Removed logger.debugs for proven functions.
This commit is contained in:
lwark
@@ -24,11 +24,9 @@ class RSLNamer(object):
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filename = Path(filename) if Path(filename).exists() else filename
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self.submission_type = sub_type
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if not self.submission_type:
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# logger.debug("Creating submission type because none exists")
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self.submission_type = self.retrieve_submission_type(filename=filename)
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logger.info(f"got submission type: {self.submission_type}")
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if self.submission_type:
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# logger.debug("Retrieving BasicSubmission subclass")
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self.sub_object = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type)
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self.parsed_name = self.retrieve_rsl_number(filename=filename, regex=self.sub_object.get_regex(submission_type=sub_type))
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if not data:
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@@ -52,7 +50,6 @@ class RSLNamer(object):
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str: parsed submission type
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"""
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def st_from_path(filename:Path) -> str:
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# logger.info(f"Using path method for {filename}.")
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if filename.exists():
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wb = load_workbook(filename)
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try:
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@@ -73,12 +70,9 @@ class RSLNamer(object):
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if filename.startswith("tmp"):
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return "Bacterial Culture"
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regex = BasicSubmission.construct_regex()
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# logger.info(f"Using string method for {filename}.")
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# logger.debug(f"Using regex: {regex}")
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m = regex.search(filename)
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try:
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submission_type = m.lastgroup
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# logger.debug(f"Got submission type: {submission_type}")
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except AttributeError as e:
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submission_type = None
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logger.critical(f"No submission type found or submission type found!: {e}")
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@@ -98,7 +92,6 @@ class RSLNamer(object):
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if check:
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if "pytest" in sys.modules:
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raise ValueError("Submission Type came back as None.")
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# logger.debug("Final option, ask the user for submission type")
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from frontend.widgets import ObjectSelector
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dlg = ObjectSelector(title="Couldn't parse submission type.",
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message="Please select submission type from list below.", obj_type=SubmissionType)
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@@ -116,21 +109,17 @@ class RSLNamer(object):
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regex (str): string to construct pattern
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filename (str): string to be parsed
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"""
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logger.info(f"Input string to be parsed: {filename}")
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if regex is None:
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regex = BasicSubmission.construct_regex()
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else:
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# logger.debug(f"Incoming regex: {regex}")
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try:
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regex = re.compile(rf'{regex}', re.IGNORECASE | re.VERBOSE)
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except re.error as e:
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regex = BasicSubmission.construct_regex()
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logger.info(f"Using regex: {regex}")
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match filename:
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case Path():
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m = regex.search(filename.stem)
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case str():
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# logger.debug(f"Using string method.")
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m = regex.search(filename)
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case _:
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m = None
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@@ -141,7 +130,6 @@ class RSLNamer(object):
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parsed_name = None
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else:
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parsed_name = None
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# logger.debug(f"Got parsed submission name: {parsed_name}")
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return parsed_name
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@classmethod
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@@ -187,8 +175,6 @@ class RSLNamer(object):
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Returns:
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str: output file name.
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"""
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# logger.debug(f"Kwargs: {kwargs}")
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# logger.debug(f"Template: {template}")
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environment = jinja_template_loading()
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template = environment.from_string(template)
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return template.render(**kwargs)
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@@ -1,6 +1,6 @@
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'''
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"""
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Contains pydantic models and accompanying validators
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'''
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"""
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from __future__ import annotations
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import uuid, re, logging, csv, sys
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from pydantic import BaseModel, field_validator, Field, model_validator
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@@ -123,18 +123,14 @@ class PydReagent(BaseModel):
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Tuple[Reagent, Report]: Reagent instance and result of function
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"""
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report = Report()
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# logger.debug("Adding extra fields.")
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if self.model_extra is not None:
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self.__dict__.update(self.model_extra)
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# logger.debug(f"Reagent SQL constructor is looking up type: {self.type}, lot: {self.lot}")
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reagent = Reagent.query(lot=self.lot, name=self.name)
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# logger.debug(f"Result: {reagent}")
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if reagent is None:
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reagent = Reagent()
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for key, value in self.__dict__.items():
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if isinstance(value, dict):
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value = value['value']
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# logger.debug(f"Reagent info item for {key}: {value}")
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# NOTE: set fields based on keys in dictionary
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match key:
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case "lot":
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@@ -149,7 +145,6 @@ class PydReagent(BaseModel):
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if isinstance(value, str):
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value = date(year=1970, month=1, day=1)
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value = datetime.combine(value, datetime.min.time())
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logger.debug(f"Expiry date coming into sql: {value} with type {type(value)}")
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reagent.expiry = value.replace(tzinfo=timezone)
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case _:
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try:
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@@ -179,14 +174,12 @@ class PydSample(BaseModel, extra='allow'):
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@model_validator(mode='after')
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@classmethod
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def validate_model(cls, data):
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# logger.debug(f"Data for pydsample: {data}")
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model = BasicSample.find_polymorphic_subclass(polymorphic_identity=data.sample_type)
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for k, v in data.model_extra.items():
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if k in model.timestamps():
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if isinstance(v, str):
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v = datetime.strptime(v, "%Y-%m-%d")
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data.__setattr__(k, v)
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# logger.debug(f"Data coming out of validation: {pformat(data)}")
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return data
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@field_validator("row", "column", "assoc_id", "submission_rank")
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@@ -238,7 +231,6 @@ class PydSample(BaseModel, extra='allow'):
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"""
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report = None
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self.__dict__.update(self.model_extra)
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# logger.debug(f"Here is the incoming sample dict: \n{self.__dict__}")
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instance = BasicSample.query_or_create(sample_type=self.sample_type, submitter_id=self.submitter_id)
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for key, value in self.__dict__.items():
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match key:
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@@ -246,7 +238,6 @@ class PydSample(BaseModel, extra='allow'):
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case "row" | "column":
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continue
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case _:
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# logger.debug(f"Setting sample field {key} to {value}")
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instance.__setattr__(key, value)
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out_associations = []
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if submission is not None:
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@@ -254,15 +245,12 @@ class PydSample(BaseModel, extra='allow'):
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submission = BasicSubmission.query(rsl_plate_num=submission)
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assoc_type = submission.submission_type_name
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for row, column, aid, submission_rank in zip(self.row, self.column, self.assoc_id, self.submission_rank):
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# logger.debug(f"Looking up association with identity: ({submission.submission_type_name} Association)")
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# logger.debug(f"Looking up association with identity: ({assoc_type} Association)")
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association = SubmissionSampleAssociation.query_or_create(association_type=f"{assoc_type} Association",
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submission=submission,
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sample=instance,
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row=row, column=column, id=aid,
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submission_rank=submission_rank,
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**self.model_extra)
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# logger.debug(f"Using submission_sample_association: {association}")
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try:
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out_associations.append(association)
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except IntegrityError as e:
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@@ -332,7 +320,6 @@ class PydEquipment(BaseModel, extra='ignore'):
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@field_validator('processes', mode='before')
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@classmethod
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def make_empty_list(cls, value):
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# logger.debug(f"Pydantic value: {value}")
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if isinstance(value, GeneratorType):
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value = [item.name for item in value]
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value = convert_nans_to_nones(value)
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@@ -355,7 +342,6 @@ class PydEquipment(BaseModel, extra='ignore'):
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Tuple[Equipment, SubmissionEquipmentAssociation]: SQL objects
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"""
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if isinstance(submission, str):
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# logger.debug(f"Got string, querying {submission}")
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submission = BasicSubmission.query(rsl_plate_num=submission)
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equipment = Equipment.query(asset_number=self.asset_number)
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if equipment is None:
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@@ -403,7 +389,6 @@ class PydEquipment(BaseModel, extra='ignore'):
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class PydSubmission(BaseModel, extra='allow'):
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filepath: Path
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submission_type: dict | None
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# For defaults
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submitter_plate_num: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
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submitted_date: dict | None
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rsl_plate_num: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
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@@ -427,7 +412,6 @@ class PydSubmission(BaseModel, extra='allow'):
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if isinstance(value, dict):
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value = value['value']
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if isinstance(value, Generator):
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# logger.debug("We have a generator")
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return [PydTips(**tips) for tips in value]
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if not value:
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return []
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@@ -436,9 +420,7 @@ class PydSubmission(BaseModel, extra='allow'):
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@field_validator('equipment', mode='before')
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@classmethod
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def convert_equipment_dict(cls, value):
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# logger.debug(f"Equipment: {value}")
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if isinstance(value, Generator):
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logger.debug("We have a generator")
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return [PydEquipment(**equipment) for equipment in value]
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if isinstance(value, dict):
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return value['value']
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@@ -454,7 +436,6 @@ class PydSubmission(BaseModel, extra='allow'):
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@field_validator("submitter_plate_num")
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@classmethod
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def enforce_with_uuid(cls, value):
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# logger.debug(f"submitter_plate_num coming into pydantic: {value}")
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if value['value'] in [None, "None"]:
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return dict(value=uuid.uuid4().hex.upper(), missing=True)
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else:
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@@ -464,7 +445,6 @@ class PydSubmission(BaseModel, extra='allow'):
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@field_validator("submitted_date", mode="before")
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@classmethod
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def rescue_date(cls, value):
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# logger.debug(f"\n\nDate coming into pydantic: {value}\n\n")
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try:
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check = value['value'] is None
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except TypeError:
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@@ -509,7 +489,6 @@ class PydSubmission(BaseModel, extra='allow'):
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@classmethod
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def lookup_submitting_lab(cls, value):
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if isinstance(value['value'], str):
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# logger.debug(f"Looking up organization {value['value']}")
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try:
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value['value'] = Organization.query(name=value['value']).name
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except AttributeError:
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@@ -540,13 +519,11 @@ class PydSubmission(BaseModel, extra='allow'):
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@field_validator("rsl_plate_num")
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@classmethod
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def rsl_from_file(cls, value, values):
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# logger.debug(f"RSL-plate initial value: {value['value']} and other values: {values.data}")
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sub_type = values.data['submission_type']['value']
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if check_not_nan(value['value']):
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value['value'] = value['value'].strip()
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return value
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else:
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# logger.debug("Constructing plate sub_type.")
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if "pytest" in sys.modules and sub_type.replace(" ", "") == "BasicSubmission":
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output = "RSL-BS-Test001"
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else:
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@@ -623,7 +600,6 @@ class PydSubmission(BaseModel, extra='allow'):
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@classmethod
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def expand_reagents(cls, value):
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if isinstance(value, Generator):
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# logger.debug("We have a generator")
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return [PydReagent(**reagent) for reagent in value]
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return value
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@@ -631,7 +607,6 @@ class PydSubmission(BaseModel, extra='allow'):
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@classmethod
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def expand_samples(cls, value):
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if isinstance(value, Generator):
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# logger.debug("We have a generator")[
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return [PydSample(**sample) for sample in value]
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return value
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@@ -656,7 +631,6 @@ class PydSubmission(BaseModel, extra='allow'):
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@field_validator("cost_centre")
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@classmethod
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def get_cost_centre(cls, value, values):
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# logger.debug(f"Value coming in for cost_centre: {value}")
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match value['value']:
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case None:
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from backend.db.models import Organization
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@@ -671,7 +645,6 @@ class PydSubmission(BaseModel, extra='allow'):
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@field_validator("contact")
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@classmethod
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def get_contact_from_org(cls, value, values):
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# logger.debug(f"Checking on value: {value}")
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match value:
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case dict():
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if isinstance(value['value'], tuple):
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@@ -684,7 +657,6 @@ class PydSubmission(BaseModel, extra='allow'):
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if check is None:
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org = Organization.query(name=values.data['submitting_lab']['value'])
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contact = org.contacts[0].name
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# logger.debug(f"Pulled: {contact}")
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if isinstance(contact, tuple):
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contact = contact[0]
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return dict(value=contact, missing=True)
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@@ -692,7 +664,6 @@ class PydSubmission(BaseModel, extra='allow'):
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return value
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def __init__(self, run_custom: bool = False, **data):
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logger.debug(f"{__name__} input data: {data}")
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super().__init__(**data)
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# NOTE: this could also be done with default_factory
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self.submission_object = BasicSubmission.find_polymorphic_subclass(
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@@ -755,13 +726,11 @@ class PydSubmission(BaseModel, extra='allow'):
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except TypeError:
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pass
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else:
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# logger.debug("Extracting 'value' from attributes")
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output = {k: self.filter_field(k) for k in fields}
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return output
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def filter_field(self, key: str):
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item = getattr(self, key)
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# logger.debug(f"Attempting deconstruction of {key}: {item} with type {type(item)}")
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match item:
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case dict():
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try:
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@@ -793,13 +762,10 @@ class PydSubmission(BaseModel, extra='allow'):
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"""
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report = Report()
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dicto = self.improved_dict()
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# logger.warning(f"\n\nQuery or create: {self.submission_type['value']}, {self.rsl_plate_num['value']}")
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instance, result = BasicSubmission.query_or_create(submission_type=self.submission_type['value'],
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rsl_plate_num=self.rsl_plate_num['value'])
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logger.debug(f"Result of query or create: {instance}")
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report.add_result(result)
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self.handle_duplicate_samples()
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# logger.debug(f"Here's our list of duplicate removed samples: {self.samples}")
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for key, value in dicto.items():
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if isinstance(value, dict):
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try:
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@@ -811,18 +777,13 @@ class PydSubmission(BaseModel, extra='allow'):
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continue
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if value is None:
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continue
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# logger.debug(f"Setting {key} to {value}")
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match key:
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case "reagents":
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for reagent in self.reagents:
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logger.debug(f"Checking reagent {reagent.lot}")
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reagent, _ = reagent.toSQL(submission=instance)
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# logger.debug(f"Association: {assoc}")
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case "samples":
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for sample in self.samples:
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sample, associations, _ = sample.toSQL(submission=instance)
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# logger.debug(f"Sample SQL object to be added to submission: {sample.__dict__}")
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# logger.debug(associations)
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for assoc in associations:
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if assoc is not None:
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if assoc not in instance.submission_sample_associations:
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@@ -830,19 +791,16 @@ class PydSubmission(BaseModel, extra='allow'):
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else:
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logger.warning(f"Sample association {assoc} is already present in {instance}")
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case "equipment":
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# logger.debug(f"Equipment: {pformat(self.equipment)}")
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for equip in self.equipment:
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if equip is None:
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continue
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equip, association = equip.toSQL(submission=instance)
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if association is not None:
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instance.submission_equipment_associations.append(association)
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logger.debug(f"Equipment associations: {instance.submission_equipment_associations}")
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case "tips":
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for tips in self.tips:
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if tips is None:
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continue
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# logger.debug(f"Converting tips: {tips} to sql.")
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try:
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association = tips.to_sql(submission=instance)
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except AttributeError:
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@@ -864,14 +822,11 @@ class PydSubmission(BaseModel, extra='allow'):
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value = value
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instance.set_attribute(key=key, value=value)
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case item if item in instance.jsons():
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# logger.debug(f"{item} is a json.")
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try:
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ii = value.items()
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except AttributeError:
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ii = {}
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logger.debug(f"ii is {ii}, value is {value}")
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for k, v in ii:
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logger.debug(f"k is {k}, v is {v}")
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if isinstance(v, datetime):
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value[k] = v.strftime("%Y-%m-%d %H:%M:%S")
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else:
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@@ -893,21 +848,17 @@ class PydSubmission(BaseModel, extra='allow'):
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else:
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logger.warning(f"{key} already == {value} so no updating.")
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try:
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# logger.debug(f"Calculating costs for procedure...")
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instance.calculate_base_cost()
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except (TypeError, AttributeError) as e:
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logger.debug(f"Looks like that kit doesn't have cost breakdown yet due to: {e}, using 0.")
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logger.error(f"Looks like that kit doesn't have cost breakdown yet due to: {e}, using 0.")
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try:
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instance.run_cost = instance.extraction_kit.cost_per_run
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except AttributeError:
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instance.run_cost = 0
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# logger.debug(f"Calculated base run cost of: {instance.run_cost}")
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# NOTE: Apply any discounts that are applicable for client and kit.
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try:
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# logger.debug("Checking and applying discounts...")
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discounts = [item.amount for item in
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Discount.query(kit_type=instance.extraction_kit, organization=instance.submitting_lab)]
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# logger.debug(f"We got discounts: {discounts}")
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if len(discounts) > 0:
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instance.run_cost = instance.run_cost - sum(discounts)
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except Exception as e:
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@@ -925,7 +876,6 @@ class PydSubmission(BaseModel, extra='allow'):
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SubmissionFormWidget: Submission form widget
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"""
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from frontend.widgets.submission_widget import SubmissionFormWidget
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# logger.debug(f"Disable: {disable}")
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return SubmissionFormWidget(parent=parent, submission=self, disable=disable)
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def to_writer(self) -> "SheetWriter":
|
||||
@@ -946,10 +896,8 @@ class PydSubmission(BaseModel, extra='allow'):
|
||||
str: Output filename
|
||||
"""
|
||||
template = self.submission_object.filename_template()
|
||||
# logger.debug(f"Using template string: {template}")
|
||||
render = self.namer.construct_export_name(template=template, **self.improved_dict(dictionaries=False)).replace(
|
||||
"/", "")
|
||||
# logger.debug(f"Template rendered as: {render}")
|
||||
return render
|
||||
|
||||
# @report_result
|
||||
@@ -964,26 +912,20 @@ class PydSubmission(BaseModel, extra='allow'):
|
||||
Report: Result object containing a message and any missing components.
|
||||
"""
|
||||
report = Report()
|
||||
# logger.debug(f"Extraction kit: {extraction_kit}. Is it a string? {isinstance(extraction_kit, str)}")
|
||||
if isinstance(extraction_kit, str):
|
||||
extraction_kit = dict(value=extraction_kit)
|
||||
if extraction_kit is not None and extraction_kit != self.extraction_kit['value']:
|
||||
self.extraction_kit['value'] = extraction_kit['value']
|
||||
# logger.debug(f"Looking up {self.extraction_kit['value']}")
|
||||
ext_kit = KitType.query(name=self.extraction_kit['value'])
|
||||
ext_kit_rtypes = [item.to_pydantic() for item in
|
||||
ext_kit.get_reagents(required=True, submission_type=self.submission_type['value'])]
|
||||
# logger.debug(f"Kit reagents: {ext_kit_rtypes}")
|
||||
# logger.debug(f"Submission reagents: {self.reagents}")
|
||||
# NOTE: Exclude any reagenttype found in this pyd not expected in kit.
|
||||
expected_check = [item.role for item in ext_kit_rtypes]
|
||||
output_reagents = [rt for rt in self.reagents if rt.role in expected_check]
|
||||
logger.debug(f"Already have these reagent types: {output_reagents}")
|
||||
missing_check = [item.role for item in output_reagents]
|
||||
missing_reagents = [rt for rt in ext_kit_rtypes if rt.role not in missing_check]
|
||||
missing_reagents += [rt for rt in output_reagents if rt.missing]
|
||||
output_reagents += [rt for rt in missing_reagents if rt not in output_reagents]
|
||||
# logger.debug(f"Missing reagents types: {missing_reagents}")
|
||||
# NOTE: if lists are equal return no problem
|
||||
if len(missing_reagents) == 0:
|
||||
result = None
|
||||
@@ -1072,7 +1014,6 @@ class PydReagentRole(BaseModel):
|
||||
instance: ReagentRole = ReagentRole.query(name=self.name)
|
||||
if instance is None:
|
||||
instance = ReagentRole(name=self.name, eol_ext=self.eol_ext)
|
||||
# logger.debug(f"This is the reagent type instance: {instance.__dict__}")
|
||||
try:
|
||||
assoc = KitTypeReagentRoleAssociation.query(reagent_role=instance, kit_type=kit)
|
||||
except StatementError:
|
||||
|
||||
Reference in New Issue
Block a user