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Autofill excel sheet

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This commit is contained in:
Landon Wark
2023-07-21 13:55:15 -05:00
parent ba35696055
commit f6e270f52d
10 changed files with 189 additions and 67 deletions
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115
src/submissions/tools/__init__.py
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@@ -10,6 +10,7 @@ import getpass
from backend.db.models import BasicSubmission, KitType
import pandas as pd
from typing import Tuple
from datetime import datetime
logger = logging.getLogger(f"submissions.{__name__}")
@@ -25,13 +26,16 @@ def check_not_nan(cell_contents) -> bool:
"""
# check for nan as a string first
try:
if "Unnamed:" in cell_contents:
cell_contents = np.nan
cell_contents = cell_contents.lower()
except AttributeError:
except (TypeError, AttributeError):
pass
if cell_contents == 'nan':
cell_contents = np.nan
if cell_contents == None:
cell_contents = np.nan
try:
if pd.isnull(cell_contents):
cell_contents = np.nan
@@ -197,7 +201,8 @@ class RSLNamer(object):
"""
Object that will enforce proper formatting on RSL plate names.
"""
def __init__(self, instr:str):
def __init__(self, ctx:dict, instr:str):
self.ctx = ctx
self.retrieve_rsl_number(in_str=instr)
if self.submission_type != None:
parser = getattr(self, f"enforce_{self.submission_type}")
@@ -205,7 +210,7 @@ class RSLNamer(object):
self.parsed_name = self.parsed_name.replace("_", "-")
def retrieve_rsl_number(self, in_str:str|Path) -> Tuple[str, str]:
def retrieve_rsl_number(self, in_str:str|Path):
"""
Uses regex to retrieve the plate number and submission type from an input string
@@ -215,37 +220,57 @@ class RSLNamer(object):
Returns:
Tuple[str, str]: tuple of (output rsl number, submission_type)
"""
if isinstance(in_str, Path):
in_str = in_str.stem
logger.debug(f"Attempting split of {in_str}")
try:
in_str = in_str.split("\\")[-1]
except AttributeError:
self.parsed_name = None
self.submission_type = None
return
logger.debug(f"Attempting match of {in_str}")
logger.debug(f"The initial plate name is: {in_str}")
if not isinstance(in_str, Path):
in_str = Path(in_str)
out_str = in_str.stem
# else:
# in_str = Path(in_str)
# logger.debug(f"Attempting split of {in_str}")
# try:
# out_str = in_str.split("\\")[-1]
# except AttributeError:
# self.parsed_name = None
# self.submission_type = None
# return
logger.debug(f"Attempting match of {out_str}")
logger.debug(f"The initial plate name is: {out_str}")
regex = re.compile(r"""
# (?P<wastewater>RSL(?:-|_)?WW(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(?:_|-)\d?((?!\d)|R)?\d(?!\d))?)|
(?P<wastewater>RSL(?:-|_)?WW(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(_|-)\d?(\D|$)R?\d?)?)|
(?P<bacterial_culture>RSL-?\d{2}-?\d{4})|
(?P<wastewater_artic>(\d{4}-\d{2}-\d{2}_(?:\d_)?artic)|(RSL(?:-|_)?AR(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(_|-)\d?(\D|$)R?\d?)?))
""", flags = re.IGNORECASE | re.VERBOSE)
m = regex.search(in_str)
try:
self.parsed_name = m.group().upper().strip(".")
logger.debug(f"Got parsed submission name: {self.parsed_name}")
self.submission_type = m.lastgroup
except AttributeError as e:
logger.critical("No RSL plate number found or submission type found!")
logger.debug(f"The cause of the above error was: {e}")
m = regex.search(out_str)
if m != None:
try:
self.parsed_name = m.group().upper().strip(".")
logger.debug(f"Got parsed submission name: {self.parsed_name}")
self.submission_type = m.lastgroup
except AttributeError as e:
logger.critical("No RSL plate number found or submission type found!")
logger.debug(f"The cause of the above error was: {e}")
else:
logger.warning(f"We're going to have to create the submission type from the excel sheet properties...")
if in_str.exists():
my_xl = pd.ExcelFile(in_str)
if my_xl.book.properties.category != None:
categories = [item.strip().title() for item in my_xl.book.properties.category.split(";")]
self.submission_type = categories[0].replace(" ", "_").lower()
else:
raise AttributeError(f"File {in_str.__str__()} has no categories.")
else:
raise FileNotFoundError()
def enforce_wastewater(self):
"""
Uses regex to enforce proper formatting of wastewater samples
"""
self.parsed_name = re.sub(r"PCR(-|_)", "", self.parsed_name)
try:
self.parsed_name = re.sub(r"PCR(-|_)", "", self.parsed_name)
except AttributeError as e:
self.parsed_name = self.construct_wastewater()
self.parsed_name = self.parsed_name.replace("RSLWW", "RSL-WW")
self.parsed_name = re.sub(r"WW(\d{4})", r"WW-\1", self.parsed_name, flags=re.IGNORECASE)
self.parsed_name = re.sub(r"(\d{4})-(\d{2})-(\d{2})", r"\1\2\3", self.parsed_name)
@@ -267,13 +292,55 @@ class RSLNamer(object):
self.parsed_name = re.sub(r"(-\dR)\d?", rf"\1 {repeat}", self.parsed_name).replace(" ", "")
def construct_wastewater(self):
today = datetime.now()
return f"RSL-WW-{today.year}{str(today.month).zfill(2)}{str(today.day).zfill(2)}"
def enforce_bacterial_culture(self):
"""
Uses regex to enforce proper formatting of bacterial culture samples
"""
self.parsed_name = re.sub(r"RSL(\d{2})", r"RSL-\1", self.parsed_name, flags=re.IGNORECASE)
try:
self.parsed_name = re.sub(r"RSL(\d{2})", r"RSL-\1", self.parsed_name, flags=re.IGNORECASE)
except AttributeError as e:
self.parsed_name = self.construct_bacterial_culture_rsl()
# year = datetime.now().year
# self.parsed_name = f"RSL-{str(year)[-2:]}-0000"
self.parsed_name = re.sub(r"RSL-(\d{2})(\d{4})", r"RSL-\1-\2", self.parsed_name, flags=re.IGNORECASE)
def construct_bacterial_culture_rsl(self) -> str:
"""
DEPRECIATED due to slowness. Search for the largest rsl number and increment by 1
Returns:
str: new RSL number
"""
logger.debug(f"Attempting to construct RSL number from scratch...")
directory = Path(self.ctx['directory_path']).joinpath("Bacteria")
year = str(datetime.now().year)[-2:]
if directory.exists():
logger.debug(f"Year: {year}")
relevant_rsls = []
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]]
logger.debug(f"All rsls: {all_xlsx}")
for item in all_xlsx:
try:
relevant_rsls.append(re.match(r"RSL-\d{2}-\d{4}", item).group(0))
except Exception as e:
logger.error(f"Regex error: {e}")
continue
logger.debug(f"Initial xlsx: {relevant_rsls}")
max_number = max([int(item[-4:]) for item in relevant_rsls])
logger.debug(f"The largest sample number is: {max_number}")
return f"RSL-{year}-{str(max_number+1).zfill(4)}"
else:
# raise FileNotFoundError(f"Unable to locate the directory: {directory.__str__()}")
return f"RSL-{year}-0000"
def enforce_wastewater_artic(self):
"""
Uses regex to enforce proper formatting of wastewater samples