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Update to reagent parser to exclude 'not applicable'

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This commit is contained in:
Landon Wark
2024-04-09 10:57:29 -05:00
parent 47bc58cd7d
commit 3889498054
4 changed files with 92 additions and 107 deletions
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166
src/submissions/backend/db/models/submissions.py
View File

@@ -32,7 +32,6 @@ from pathlib import Path
from jinja2.exceptions import TemplateNotFound
from jinja2 import Template
logger = logging.getLogger(f"submissions.{__name__}")
class BasicSubmission(BaseClass):
@@ -593,7 +592,7 @@ class BasicSubmission(BaseClass):
return input_excel
@classmethod
def enforce_name(cls, instr:str, data:dict|None=None) -> str:
def enforce_name(cls, instr:str, data:dict|None={}) -> str:
"""
Custom naming method for this class.
@@ -604,8 +603,40 @@ class BasicSubmission(BaseClass):
Returns:
str: Updated name.
"""
logger.info(f"Hello from {cls.__mapper_args__['polymorphic_identity']} Enforcer!")
return instr
# logger.info(f"Hello from {cls.__mapper_args__['polymorphic_identity']} Enforcer!")
# return instr
from backend.validators import RSLNamer
defaults = cls.get_default_info()
data['abbreviation'] = defaults['abbreviation']
if 'submission_type' not in data.keys() or data['submission_type'] in [None, ""]:
data['submission_type'] = defaults['submission_type']
# outstr = super().enforce_name(instr=instr, data=data)
if instr in [None, ""]:
outstr = RSLNamer.construct_new_plate_name(data=data)
else:
outstr = instr
if re.search(rf"{data['abbreviation']}", outstr, flags=re.IGNORECASE) is None:
outstr = re.sub(rf"RSL-?", rf"RSL-{data['abbreviation']}-", outstr, flags=re.IGNORECASE)
try:
outstr = re.sub(r"(\d{4})-(\d{2})-(\d{2})", r"\1\2\3", outstr)
outstr = re.sub(rf"{data['abbreviation']}(\d{6})", rf"{data['abbreviation']}-\1", outstr, flags=re.IGNORECASE).upper()
except (AttributeError, TypeError) as e:
outstr = RSLNamer.construct_new_plate_name(data=data)
try:
plate_number = re.search(r"(?:(-|_)\d)(?!\d)", outstr).group().strip("_").strip("-")
# logger.debug(f"Plate number is: {plate_number}")
except AttributeError as e:
plate_number = "1"
outstr = re.sub(r"(\d{8})(-|_)?\d?(R\d?)?", rf"\1-{plate_number}\3", outstr)
# logger.debug(f"After addition of plate number the plate name is: {outstr}")
try:
repeat = re.search(r"-\dR(?P<repeat>\d)?", outstr).groupdict()['repeat']
if repeat == None:
repeat = "1"
except AttributeError as e:
repeat = ""
return re.sub(r"(-\dR)\d?", rf"\1 {repeat}", outstr).replace(" ", "")
# return outstr
@classmethod
def parse_pcr(cls, xl:pd.DataFrame, rsl_number:str) -> list:
@@ -1052,42 +1083,6 @@ class BacterialCulture(BasicSubmission):
input_excel["Sample List"].cell(row=15, column=2, value=getuser())
return input_excel
@classmethod
def enforce_name(cls, instr:str, data:dict|None={}) -> str:
"""
Extends parent
"""
from backend.validators import RSLNamer
defaults = cls.get_default_info()
data['abbreviation'] = defaults['abbreviation']
if 'submission_type' not in data.keys() or data['submission_type'] in [None, ""]:
data['submission_type'] = defaults['submission_type']
outstr = super().enforce_name(instr=instr, data=data)
if outstr in [None, ""]:
outstr = RSLNamer.construct_new_plate_name(data=data)
if re.search(rf"{data['abbreviation']}", outstr, flags=re.IGNORECASE) is None:
outstr = re.sub(rf"RSL-?", rf"RSL-{data['abbreviation']}-", outstr, flags=re.IGNORECASE)
try:
outstr = re.sub(r"(\d{4})-(\d{2})-(\d{2})", r"\1\2\3", outstr)
outstr = re.sub(rf"{data['abbreviation']}(\d{6})", rf"{data['abbreviation']}-\1", outstr, flags=re.IGNORECASE).upper()
except (AttributeError, TypeError) as e:
outstr = RSLNamer.construct_new_plate_name(data=data)
try:
plate_number = re.search(r"(?:(-|_)\d)(?!\d)", outstr).group().strip("_").strip("-")
# logger.debug(f"Plate number is: {plate_number}")
except AttributeError as e:
plate_number = "1"
outstr = re.sub(r"(\d{8})(-|_)?\d?(R\d?)?", rf"\1-{plate_number}\3", outstr)
# logger.debug(f"After addition of plate number the plate name is: {outstr}")
try:
repeat = re.search(r"-\dR(?P<repeat>\d)?", outstr).groupdict()['repeat']
if repeat == None:
repeat = "1"
except AttributeError as e:
repeat = ""
return re.sub(r"(-\dR)\d?", rf"\1 {repeat}", outstr).replace(" ", "")
# return outstr
@classmethod
def get_regex(cls) -> str:
"""
@@ -1227,37 +1222,17 @@ class Wastewater(BasicSubmission):
return samples
@classmethod
def enforce_name(cls, instr:str, data:dict|None=None) -> str:
def enforce_name(cls, instr:str, data:dict|None={}) -> str:
"""
Extends parent
"""
from backend.validators import RSLNamer
defaults = cls.get_default_info()
data['abbreviation'] = defaults['abbreviation']
outstr = super().enforce_name(instr=instr, data=data)
try:
outstr = re.sub(r"PCR(-|_)", "", outstr)
# Deal with PCR file.
instr = re.sub(r"PCR(-|_)", "", instr)
except (AttributeError, TypeError) as e:
logger.error(f"Problem using regex: {e}")
outstr = RSLNamer.construct_new_plate_name(data=data)
outstr = outstr.replace("RSLWW", "RSL-WW")
outstr = re.sub(r"WW(\d{4})", r"WW-\1", outstr, flags=re.IGNORECASE)
outstr = re.sub(r"(\d{4})-(\d{2})-(\d{2})", r"\1\2\3", outstr)
# logger.debug(f"Coming out of the preliminary parsing, the plate name is {outstr}")
try:
plate_number = re.search(r"(?:(-|_)\d)(?!\d)", outstr).group().strip("_").strip("-")
# logger.debug(f"Plate number is: {plate_number}")
except AttributeError as e:
plate_number = "1"
outstr = re.sub(r"(\d{8})(-|_)?\d?(R\d?)?", rf"\1-{plate_number}\3", outstr)
# logger.debug(f"After addition of plate number the plate name is: {outstr}")
try:
repeat = re.search(r"-\dR(?P<repeat>\d)?", outstr).groupdict()['repeat']
if repeat == None:
repeat = "1"
except AttributeError as e:
repeat = ""
return re.sub(r"(-\dR)\d?", rf"\1 {repeat}", outstr).replace(" ", "")
outstr = super().enforce_name(instr=instr, data=data)
return outstr
@classmethod
def get_regex(cls) -> str:
@@ -1275,8 +1250,9 @@ class Wastewater(BasicSubmission):
Extends parent
"""
samples = super().adjust_autofill_samples(samples)
return [item for item in samples if not item.submitter_id.startswith("EN")]
samples = [item for item in samples if not item.submitter_id.startswith("EN")]
return samples
@classmethod
def custom_sample_autofill_row(cls, sample, worksheet: Worksheet) -> int:
"""
@@ -1325,8 +1301,8 @@ class WastewaterArtic(BasicSubmission):
return output
@classmethod
def get_abbreviation(cls) -> str:
return "AR"
def get_default_info(cls) -> str:
return dict(abbreviation="AR", submission_type="Wastewater Artic")
@classmethod
def parse_info(cls, input_dict:dict, xl:pd.ExcelFile|None=None) -> dict:
@@ -1350,6 +1326,28 @@ class WastewaterArtic(BasicSubmission):
input_dict['source_plates'] = plates
return input_dict
@classmethod
def enforce_name(cls, instr:str, data:dict|None={}) -> str:
"""
Extends parent
"""
try:
# Deal with PCR file.
instr = re.sub(r"Artic", "", instr, flags=re.IGNORECASE)
except (AttributeError, TypeError) as e:
logger.error(f"Problem using regex: {e}")
try:
check = instr.startswith("RSL")
except AttributeError:
check = False
if not check:
try:
instr = "RSL" + instr
except:
instr = "RSL"
outstr = super().enforce_name(instr=instr, data=data)
return outstr
@classmethod
def parse_samples(cls, input_dict: dict) -> dict:
"""
@@ -1420,27 +1418,6 @@ class WastewaterArtic(BasicSubmission):
year = f"20{year}"
return f"EN{year}{month}{day}-{en_num}"
@classmethod
def enforce_name(cls, instr:str|None=None, data:dict|None=None) -> str:
"""
Extends parent
"""
from backend.validators import RSLNamer
data['abbreviation'] = cls.get_abbreviation()
outstr = super().enforce_name(instr=instr, data=data)
try:
outstr = re.sub(r"(\d{4})-(\d{2})-(\d{2})", r"RSL-AR-\1\2\3", outstr, flags=re.IGNORECASE)
except (AttributeError, TypeError):
if instr != None:
data['rsl_plate_num'] = instr
# logger.debug(f"Create new plate name from submission parameters")
outstr = RSLNamer.construct_new_plate_name(data=data)
try:
plate_number = int(re.search(r"_|-\d?_", outstr).group().strip("_").strip("-"))
except (AttributeError, ValueError) as e:
plate_number = 1
return re.sub(r"(_|-\d)?_ARTIC", f"-{plate_number}", outstr)
@classmethod
def get_regex(cls) -> str:
"""
@@ -1676,10 +1653,11 @@ class WastewaterArtic(BasicSubmission):
self.gel_info = output
dt = datetime.strftime(datetime.now(), "%Y-%m-%d %H:%M:%S")
com = dict(text=comment, name=getuser(), time=dt)
if self.comment is not None:
self.comment.append(com)
else:
self.comment = [com]
if com['text'] != None and com['text'] != "":
if self.comment is not None:
self.comment.append(com)
else:
self.comment = [com]
logger.debug(pformat(self.gel_info))
with ZipFile(self.__directory_path__.joinpath("submission_imgs.zip"), 'a') as zipf:
# Add a file located at the source_path to the destination within the zip

3
src/submissions/backend/excel/parser.py
View File

@@ -266,7 +266,8 @@ class ReagentParser(object):
# logger.debug(f"Got lot for {item}-{name}: {lot} as {type(lot)}")
lot = str(lot)
logger.debug(f"Going into pydantic: name: {name}, lot: {lot}, expiry: {expiry}, type: {item.strip()}, comment: {comment}")
listo.append(PydReagent(type=item.strip(), lot=lot, expiry=expiry, name=name, comment=comment, missing=missing))
if name.lower() != "not applicable":
listo.append(PydReagent(type=item.strip(), lot=lot, expiry=expiry, name=name, comment=comment, missing=missing))
return listo
class SampleParser(object):

25
src/submissions/backend/validators/pydant.py
View File

@@ -138,19 +138,19 @@ class PydReagent(BaseModel):
# NOTE: this will now be done only in the reporting phase to account for potential changes in end-of-life extensions
return reagent, report
def toForm(self, parent:QWidget, extraction_kit:str) -> QComboBox:
"""
Converts this instance into a form widget
# def toForm(self, parent:QWidget, extraction_kit:str) -> QComboBox:
# """
# Converts this instance into a form widget
Args:
parent (QWidget): Parent widget of the constructed object
extraction_kit (str): Name of extraction kit used
# Args:
# parent (QWidget): Parent widget of the constructed object
# extraction_kit (str): Name of extraction kit used
Returns:
QComboBox: Form object.
"""
from frontend.widgets.submission_widget import ReagentFormWidget
return ReagentFormWidget(parent=parent, reagent=self, extraction_kit=extraction_kit)
# Returns:
# QComboBox: Form object.
# """
# from frontend.widgets.submission_widget import ReagentFormWidget
# return ReagentFormWidget(parent=parent, reagent=self, extraction_kit=extraction_kit)
class PydSample(BaseModel, extra='allow'):
@@ -705,16 +705,19 @@ class PydSubmission(BaseModel, extra='allow'):
# logger.debug("Sorting samples by row/column")
samples = sorted(self.samples, key=attrgetter('column', 'row'))
submission_obj = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type)
# custom function to adjust values for writing.
samples = submission_obj.adjust_autofill_samples(samples=samples)
logger.debug(f"Samples: {pformat(samples)}")
# Fail safe against multiple instances of the same sample
for iii, sample in enumerate(samples, start=1):
logger.debug(f"Sample: {sample}")
# custom function to find the row of this sample
row = submission_obj.custom_sample_autofill_row(sample, worksheet=worksheet)
logger.debug(f"Writing to {row}")
if row == None:
row = sample_info['lookup_table']['start_row'] + iii
fields = [field for field in list(sample.model_fields.keys()) + list(sample.model_extra.keys()) if field in sample_info['sample_columns'].keys()]
logger.debug(f"Here are the fields we are going to fill:\n\t{fields}")
for field in fields:
column = sample_info['sample_columns'][field]
value = getattr(sample, field)

5
src/submissions/frontend/widgets/submission_widget.py
View File

@@ -280,7 +280,10 @@ class SubmissionFormWidget(QWidget):
if key not in self.ignore:
match value:
case PydReagent():
widget = self.ReagentFormWidget(self, reagent=value, extraction_kit=extraction_kit)
if value.name.lower() != "not applicable":
widget = self.ReagentFormWidget(self, reagent=value, extraction_kit=extraction_kit)
else:
widget = None
case _:
widget = self.InfoItem(self, key=key, value=value, submission_type=submission_type)
return widget