Update to reagent parser to exclude 'not applicable'
This commit is contained in:
Landon Wark
@@ -32,7 +32,6 @@ from pathlib import Path
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from jinja2.exceptions import TemplateNotFound
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from jinja2 import Template
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logger = logging.getLogger(f"submissions.{__name__}")
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class BasicSubmission(BaseClass):
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@@ -593,7 +592,7 @@ class BasicSubmission(BaseClass):
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return input_excel
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@classmethod
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def enforce_name(cls, instr:str, data:dict|None=None) -> str:
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def enforce_name(cls, instr:str, data:dict|None={}) -> str:
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"""
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Custom naming method for this class.
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@@ -604,8 +603,40 @@ class BasicSubmission(BaseClass):
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Returns:
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str: Updated name.
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"""
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logger.info(f"Hello from {cls.__mapper_args__['polymorphic_identity']} Enforcer!")
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return instr
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# logger.info(f"Hello from {cls.__mapper_args__['polymorphic_identity']} Enforcer!")
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# return instr
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from backend.validators import RSLNamer
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defaults = cls.get_default_info()
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data['abbreviation'] = defaults['abbreviation']
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if 'submission_type' not in data.keys() or data['submission_type'] in [None, ""]:
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data['submission_type'] = defaults['submission_type']
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# outstr = super().enforce_name(instr=instr, data=data)
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if instr in [None, ""]:
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outstr = RSLNamer.construct_new_plate_name(data=data)
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else:
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outstr = instr
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if re.search(rf"{data['abbreviation']}", outstr, flags=re.IGNORECASE) is None:
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outstr = re.sub(rf"RSL-?", rf"RSL-{data['abbreviation']}-", outstr, flags=re.IGNORECASE)
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try:
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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(rf"{data['abbreviation']}(\d{6})", rf"{data['abbreviation']}-\1", outstr, flags=re.IGNORECASE).upper()
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except (AttributeError, TypeError) as e:
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outstr = RSLNamer.construct_new_plate_name(data=data)
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try:
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plate_number = re.search(r"(?:(-|_)\d)(?!\d)", outstr).group().strip("_").strip("-")
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# logger.debug(f"Plate number is: {plate_number}")
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except AttributeError as e:
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plate_number = "1"
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outstr = re.sub(r"(\d{8})(-|_)?\d?(R\d?)?", rf"\1-{plate_number}\3", outstr)
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# logger.debug(f"After addition of plate number the plate name is: {outstr}")
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try:
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repeat = re.search(r"-\dR(?P<repeat>\d)?", outstr).groupdict()['repeat']
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if repeat == None:
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repeat = "1"
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except AttributeError as e:
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repeat = ""
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return re.sub(r"(-\dR)\d?", rf"\1 {repeat}", outstr).replace(" ", "")
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# return outstr
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@classmethod
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def parse_pcr(cls, xl:pd.DataFrame, rsl_number:str) -> list:
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@@ -1052,42 +1083,6 @@ class BacterialCulture(BasicSubmission):
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input_excel["Sample List"].cell(row=15, column=2, value=getuser())
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return input_excel
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@classmethod
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def enforce_name(cls, instr:str, data:dict|None={}) -> str:
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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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defaults = cls.get_default_info()
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data['abbreviation'] = defaults['abbreviation']
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if 'submission_type' not in data.keys() or data['submission_type'] in [None, ""]:
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data['submission_type'] = defaults['submission_type']
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outstr = super().enforce_name(instr=instr, data=data)
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if outstr in [None, ""]:
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outstr = RSLNamer.construct_new_plate_name(data=data)
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if re.search(rf"{data['abbreviation']}", outstr, flags=re.IGNORECASE) is None:
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outstr = re.sub(rf"RSL-?", rf"RSL-{data['abbreviation']}-", outstr, flags=re.IGNORECASE)
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try:
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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(rf"{data['abbreviation']}(\d{6})", rf"{data['abbreviation']}-\1", outstr, flags=re.IGNORECASE).upper()
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except (AttributeError, TypeError) as e:
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outstr = RSLNamer.construct_new_plate_name(data=data)
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try:
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plate_number = re.search(r"(?:(-|_)\d)(?!\d)", outstr).group().strip("_").strip("-")
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# logger.debug(f"Plate number is: {plate_number}")
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except AttributeError as e:
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plate_number = "1"
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outstr = re.sub(r"(\d{8})(-|_)?\d?(R\d?)?", rf"\1-{plate_number}\3", outstr)
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# logger.debug(f"After addition of plate number the plate name is: {outstr}")
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try:
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repeat = re.search(r"-\dR(?P<repeat>\d)?", outstr).groupdict()['repeat']
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if repeat == None:
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repeat = "1"
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except AttributeError as e:
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repeat = ""
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return re.sub(r"(-\dR)\d?", rf"\1 {repeat}", outstr).replace(" ", "")
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# return outstr
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@classmethod
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def get_regex(cls) -> str:
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"""
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@@ -1227,37 +1222,17 @@ class Wastewater(BasicSubmission):
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return samples
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@classmethod
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def enforce_name(cls, instr:str, data:dict|None=None) -> str:
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def enforce_name(cls, instr:str, data:dict|None={}) -> str:
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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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defaults = cls.get_default_info()
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data['abbreviation'] = defaults['abbreviation']
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outstr = super().enforce_name(instr=instr, data=data)
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try:
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outstr = re.sub(r"PCR(-|_)", "", outstr)
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# Deal with PCR file.
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instr = re.sub(r"PCR(-|_)", "", instr)
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except (AttributeError, TypeError) as e:
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logger.error(f"Problem using regex: {e}")
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outstr = RSLNamer.construct_new_plate_name(data=data)
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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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# logger.debug(f"Coming out of the preliminary parsing, the plate name is {outstr}")
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try:
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plate_number = re.search(r"(?:(-|_)\d)(?!\d)", outstr).group().strip("_").strip("-")
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# logger.debug(f"Plate number is: {plate_number}")
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except AttributeError as e:
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plate_number = "1"
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outstr = re.sub(r"(\d{8})(-|_)?\d?(R\d?)?", rf"\1-{plate_number}\3", outstr)
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# logger.debug(f"After addition of plate number the plate name is: {outstr}")
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try:
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repeat = re.search(r"-\dR(?P<repeat>\d)?", outstr).groupdict()['repeat']
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if repeat == None:
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repeat = "1"
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except AttributeError as e:
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repeat = ""
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return re.sub(r"(-\dR)\d?", rf"\1 {repeat}", outstr).replace(" ", "")
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outstr = super().enforce_name(instr=instr, 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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@@ -1275,8 +1250,9 @@ class Wastewater(BasicSubmission):
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Extends parent
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"""
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samples = super().adjust_autofill_samples(samples)
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return [item for item in samples if not item.submitter_id.startswith("EN")]
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samples = [item for item in samples if not item.submitter_id.startswith("EN")]
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return samples
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@classmethod
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def custom_sample_autofill_row(cls, sample, worksheet: Worksheet) -> int:
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"""
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@@ -1325,8 +1301,8 @@ class WastewaterArtic(BasicSubmission):
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return output
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@classmethod
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def get_abbreviation(cls) -> str:
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return "AR"
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def get_default_info(cls) -> str:
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return dict(abbreviation="AR", submission_type="Wastewater Artic")
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@classmethod
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def parse_info(cls, input_dict:dict, xl:pd.ExcelFile|None=None) -> dict:
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@@ -1350,6 +1326,28 @@ class WastewaterArtic(BasicSubmission):
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input_dict['source_plates'] = plates
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return input_dict
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@classmethod
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def enforce_name(cls, instr:str, data:dict|None={}) -> str:
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"""
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Extends parent
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"""
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try:
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# Deal with PCR file.
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instr = re.sub(r"Artic", "", instr, flags=re.IGNORECASE)
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except (AttributeError, TypeError) as e:
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logger.error(f"Problem using regex: {e}")
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try:
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check = instr.startswith("RSL")
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except AttributeError:
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check = False
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if not check:
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try:
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instr = "RSL" + instr
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except:
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instr = "RSL"
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outstr = super().enforce_name(instr=instr, data=data)
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return outstr
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@classmethod
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def parse_samples(cls, input_dict: dict) -> dict:
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"""
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@@ -1420,27 +1418,6 @@ class WastewaterArtic(BasicSubmission):
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year = f"20{year}"
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return f"EN{year}{month}{day}-{en_num}"
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@classmethod
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def enforce_name(cls, instr:str|None=None, data:dict|None=None) -> str:
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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'] = cls.get_abbreviation()
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outstr = super().enforce_name(instr=instr, data=data)
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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, TypeError):
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if instr != None:
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data['rsl_plate_num'] = instr
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# logger.debug(f"Create new plate name from submission parameters")
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outstr = RSLNamer.construct_new_plate_name(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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plate_number = 1
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return re.sub(r"(_|-\d)?_ARTIC", f"-{plate_number}", outstr)
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@classmethod
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def get_regex(cls) -> str:
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"""
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@@ -1676,10 +1653,11 @@ class WastewaterArtic(BasicSubmission):
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self.gel_info = output
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dt = datetime.strftime(datetime.now(), "%Y-%m-%d %H:%M:%S")
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com = dict(text=comment, name=getuser(), time=dt)
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if self.comment is not None:
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self.comment.append(com)
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else:
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self.comment = [com]
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if com['text'] != None and com['text'] != "":
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if self.comment is not None:
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self.comment.append(com)
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else:
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self.comment = [com]
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logger.debug(pformat(self.gel_info))
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with ZipFile(self.__directory_path__.joinpath("submission_imgs.zip"), 'a') as zipf:
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# Add a file located at the source_path to the destination within the zip
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