Moments before disaster.
This commit is contained in:
Landon Wark
@@ -15,7 +15,7 @@ import pandas as pd
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from openpyxl import Workbook
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from . import BaseClass
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from tools import check_not_nan, row_map, query_return, setup_lookup, jinja_template_loading
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from datetime import datetime, date
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from datetime import datetime, date, time
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from typing import List
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from dateutil.parser import parse
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from dateutil.parser._parser import ParserError
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@@ -397,7 +397,7 @@ class BasicSubmission(BaseClass):
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return cls.find_polymorphic_subclass(submission_type.name)
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case _:
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pass
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if len(attrs) == 0 or attrs == None:
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if attrs == None or len(attrs) == 0:
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return cls
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if any([not hasattr(cls, attr) for attr in attrs]):
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# looks for first model that has all included kwargs
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@@ -675,6 +675,7 @@ class BasicSubmission(BaseClass):
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logger.warning(f"End date with no start date, using Jan 1, 2023")
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start_date = date(2023, 1, 1)
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if start_date != None:
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logger.debug(f"Querying with start date: {start_date} and end date: {end_date}")
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match start_date:
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case date():
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start_date = start_date.strftime("%Y-%m-%d")
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@@ -683,14 +684,19 @@ class BasicSubmission(BaseClass):
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case _:
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start_date = parse(start_date).strftime("%Y-%m-%d")
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match end_date:
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case date():
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case date() | datetime():
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end_date = end_date.strftime("%Y-%m-%d")
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case int():
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end_date = datetime.fromordinal(datetime(1900, 1, 1).toordinal() + end_date - 2).date().strftime("%Y-%m-%d")
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case _:
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end_date = parse(end_date).strftime("%Y-%m-%d")
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# logger.debug(f"Looking up BasicSubmissions from start date: {start_date} and end date: {end_date}")
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query = query.filter(cls.submitted_date.between(start_date, end_date))
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logger.debug(f"Start date {start_date} == End date {end_date}: {start_date==end_date}")
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if start_date == end_date:
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start_date = datetime.strptime(start_date, "%Y-%m-%d").strftime("%Y-%m-%d %H:%M:%S.%f")
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query = query.filter(cls.submitted_date==start_date)
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else:
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query = query.filter(cls.submitted_date.between(start_date, end_date))
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# by reagent (for some reason)
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match reagent:
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case str():
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@@ -846,42 +852,55 @@ class BacterialCulture(BasicSubmission):
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"""
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Extends parent
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"""
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from backend.validators import RSLNamer
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data['abbreviation'] = "BC"
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outstr = super().enforce_name(instr=instr, data=data)
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def construct(data:dict|None=None) -> str:
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"""
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Create default plate name.
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# def construct(data:dict|None=None) -> str:
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# """
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# Create default plate name.
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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 = cls.__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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# 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 = cls.__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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# outstr = re.sub(r"RSL(\d{2})", r"RSL-\1", outstr, flags=re.IGNORECASE)
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# except (AttributeError, TypeError) as e:
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# outstr = construct()
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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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# return re.sub(r"RSL-(\d{2})(\d{4})", r"RSL-\1-\2", outstr, flags=re.IGNORECASE)
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# def construct():
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# previous = cls.query(start_date=date.today(), end_date=date.today(), submission_type=cls.__name__)
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# max = len(previous)
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# return f"RSL-BC-{date.today().strftime('%Y%m%d')}-{max+1}"
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try:
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outstr = re.sub(r"RSL(\d{2})", r"RSL-\1", outstr, flags=re.IGNORECASE)
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outstr = re.sub(r"(\d{4})-(\d{2})-(\d{2})", r"\1\2\3", outstr)
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outstr = re.sub(r"BC(\d{6})", r"BC-\1", outstr, flags=re.IGNORECASE)
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except (AttributeError, TypeError) as e:
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outstr = construct()
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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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return re.sub(r"RSL-(\d{2})(\d{4})", r"RSL-\1-\2", outstr, flags=re.IGNORECASE)
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# outstr = construct()
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outstr = RSLNamer.construct_new_plate_name(data=data)
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return outstr
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@classmethod
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def get_regex(cls) -> str:
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@@ -992,27 +1011,30 @@ class Wastewater(BasicSubmission):
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"""
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Extends parent
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"""
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from backend.validators import RSLNamer
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data['abbreviation'] = "WW"
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outstr = super().enforce_name(instr=instr, data=data)
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def construct(data:dict|None=None):
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if "submitted_date" in data.keys():
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if data['submitted_date']['value'] != None:
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today = data['submitted_date']['value']
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else:
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today = datetime.now()
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else:
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today = re.search(r"\d{4}(_|-)?\d{2}(_|-)?\d{2}", instr)
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try:
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today = parse(today.group())
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except AttributeError:
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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)}"
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if outstr == None:
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outstr = construct(data)
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# def construct(data:dict|None=None):
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# if "submitted_date" in data.keys():
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# if data['submitted_date']['value'] != None:
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# today = data['submitted_date']['value']
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# else:
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# today = datetime.now()
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# else:
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# today = re.search(r"\d{4}(_|-)?\d{2}(_|-)?\d{2}", instr)
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# try:
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# today = parse(today.group())
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# except AttributeError:
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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)}"
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# if outstr == None:
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# outstr = construct(data)
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try:
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outstr = re.sub(r"PCR(-|_)", "", outstr)
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except AttributeError as e:
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logger.error(f"Problem using regex: {e}")
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outstr = construct(data)
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# outstr = construct(data)
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outstr = RSLNamer.construct_new_plate_name(instr=outstr)
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outstr = outstr.replace("RSLWW", "RSL-WW")
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outstr = re.sub(r"WW(\d{4})", r"WW-\1", outstr, flags=re.IGNORECASE)
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outstr = re.sub(r"(\d{4})-(\d{2})-(\d{2})", r"\1\2\3", outstr)
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@@ -1094,14 +1116,17 @@ class WastewaterArtic(BasicSubmission):
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"""
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Extends parent
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"""
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from backend.validators import RSLNamer
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data['abbreviation'] = "AR"
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outstr = super().enforce_name(instr=instr, data=data)
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def construct(data:dict|None=None):
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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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# def construct(data:dict|None=None):
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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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outstr = re.sub(r"(\d{4})-(\d{2})-(\d{2})", r"RSL-AR-\1\2\3", outstr, flags=re.IGNORECASE)
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except AttributeError:
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outstr = construct()
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# outstr = construct()
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outstr = RSLNamer.construct_new_plate_name(instr=outstr, data=data)
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try:
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plate_number = int(re.search(r"_|-\d?_", outstr).group().strip("_").strip("-"))
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except (AttributeError, ValueError) as e:
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