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