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Addition of WW artic parsers, large-scale shake-up of parser structure.

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This commit is contained in:
Landon Wark
2023-06-08 14:43:36 -05:00
parent 1d6823705c
commit a7132cd1b4
14 changed files with 376 additions and 56 deletions
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47
src/submissions/tools/__init__.py
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@@ -83,7 +83,10 @@ def check_kit_integrity(sub:BasicSubmission|KitType, reagenttypes:list|None=None
case BasicSubmission():
ext_kit_rtypes = [reagenttype.name for reagenttype in sub.extraction_kit.reagent_types]
# Overwrite function parameter reagenttypes
reagenttypes = [reagent.type.name for reagent in sub.reagents]
try:
reagenttypes = [reagent.type.name for reagent in sub.reagents]
except AttributeError as e:
logger.error(f"Problem parsing reagents: {[f'{reagent.lot}, {reagent.type}' for reagent in sub.reagents]}")
case KitType():
ext_kit_rtypes = [reagenttype.name for reagenttype in sub.reagent_types]
logger.debug(f"Kit reagents: {ext_kit_rtypes}")
@@ -191,9 +194,12 @@ class RSLNamer(object):
self.submission_type = None
return
logger.debug(f"Attempting match of {in_str}")
print(f"The initial plate name is: {in_str}")
regex = re.compile(r"""
(?P<wastewater>RSL(?:-|_)?WW(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(?:_|-)\d?(?!\d)R?\d(?!\d))?)|
(?P<bacterial_culture>RSL-?\d{2}-?\d{4})
# (?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:
@@ -212,6 +218,25 @@ class RSLNamer(object):
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)
print(f"Coming out of the preliminary parsing, the plate name is {self.parsed_name}")
try:
plate_number = re.search(r"(?:(-|_)\d)(?!\d)", self.parsed_name).group().strip("_").strip("-")
print(f"Plate number is: {plate_number}")
except AttributeError as e:
plate_number = "1"
# self.parsed_name = re.sub(r"(\d{8})(-|_\d)?(R\d)?", fr"\1-{plate_number}\3", self.parsed_name)
self.parsed_name = re.sub(r"(\d{8})(-|_)?\d?(R\d?)?", rf"\1-{plate_number}\3", self.parsed_name)
print(f"After addition of plate number the plate name is: {self.parsed_name}")
try:
repeat = re.search(r"-\dR(?P<repeat>\d)?", self.parsed_name).groupdict()['repeat']
if repeat == None:
repeat = "1"
except AttributeError as e:
repeat = ""
self.parsed_name = re.sub(r"(-\dR)\d?", rf"\1 {repeat}", self.parsed_name).replace(" ", "")
def enforce_bacterial_culture(self):
"""
@@ -219,4 +244,20 @@ class RSLNamer(object):
"""
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)
def enforce_wastewater_artic(self):
self.parsed_name = re.sub(r"(\d{4})-(\d{2})-(\d{2})", r"RSL-AR-\1\2\3", self.parsed_name, flags=re.IGNORECASE)
try:
plate_number = int(re.search(r"_\d?_", self.parsed_name).group().strip("_"))
except AttributeError as e:
plate_number = 1
self.parsed_name = re.sub(r"(_\d)?_ARTIC", f"-{plate_number}", self.parsed_name)
def massage_common_reagents(reagent_name:str):
logger.debug(f"Attempting to massage {reagent_name}")
if reagent_name.endswith("water") or "H2O" in reagent_name:
reagent_name = "molecular_grade_water"
reagent_name = reagent_name.replace("µ", "u")
return reagent_name