Last minute save of new pcr parser.

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

@@ -156,11 +156,11 @@ class KitType(BaseClass):
                 # logger.debug(f"Constructing xl map with str {submission_type}")
                 assocs = [item for item in self.kit_reagenttype_associations if
                           item.submission_type.name == submission_type]
-                st_assoc = [item for item in self.used_for if submission_type == item.name][0]
+                # st_assoc = [item for item in self.used_for if submission_type == item.name][0]
             case SubmissionType():
                 # logger.debug(f"Constructing xl map with SubmissionType {submission_type}")
                 assocs = [item for item in self.kit_reagenttype_associations if item.submission_type == submission_type]
-                st_assoc = submission_type
+                # st_assoc = submission_type
             case _:
                 raise ValueError(f"Wrong variable type: {type(submission_type)} used!")
         # logger.debug("Get all KitTypeReagentTypeAssociation for SubmissionType")
@@ -279,9 +279,9 @@ class ReagentType(BaseClass):
             ReagentType|List[ReagentType]: ReagentType or list of ReagentTypes matching filter.
         """
         query: Query = cls.__database_session__.query(cls)
-        if (kit_type != None and reagent == None) or (reagent != None and kit_type == None):
+        if (kit_type is not None and reagent is None) or (reagent is not None and kit_type is None):
             raise ValueError("Cannot filter without both reagent and kit type.")
-        elif kit_type == None and reagent == None:
+        elif kit_type is None and reagent is None:
             pass
         else:
             match kit_type:
@@ -296,7 +296,7 @@ class ReagentType(BaseClass):
                     reagent = Reagent.query(lot_number=reagent)
                 case _:
                     pass
-            assert reagent.type != []
+            assert reagent.type
             # logger.debug(f"Looking up reagent type for {type(kit_type)} {kit_type} and {type(reagent)} {reagent}")
             # logger.debug(f"Kit reagent types: {kit_type.reagent_types}")
             result = list(set(kit_type.reagent_types).intersection(reagent.type))
@@ -353,7 +353,7 @@ class Reagent(BaseClass):
                                     "submission")  #: Association proxy to SubmissionSampleAssociation.samples
 
     def __repr__(self):
-        if self.name != None:
+        if self.name is not None:
             return f"<Reagent({self.name}-{self.lot})>"
         else:
             return f"<Reagent({self.type.name}-{self.lot})>"
@@ -368,7 +368,7 @@ class Reagent(BaseClass):
         Returns:
             dict: representation of the reagent's attributes
         """
-        if extraction_kit != None:
+        if extraction_kit is not None:
             # Get the intersection of this reagent's ReagentType and all ReagentTypes in KitType
             try:
                 reagent_role = list(set(self.type).intersection(extraction_kit.reagent_types))[0]
@@ -412,10 +412,10 @@ class Reagent(BaseClass):
         report = Report()
         logger.debug(f"Attempting update of reagent type at intersection of ({self}), ({kit})")
         rt = ReagentType.query(kit_type=kit, reagent=self, limit=1)
-        if rt != None:
+        if rt is not None:
             logger.debug(f"got reagenttype {rt}")
             assoc = KitTypeReagentTypeAssociation.query(kit_type=kit, reagent_type=rt)
-            if assoc != None:
+            if assoc is not None:
                 if assoc.last_used != self.lot:
                     logger.debug(f"Updating {assoc} last used to {self.lot}")
                     assoc.last_used = self.lot
@@ -658,14 +658,10 @@ class SubmissionType(BaseClass):
         output = {}
         # logger.debug("Iterating through equipment roles")
         for item in self.submissiontype_equipmentrole_associations:
-            map = item.uses
+            emap = item.uses
-            if map is None:
+            if emap is None:
-                map = {}
+                emap = {}
-            # try:
+            output[item.equipment_role.name] = emap
-            output[item.equipment_role.name] = map
-            # except TypeError:
-            #     pass
-            # output.append(map)
         return output
 
     def get_equipment(self, extraction_kit: str | KitType | None = None) -> List['PydEquipmentRole']:
@@ -737,7 +733,7 @@ class SubmissionType(BaseClass):
         match key:
             case str():
                 # logger.debug(f"Looking up submission type by info-map key str: {key}")
-                query = query.filter(cls.info_map.op('->')(key) != None)
+                query = query.filter(cls.info_map.op('->')(key) is not None)
             case _:
                 pass
         return cls.execute_query(query=query, limit=limit)

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

@@ -735,20 +735,46 @@ class BasicSubmission(BaseClass):
         return re.sub(rf"{abb}(\d)", rf"{abb}-\1", outstr)
         # return outstr
 
+    # @classmethod
+    # def parse_pcr(cls, xl: pd.DataFrame, rsl_number: str) -> list:
+    #     """
+    #     Perform custom parsing of pcr info.
+    #
+    #     Args:
+    #         xl (pd.DataFrame): pcr info form
+    #         rsl_number (str): rsl plate num of interest
+    #
+    #     Returns:
+    #         list: _description_
+    #     """
+    #     logger.debug(f"Hello from {cls.__mapper_args__['polymorphic_identity']} PCR parser!")
+    #     return []
     @classmethod
-    def parse_pcr(cls, xl: pd.DataFrame, rsl_number: str) -> list:
+    def parse_pcr(cls, xl: Workbook, rsl_plate_num: str) -> list:
         """
         Perform custom parsing of pcr info.
 
         Args:
             xl (pd.DataFrame): pcr info form
-            rsl_number (str): rsl plate num of interest
+            rsl_plate_number (str): rsl plate num of interest
 
         Returns:
             list: _description_
         """
         logger.debug(f"Hello from {cls.__mapper_args__['polymorphic_identity']} PCR parser!")
-        return []
+        pcr_sample_map = cls.get_submission_type().sample_map['pcr_samples']
+        logger.debug(f'sample map: {pcr_sample_map}')
+        main_sheet = xl[pcr_sample_map['main_sheet']]
+        samples = []
+        fields = {k: v for k, v in pcr_sample_map.items() if k not in ['main_sheet', 'start_row']}
+        for row in main_sheet.iter_rows(min_row=pcr_sample_map['start_row']):
+            idx = row[0].row
+            sample = {}
+            for k, v in fields.items():
+                sheet = xl[v['sheet']]
+                sample[k] = sheet.cell(row=idx, column=v['column']).value
+            samples.append(sample)
+        return samples
 
     @classmethod
     def filename_template(cls) -> str:
@@ -1314,46 +1340,74 @@ class Wastewater(BasicSubmission):
             input_dict['csv'] = xl["Copy to import file"]
         return input_dict
 
+    # @classmethod
+    # def parse_pcr(cls, xl: pd.ExcelFile, rsl_number: str) -> list:
+    #     """
+    #     Parse specific to wastewater samples.
+    #     """
+    #     samples = super().parse_pcr(xl=xl, rsl_number=rsl_number)
+    #     df = xl.parse(sheet_name="Results", dtype=object).fillna("")
+    #     column_names = ["Well", "Well Position", "Omit", "Sample", "Target", "Task", " Reporter", "Quencher",
+    #                     "Amp Status", "Amp Score", "Curve Quality", "Result Quality Issues", "Cq", "Cq Confidence",
+    #                     "Cq Mean", "Cq SD", "Auto Threshold", "Threshold", "Auto Baseline", "Baseline Start",
+    #                     "Baseline End"]
+    #     samples_df = df.iloc[23:][0:]
+    #     logger.debug(f"Dataframe of PCR results:\n\t{samples_df}")
+    #     samples_df.columns = column_names
+    #     logger.debug(f"Samples columns: {samples_df.columns}")
+    #     well_call_df = xl.parse(sheet_name="Well Call").iloc[24:][0:].iloc[:, -1:]
+    #     try:
+    #         samples_df['Assessment'] = well_call_df.values
+    #     except ValueError:
+    #         logger.error("Well call number doesn't match sample number")
+    #     logger.debug(f"Well call df: {well_call_df}")
+    #     for _, row in samples_df.iterrows():
+    #         try:
+    #             sample_obj = [sample for sample in samples if sample['sample'] == row[3]][0]
+    #         except IndexError:
+    #             sample_obj = dict(
+    #                 sample=row['Sample'],
+    #                 plate_rsl=rsl_number,
+    #             )
+    #         logger.debug(f"Got sample obj: {sample_obj}")
+    #         if isinstance(row['Cq'], float):
+    #             sample_obj[f"ct_{row['Target'].lower()}"] = row['Cq']
+    #         else:
+    #             sample_obj[f"ct_{row['Target'].lower()}"] = 0.0
+    #         try:
+    #             sample_obj[f"{row['Target'].lower()}_status"] = row['Assessment']
+    #         except KeyError:
+    #             logger.error(f"No assessment for {sample_obj['sample']}")
+    #         samples.append(sample_obj)
+    #     return samples
     @classmethod
-    def parse_pcr(cls, xl: pd.ExcelFile, rsl_number: str) -> list:
+    def parse_pcr(cls, xl: Workbook, rsl_plate_num: str) -> list:
         """
         Parse specific to wastewater samples.
         """
-        samples = super().parse_pcr(xl=xl, rsl_number=rsl_number)
+        samples = super().parse_pcr(xl=xl, rsl_plate_num=rsl_plate_num)
-        df = xl.parse(sheet_name="Results", dtype=object).fillna("")
+        logger.debug(f'Samples from parent pcr parser: {pformat(samples)}')
-        column_names = ["Well", "Well Position", "Omit", "Sample", "Target", "Task", " Reporter", "Quencher",
+        output = []
-                        "Amp Status", "Amp Score", "Curve Quality", "Result Quality Issues", "Cq", "Cq Confidence",
+        for sample in samples:
-                        "Cq Mean", "Cq SD", "Auto Threshold", "Threshold", "Auto Baseline", "Baseline Start",
+            sample['sample'] = re.sub('-N\\d$', '', sample['sample'])
-                        "Baseline End"]
+            if sample['sample'] in [item['sample'] for item in output]:
-        samples_df = df.iloc[23:][0:]
+                continue
-        logger.debug(f"Dataframe of PCR results:\n\t{samples_df}")
+            sample[f"ct_{sample['target'].lower()}"] = sample['ct'] if isinstance(sample['ct'], float) else 0.0
-        samples_df.columns = column_names
+            sample[f"{sample['target'].lower()}_status"] = sample['assessment']
-        logger.debug(f"Samples columns: {samples_df.columns}")
+            other_targets = [s for s in samples if re.sub('-N\\d$', '', s['sample']) == sample['sample']]
-        well_call_df = xl.parse(sheet_name="Well Call").iloc[24:][0:].iloc[:, -1:]
+            for s in other_targets:
-        try:
+                sample[f"ct_{s['target'].lower()}"] = s['ct'] if isinstance(s['ct'], float) else 0.0
-            samples_df['Assessment'] = well_call_df.values
+                sample[f"{s['target'].lower()}_status"] = s['assessment']
-        except ValueError:
-            logger.error("Well call number doesn't match sample number")
-        logger.debug(f"Well call df: {well_call_df}")
-        for _, row in samples_df.iterrows():
             try:
-                sample_obj = [sample for sample in samples if sample['sample'] == row[3]][0]
+                del sample['ct']
-            except IndexError:
-                sample_obj = dict(
-                    sample=row['Sample'],
-                    plate_rsl=rsl_number,
-                )
-            logger.debug(f"Got sample obj: {sample_obj}")
-            if isinstance(row['Cq'], float):
-                sample_obj[f"ct_{row['Target'].lower()}"] = row['Cq']
-            else:
-                sample_obj[f"ct_{row['Target'].lower()}"] = 0.0
-            try:
-                sample_obj[f"{row['Target'].lower()}_status"] = row['Assessment']
             except KeyError:
-                logger.error(f"No assessment for {sample_obj['sample']}")
+                pass
-            samples.append(sample_obj)
+            try:
-        return samples
+                del sample['assessment']
+            except KeyError:
+                pass
+            output.append(sample)
+        return output
 
     @classmethod
     def enforce_name(cls, instr: str, data: dict | None = {}) -> str:

src/submissions/backend/excel/parser.py

@@ -732,67 +732,113 @@ class EquipmentParser(object):
         return output
 
 
+# class PCRParser(object):
+#     """
+#     Object to pull data from Design and Analysis PCR export file.
+#     """
+#
+#     def __init__(self, filepath: Path | None = None) -> None:
+#         """
+#         Initializes object.
+#
+#         Args:
+#             filepath (Path | None, optional): file to parse. Defaults to None.
+#         """
+#         logger.debug(f"Parsing {filepath.__str__()}")
+#         if filepath == None:
+#             logger.error(f"No filepath given.")
+#             self.xl = None
+#         else:
+#             try:
+#                 self.xl = pd.ExcelFile(filepath.__str__())
+#             except ValueError as e:
+#                 logger.error(f"Incorrect value: {e}")
+#                 self.xl = None
+#             except PermissionError:
+#                 logger.error(f"Couldn't get permissions for {filepath.__str__()}. Operation might have been cancelled.")
+#                 return
+#         self.parse_general(sheet_name="Results")
+#         namer = RSLNamer(filename=filepath.__str__())
+#         self.plate_num = namer.parsed_name
+#         self.submission_type = namer.submission_type
+#         logger.debug(f"Set plate number to {self.plate_num} and type to {self.submission_type}")
+#         parser = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type)
+#         self.samples = parser.parse_pcr(xl=self.xl, rsl_number=self.plate_num)
+#
+#     def parse_general(self, sheet_name: str):
+#         """
+#         Parse general info rows for all types of PCR results
+#
+#         Args:
+#             sheet_name (str): Name of sheet in excel workbook that holds info.
+#         """
+#         self.pcr = {}
+#         df = self.xl.parse(sheet_name=sheet_name, dtype=object).fillna("")
+#         self.pcr['comment'] = df.iloc[0][1]
+#         self.pcr['operator'] = df.iloc[1][1]
+#         self.pcr['barcode'] = df.iloc[2][1]
+#         self.pcr['instrument'] = df.iloc[3][1]
+#         self.pcr['block_type'] = df.iloc[4][1]
+#         self.pcr['instrument_name'] = df.iloc[5][1]
+#         self.pcr['instrument_serial'] = df.iloc[6][1]
+#         self.pcr['heated_cover_serial'] = df.iloc[7][1]
+#         self.pcr['block_serial'] = df.iloc[8][1]
+#         self.pcr['run-start'] = df.iloc[9][1]
+#         self.pcr['run_end'] = df.iloc[10][1]
+#         self.pcr['run_duration'] = df.iloc[11][1]
+#         self.pcr['sample_volume'] = df.iloc[12][1]
+#         self.pcr['cover_temp'] = df.iloc[13][1]
+#         self.pcr['passive_ref'] = df.iloc[14][1]
+#         self.pcr['pcr_step'] = df.iloc[15][1]
+#         self.pcr['quant_cycle_method'] = df.iloc[16][1]
+#         self.pcr['analysis_time'] = df.iloc[17][1]
+#         self.pcr['software'] = df.iloc[18][1]
+#         self.pcr['plugin'] = df.iloc[19][1]
+#         self.pcr['exported_on'] = df.iloc[20][1]
+#         self.pcr['imported_by'] = getuser()
+
 class PCRParser(object):
-    """
+    """Object to pull data from Design and Analysis PCR export file."""
-    Object to pull data from Design and Analysis PCR export file.
-    """
 
-    def __init__(self, filepath: Path | None = None) -> None:
+    def __init__(self, filepath: Path | None=None, submission: BasicSubmission | None=None) -> None:
         """
-        Initializes object.
+         Initializes object.
 
-        Args:
+         Args:
-            filepath (Path | None, optional): file to parse. Defaults to None.
+             filepath (Path | None, optional): file to parse. Defaults to None.
-        """
+         """
-        logger.debug(f"Parsing {filepath.__str__()}")
+        logger.debug(f'Parsing {filepath.__str__()}')
-        if filepath == None:
+        if filepath is None:
-            logger.error(f"No filepath given.")
+            logger.error('No filepath given.')
             self.xl = None
         else:
             try:
-                self.xl = pd.ExcelFile(filepath.__str__())
+                self.xl = load_workbook(filepath)
             except ValueError as e:
-                logger.error(f"Incorrect value: {e}")
+                logger.error(f'Incorrect value: {e}')
                 self.xl = None
             except PermissionError:
-                logger.error(f"Couldn't get permissions for {filepath.__str__()}. Operation might have been cancelled.")
+                logger.error(f'Couldn\'t get permissions for {filepath.__str__()}. Operation might have been cancelled.')
-                return
+                return None
-        self.parse_general(sheet_name="Results")
+        if submission is None:
-        namer = RSLNamer(filename=filepath.__str__())
+            self.submission_obj = Wastewater
-        self.plate_num = namer.parsed_name
+            rsl_plate_num = None
-        self.submission_type = namer.submission_type
+        else:
-        logger.debug(f"Set plate number to {self.plate_num} and type to {self.submission_type}")
+            self.submission_obj = submission
-        parser = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type)
+            rsl_plate_num = self.submission_obj.rsl_plate_num
-        self.samples = parser.parse_pcr(xl=self.xl, rsl_number=self.plate_num)
+        self.pcr = self.parse_general()
+        self.samples = self.submission_obj.parse_pcr(xl=self.xl, rsl_plate_num=rsl_plate_num)
 
-    def parse_general(self, sheet_name: str):
+    def parse_general(self):
         """
         Parse general info rows for all types of PCR results
 
         Args:
             sheet_name (str): Name of sheet in excel workbook that holds info.
-        """
+         """
-        self.pcr = {}
+        info_map = self.submission_obj.get_submission_type().sample_map['pcr_general_info']
-        df = self.xl.parse(sheet_name=sheet_name, dtype=object).fillna("")
+        sheet = self.xl[info_map['sheet']]
-        self.pcr['comment'] = df.iloc[0][1]
+        iter_rows = sheet.iter_rows(min_row=info_map['start_row'], max_row=info_map['end_row'])
-        self.pcr['operator'] = df.iloc[1][1]
+        pcr = {row[0].value.lower().replace(' ', '_'): row[1].value for row in iter_rows}
-        self.pcr['barcode'] = df.iloc[2][1]
+        pcr['imported_by'] = getuser()
-        self.pcr['instrument'] = df.iloc[3][1]
+        return pcr
-        self.pcr['block_type'] = df.iloc[4][1]
-        self.pcr['instrument_name'] = df.iloc[5][1]
-        self.pcr['instrument_serial'] = df.iloc[6][1]
-        self.pcr['heated_cover_serial'] = df.iloc[7][1]
-        self.pcr['block_serial'] = df.iloc[8][1]
-        self.pcr['run-start'] = df.iloc[9][1]
-        self.pcr['run_end'] = df.iloc[10][1]
-        self.pcr['run_duration'] = df.iloc[11][1]
-        self.pcr['sample_volume'] = df.iloc[12][1]
-        self.pcr['cover_temp'] = df.iloc[13][1]
-        self.pcr['passive_ref'] = df.iloc[14][1]
-        self.pcr['pcr_step'] = df.iloc[15][1]
-        self.pcr['quant_cycle_method'] = df.iloc[16][1]
-        self.pcr['analysis_time'] = df.iloc[17][1]
-        self.pcr['software'] = df.iloc[18][1]
-        self.pcr['plugin'] = df.iloc[19][1]
-        self.pcr['exported_on'] = df.iloc[20][1]
-        self.pcr['imported_by'] = getuser()