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Before creating info and reagent parser classes.

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This commit is contained in:
Landon Wark
2023-08-21 13:50:38 -05:00
parent af810ae528
commit b6de159631
20 changed files with 1176 additions and 571 deletions
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70
src/submissions/tools/__init__.py
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@@ -18,8 +18,6 @@ from sqlalchemy import create_engine
from pydantic import field_validator
from pydantic_settings import BaseSettings, SettingsConfigDict
from typing import Any, Tuple
import __init__ as package
logger = logging.getLogger(f"submissions.{__name__}")
@@ -50,7 +48,7 @@ def check_not_nan(cell_contents) -> bool:
"""
# check for nan as a string first
try:
if "Unnamed:" in cell_contents:
if "Unnamed:" in cell_contents or "blank" in cell_contents.lower():
cell_contents = np.nan
cell_contents = cell_contents.lower()
except (TypeError, AttributeError):
@@ -59,7 +57,6 @@ def check_not_nan(cell_contents) -> bool:
cell_contents = np.nan
if cell_contents == None:
cell_contents = np.nan
try:
if pd.isnull(cell_contents):
cell_contents = np.nan
@@ -170,11 +167,12 @@ class RSLNamer(object):
"""
Object that will enforce proper formatting on RSL plate names.
"""
def __init__(self, ctx, instr:str):
def __init__(self, ctx, instr:str, sub_type:str|None=None):
self.ctx = ctx
self.submission_type = sub_type
self.retrieve_rsl_number(in_str=instr)
if self.submission_type != None:
parser = getattr(self, f"enforce_{self.submission_type}")
parser = getattr(self, f"enforce_{self.submission_type.lower()}")
parser()
self.parsed_name = self.parsed_name.replace("_", "-")
@@ -187,35 +185,37 @@ class RSLNamer(object):
"""
if not isinstance(in_str, Path):
in_str = Path(in_str)
out_str = in_str.stem
logger.debug(f"Attempting match of {out_str}")
logger.debug(f"The initial plate name is: {out_str}")
self.out_str = in_str.stem
logger.debug(f"Attempting match of {self.out_str}")
logger.debug(f"The initial plate name is: {self.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(out_str)
# (?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(self.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()
self.parsed_name = m.group().upper().strip(".")
logger.debug(f"Got parsed submission name: {self.parsed_name}")
if self.submission_type == None:
try:
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}")
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()
# else:
# raise ValueError(f"No parsed name could be created for {self.out_str}.")
def enforce_wastewater(self):
"""
@@ -223,10 +223,11 @@ class RSLNamer(object):
"""
def construct():
today = datetime.now()
return f"RSL-WW-{today.year}{str(today.month).zfill(2)}{str(today.day).zfill(2)}"
return f"RSL-WW-{today.year}{str(today.month).zfill(2)}{str(today.day).zfill(2)}"
try:
self.parsed_name = re.sub(r"PCR(-|_)", "", self.parsed_name)
except AttributeError as e:
logger.error(f"Problem using regex: {e}")
self.parsed_name = construct()
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)
@@ -413,6 +414,7 @@ class Settings(BaseSettings):
@field_validator('package', mode="before")
@classmethod
def import_package(cls, value):
import __init__ as package
if value == None:
return package