lot=lot))
+                    # output.append(
+                    yield dict(name=eq.name, role=k, lot=lot)
                 except AttributeError:
                     logger.error(f"Unable to add {eq} to PydTips list.")
                 # logger.debug(f"Here is the output so far: {pformat(output)}")
-        return output
+        # return output
 
 
 class PCRParser(object):

src/submissions/backend/validators/pydant.py

@@ -582,7 +582,7 @@ class PydSubmission(BaseModel, extra='allow'):
 
     @field_validator("samples")
     @classmethod
-    def assign_ids(cls, value, values):
+    def assign_ids(cls, value):
         starting_id = SubmissionSampleAssociation.autoincrement_id()
         output = []
         for iii, sample in enumerate(value, start=starting_id):