Better flexibility with parsers pulling methods from database objects.
This commit is contained in:
Landon Wark
@@ -134,153 +134,6 @@ def massage_common_reagents(reagent_name:str):
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reagent_name = reagent_name.replace("µ", "u")
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return reagent_name
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# class RSLNamer(object):
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# """
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# Object that will enforce proper formatting on RSL plate names.
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# NOTE: Depreciated in favour of object based methods in 'submissions.py'
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# """
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# def __init__(self, ctx, instr:str, sub_type:str|None=None):
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# self.ctx = ctx
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# self.submission_type = sub_type
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# self.retrieve_rsl_number(in_str=instr)
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# if self.submission_type != None:
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# # custom_enforcer = get_polymorphic_subclass(BasicSubmission, self.submission_type).enforce_naming_schema
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# parser = getattr(self, f"enforce_{self.submission_type.replace(' ', '_').lower()}")
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# parser()
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# self.parsed_name = self.parsed_name.replace("_", "-")
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# def retrieve_rsl_number(self, in_str:str|Path):
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# """
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# Uses regex to retrieve the plate number and submission type from an input string
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# Args:
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# in_str (str): string to be parsed
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# """
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# if not isinstance(in_str, Path):
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# in_str = Path(in_str)
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# self.out_str = in_str.stem
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# logger.debug(f"Attempting match of {self.out_str}")
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# logger.debug(f"The initial plate name is: {self.out_str}")
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# regex = re.compile(r"""
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# # (?P<wastewater>RSL(?:-|_)?WW(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(?:_|-)\d?((?!\d)|R)?\d(?!\d))?)|
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# (?P<wastewater>RSL(?:-|_)?WW(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(_|-)\d?(\D|$)R?\d?)?)|
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# (?P<bacterial_culture>RSL-?\d{2}-?\d{4})|
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# (?P<wastewater_artic>(\d{4}-\d{2}-\d{2}(?:-|_)(?:\d_)?artic)|(RSL(?:-|_)?AR(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(_|-)\d?(\D|$)R?\d?)?))
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# """, flags = re.IGNORECASE | re.VERBOSE)
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# m = regex.search(self.out_str)
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# if m != None:
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# self.parsed_name = m.group().upper().strip(".")
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# logger.debug(f"Got parsed submission name: {self.parsed_name}")
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# if self.submission_type == None:
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# try:
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# self.submission_type = m.lastgroup
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# except AttributeError as e:
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# logger.critical("No RSL plate number found or submission type found!")
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# logger.debug(f"The cause of the above error was: {e}")
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# logger.warning(f"We're going to have to create the submission type from the excel sheet properties...")
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# if in_str.exists():
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# my_xl = pd.ExcelFile(in_str)
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# if my_xl.book.properties.category != None:
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# categories = [item.strip().title() for item in my_xl.book.properties.category.split(";")]
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# self.submission_type = categories[0].replace(" ", "_").lower()
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# else:
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# raise AttributeError(f"File {in_str.__str__()} has no categories.")
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# else:
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# raise FileNotFoundError()
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# # else:
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# # raise ValueError(f"No parsed name could be created for {self.out_str}.")
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# def enforce_wastewater(self):
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# """
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# Uses regex to enforce proper formatting of wastewater samples
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# """
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# def construct():
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# today = datetime.now()
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# return f"RSL-WW-{today.year}{str(today.month).zfill(2)}{str(today.day).zfill(2)}-1"
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# try:
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# self.parsed_name = re.sub(r"PCR(-|_)", "", self.parsed_name)
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# except AttributeError as e:
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# logger.error(f"Problem using regex: {e}")
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# self.parsed_name = construct()
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# self.parsed_name = self.parsed_name.replace("RSLWW", "RSL-WW")
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# self.parsed_name = re.sub(r"WW(\d{4})", r"WW-\1", self.parsed_name, flags=re.IGNORECASE)
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# self.parsed_name = re.sub(r"(\d{4})-(\d{2})-(\d{2})", r"\1\2\3", self.parsed_name)
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# logger.debug(f"Coming out of the preliminary parsing, the plate name is {self.parsed_name}")
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# try:
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# plate_number = re.search(r"(?:(-|_)\d)(?!\d)", self.parsed_name).group().strip("_").strip("-")
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# logger.debug(f"Plate number is: {plate_number}")
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# except AttributeError as e:
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# plate_number = "1"
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# # self.parsed_name = re.sub(r"(\d{8})(-|_\d)?(R\d)?", fr"\1-{plate_number}\3", self.parsed_name)
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# self.parsed_name = re.sub(r"(\d{8})(-|_)?\d?(R\d?)?", rf"\1-{plate_number}\3", self.parsed_name)
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# logger.debug(f"After addition of plate number the plate name is: {self.parsed_name}")
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# try:
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# repeat = re.search(r"-\dR(?P<repeat>\d)?", self.parsed_name).groupdict()['repeat']
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# if repeat == None:
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# repeat = "1"
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# except AttributeError as e:
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# repeat = ""
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# self.parsed_name = re.sub(r"(-\dR)\d?", rf"\1 {repeat}", self.parsed_name).replace(" ", "")
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# def enforce_bacterial_culture(self):
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# """
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# Uses regex to enforce proper formatting of bacterial culture samples
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# """
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# def construct(ctx) -> str:
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# """
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# DEPRECIATED due to slowness. Search for the largest rsl number and increment by 1
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# Returns:
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# str: new RSL number
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# """
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# logger.debug(f"Attempting to construct RSL number from scratch...")
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# # directory = Path(self.ctx['directory_path']).joinpath("Bacteria")
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# directory = Path(ctx.directory_path).joinpath("Bacteria")
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# year = str(datetime.now().year)[-2:]
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# if directory.exists():
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# logger.debug(f"Year: {year}")
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# relevant_rsls = []
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# all_xlsx = [item.stem for item in directory.rglob("*.xlsx") if bool(re.search(r"RSL-\d{2}-\d{4}", item.stem)) and year in item.stem[4:6]]
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# logger.debug(f"All rsls: {all_xlsx}")
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# for item in all_xlsx:
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# try:
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# relevant_rsls.append(re.match(r"RSL-\d{2}-\d{4}", item).group(0))
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# except Exception as e:
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# logger.error(f"Regex error: {e}")
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# continue
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# logger.debug(f"Initial xlsx: {relevant_rsls}")
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# max_number = max([int(item[-4:]) for item in relevant_rsls])
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# logger.debug(f"The largest sample number is: {max_number}")
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# return f"RSL-{year}-{str(max_number+1).zfill(4)}"
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# else:
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# # raise FileNotFoundError(f"Unable to locate the directory: {directory.__str__()}")
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# return f"RSL-{year}-0000"
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# try:
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# self.parsed_name = re.sub(r"RSL(\d{2})", r"RSL-\1", self.parsed_name, flags=re.IGNORECASE)
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# except AttributeError as e:
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# self.parsed_name = construct(ctx=self.ctx)
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# # year = datetime.now().year
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# # self.parsed_name = f"RSL-{str(year)[-2:]}-0000"
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# self.parsed_name = re.sub(r"RSL-(\d{2})(\d{4})", r"RSL-\1-\2", self.parsed_name, flags=re.IGNORECASE)
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# def enforce_wastewater_artic(self):
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# """
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# Uses regex to enforce proper formatting of wastewater samples
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# """
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# def construct():
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# today = datetime.now()
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# return f"RSL-AR-{today.year}{str(today.month).zfill(2)}{str(today.day).zfill(2)}"
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# try:
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# self.parsed_name = re.sub(r"(\d{4})-(\d{2})-(\d{2})", r"RSL-AR-\1\2\3", self.parsed_name, flags=re.IGNORECASE)
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# except AttributeError:
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# self.parsed_name = construct()
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# try:
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# plate_number = int(re.search(r"_|-\d?_", self.parsed_name).group().strip("_").strip("-"))
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# except (AttributeError, ValueError) as e:
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# plate_number = 1
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# self.parsed_name = re.sub(r"(_|-\d)?_ARTIC", f"-{plate_number}", self.parsed_name)
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class GroupWriteRotatingFileHandler(handlers.RotatingFileHandler):
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def doRollover(self):
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