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hitpicking complete, pre-addition of WW-Arctic parsers and models.

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Landon Wark
2023-05-31 09:44:20 -05:00
parent 01d95e80f5
commit 1d6823705c
17 changed files with 334 additions and 247 deletions
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19
src/submissions/tools/__init__.py
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@@ -92,14 +92,12 @@ def check_kit_integrity(sub:BasicSubmission|KitType, reagenttypes:list|None=None
check = set(ext_kit_rtypes) == set(reagenttypes)
logger.debug(f"Checking if reagents match kit contents: {check}")
# what reagent types are in both lists?
# common = list(set(ext_kit_rtypes).intersection(reagenttypes))
missing = list(set(ext_kit_rtypes).difference(reagenttypes))
logger.debug(f"Missing reagents types: {missing}")
# if lists are equal return no problem
if len(missing)==0:
result = None
else:
# missing = [x for x in ext_kit_rtypes if x not in common]
result = {'message' : f"The submission you are importing is missing some reagents expected by the kit.\n\nIt looks like you are missing: {[item.upper() for item in missing]}\n\nAlternatively, you may have set the wrong extraction kit.\n\nThe program will populate lists using existing reagents.\n\nPlease make sure you check the lots carefully!", 'missing': missing}
return result
@@ -168,7 +166,6 @@ class RSLNamer(object):
Object that will enforce proper formatting on RSL plate names.
"""
def __init__(self, instr:str):
# self.parsed_name, self.submission_type = self.retrieve_rsl_number(instr)
self.retrieve_rsl_number(in_str=instr)
if self.submission_type != None:
parser = getattr(self, f"enforce_{self.submission_type}")
@@ -195,12 +192,13 @@ class RSLNamer(object):
return
logger.debug(f"Attempting match of {in_str}")
regex = re.compile(r"""
(?P<wastewater>RSL(?:-|_)?WW(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(?:_|-)R?\d(?!\d))?)|
(?P<wastewater>RSL(?:-|_)?WW(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(?:_|-)\d?(?!\d)R?\d(?!\d))?)|
(?P<bacterial_culture>RSL-?\d{2}-?\d{4})
""", flags = re.IGNORECASE | re.VERBOSE)
m = regex.search(in_str)
try:
self.parsed_name = m.group().upper()
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!")
@@ -210,11 +208,8 @@ class RSLNamer(object):
"""
Uses regex to enforce proper formatting of wastewater samples
"""
# self.parsed_name = re.sub(r"(\d)-(\d)", "\1\2", self.parsed_name)
# year = str(date.today().year)[:2]
self.parsed_name = re.sub(r"PCR(-|_)", "", self.parsed_name)
self.parsed_name = self.parsed_name.replace("RSLWW", "RSL-WW")
# .replace(f"WW{year}", f"WW-{year}")
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)
@@ -222,14 +217,6 @@ class RSLNamer(object):
"""
Uses regex to enforce proper formatting of bacterial culture samples
"""
# year = str(date.today().year)[2:]
# self.parsed_name = self.parsed_name.replace(f"RSL{year}", f"RSL-{year}")
# reg_year = re.compile(fr"{year}(?P<rsl>\d\d\d\d)")
self.parsed_name = re.sub(r"RSL(\d{2})", r"RSL-\1", self.parsed_name, flags=re.IGNORECASE)
self.parsed_name = re.sub(r"RSL-(\d{2})(\d{4})", r"RSL-\1-\2", self.parsed_name, flags=re.IGNORECASE)
# year = regex.group('year')
# rsl = regex.group('rsl')
# self.parsed_name = re.sub(fr"{year}(\d\d\d\d)", fr"{year}-\1", self.parsed_name)
# plate_search = reg_year.search(self.parsed_name)
# if plate_search != None:
# self.parsed_name = re.sub(reg_year, f"{year}-{plate_search.group('rsl')}", self.parsed_name)