Code cleanup, dependency update, various bug fixes
This commit is contained in:
lwark
@@ -23,7 +23,7 @@ class RSLNamer(object):
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if self.submission_type is None:
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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.debug(f"got submission type: {self.submission_type}")
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# logger.debug(f"got submission type: {self.submission_type}")
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if self.submission_type is not None:
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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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@@ -47,7 +47,7 @@ class RSLNamer(object):
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"""
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match filename:
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case Path():
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logger.debug(f"Using path method for {filename}.")
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# logger.debug(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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@@ -67,7 +67,7 @@ class RSLNamer(object):
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submission_type = cls.retrieve_submission_type(filename=filename.stem.__str__())
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case str():
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regex = BasicSubmission.construct_regex()
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logger.debug(f"Using string method for {filename}.")
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# logger.debug(f"Using string method for {filename}.")
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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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@@ -100,17 +100,17 @@ 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.debug(f"Input string to be parsed: {filename}")
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# logger.debug(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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regex = re.compile(rf'{regex}', re.IGNORECASE | re.VERBOSE)
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logger.debug(f"Using regex: {regex}")
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# logger.debug(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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# 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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@@ -121,7 +121,7 @@ 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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# 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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@@ -167,8 +167,8 @@ 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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# 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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@@ -134,15 +134,15 @@ class PydReagent(BaseModel):
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# logger.debug("Adding extra fields.")
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if self.model_extra != 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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# logger.debug(f"Reagent SQL constructor is looking up type: {self.type}, lot: {self.lot}")
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reagent = Reagent.query(lot_number=self.lot, name=self.name)
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logger.debug(f"Result: {reagent}")
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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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# logger.debug(f"Reagent info item for {key}: {value}")
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# set fields based on keys in dictionary
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match key:
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case "lot":
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@@ -191,7 +191,7 @@ 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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# 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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print(k, v)
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@@ -200,7 +200,7 @@ class PydSample(BaseModel, extra='allow'):
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v = datetime.strptime(v, "%Y-%m-%d")
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data.__setattr__(k, v)
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# print(dir(data))
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logger.debug(f"Data coming out of validation: {pformat(data)}")
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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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@@ -233,7 +233,7 @@ 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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# 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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@@ -246,8 +246,8 @@ class PydSample(BaseModel, extra='allow'):
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if submission is not None:
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assoc_type = self.sample_type.replace("Sample", "").strip()
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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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# 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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@@ -357,7 +357,7 @@ 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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# logger.debug(f"Equipment: {value}")
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if isinstance(value, dict):
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return value['value']
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return value
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@@ -381,7 +381,7 @@ 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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# logger.debug(f"\n\nDate coming into pydantic: {value}\n\n")
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try:
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check = value['value'] == None
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except TypeError:
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@@ -426,7 +426,7 @@ 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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# 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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@@ -457,12 +457,12 @@ 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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# 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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return value
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else:
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logger.debug("Constructing plate name.")
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# logger.debug("Constructing plate name.")
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output = RSLNamer(filename=values.data['filepath'].__str__(), sub_type=sub_type,
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data=values.data).parsed_name
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return dict(value=output, missing=True)
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@@ -649,32 +649,32 @@ class PydSubmission(BaseModel, extra='allow'):
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rsl_plate_num=self.rsl_plate_num['value'])
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result = Result(msg=msg, code=code)
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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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# logger.debug(f"Here's our list of duplicate removed samples: {self.samples}")
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# for key, value in self.__dict__.items():
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for key, value in dicto.items():
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if isinstance(value, dict):
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value = value['value']
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logger.debug(f"Setting {key} to {value}")
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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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if code == 1:
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instance.submission_reagent_associations = []
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logger.debug(f"Looking through {self.reagents}")
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# logger.debug(f"Looking through {self.reagents}")
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for reagent in self.reagents:
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reagent, assoc = reagent.toSQL(submission=instance)
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logger.debug(f"Association: {assoc}")
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# logger.debug(f"Association: {assoc}")
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if assoc is not None:# and assoc not in instance.submission_reagent_associations:
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instance.submission_reagent_associations.append(assoc)
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# instance.reagents.append(reagent)
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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(f"Sample SQL object to be added to submission: {sample.__dict__}")
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for assoc in associations:
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if assoc is not None and assoc not in instance.submission_sample_associations:
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instance.submission_sample_associations.append(assoc)
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case "equipment":
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logger.debug(f"Equipment: {pformat(self.equipment)}")
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# logger.debug(f"Equipment: {pformat(self.equipment)}")
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try:
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if equip is None:
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continue
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@@ -684,11 +684,11 @@ class PydSubmission(BaseModel, extra='allow'):
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equip, association = equip.toSQL(submission=instance)
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if association is not None:
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association.save()
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logger.debug(
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f"Equipment association SQL object to be added to submission: {association.__dict__}")
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# logger.debug(
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# f"Equipment association SQL object to be added to submission: {association.__dict__}")
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instance.submission_equipment_associations.append(association)
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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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# 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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@@ -701,38 +701,38 @@ class PydSubmission(BaseModel, extra='allow'):
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try:
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instance.set_attribute(key=key, value=value)
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except AttributeError as e:
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logger.debug(f"Could not set attribute: {key} to {value} due to: \n\n {e}")
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logger.error(f"Could not set attribute: {key} to {value} due to: \n\n {e}")
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continue
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except KeyError:
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continue
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try:
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logger.debug(f"Calculating costs for procedure...")
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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 full plate cost.")
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# logger.debug(f"Looks like that kit doesn't have cost breakdown yet due to: {e}, using full plate cost.")
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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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# logger.debug(f"Calculated base run cost of: {instance.run_cost}")
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# 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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# 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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# logger.debug(f"We got discounts: {discounts}")
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if len(discounts) > 0:
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discounts = sum(discounts)
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instance.run_cost = instance.run_cost - discounts
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except Exception as e:
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logger.error(f"An unknown exception occurred when calculating discounts: {e}")
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# We need to make sure there's a proper rsl plate number
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logger.debug(f"We've got a total cost of {instance.run_cost}")
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try:
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logger.debug(f"Constructed instance: {instance}")
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except AttributeError as e:
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logger.debug(f"Something went wrong constructing instance {self.rsl_plate_num}: {e}")
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logger.debug(f"Constructed submissions message: {msg}")
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# logger.debug(f"We've got a total cost of {instance.run_cost}")
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# try:
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# logger.debug(f"Constructed instance: {instance}")
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# except AttributeError as e:
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# logger.debug(f"Something went wrong constructing instance {self.rsl_plate_num}: {e}")
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# logger.debug(f"Constructed submissions message: {msg}")
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return instance, result
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def to_form(self, parent: QWidget):
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@@ -777,26 +777,26 @@ class PydSubmission(BaseModel, extra='allow'):
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Report: Result object containing a message and any missing components.
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"""
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report = Report()
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logger.debug(f"Extraction kit: {extraction_kit}. Is it a string? {isinstance(extraction_kit, str)}")
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# logger.debug(f"Extraction kit: {extraction_kit}. Is it a string? {isinstance(extraction_kit, str)}")
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if isinstance(extraction_kit, str):
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extraction_kit = dict(value=extraction_kit)
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if extraction_kit is not None and extraction_kit != self.extraction_kit['value']:
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self.extraction_kit['value'] = extraction_kit['value']
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logger.debug(f"Looking up {self.extraction_kit['value']}")
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# logger.debug(f"Looking up {self.extraction_kit['value']}")
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ext_kit = KitType.query(name=self.extraction_kit['value'])
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ext_kit_rtypes = [item.to_pydantic() for item in
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ext_kit.get_reagents(required=True, submission_type=self.submission_type['value'])]
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logger.debug(f"Kit reagents: {ext_kit_rtypes}")
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logger.debug(f"Submission reagents: {self.reagents}")
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# logger.debug(f"Kit reagents: {ext_kit_rtypes}")
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# logger.debug(f"Submission reagents: {self.reagents}")
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# Exclude any reagenttype found in this pyd not expected in kit.
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expected_check = [item.type for item in ext_kit_rtypes]
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output_reagents = [rt for rt in self.reagents if rt.type in expected_check]
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logger.debug(f"Already have these reagent types: {output_reagents}")
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# logger.debug(f"Already have these reagent types: {output_reagents}")
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missing_check = [item.type for item in output_reagents]
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missing_reagents = [rt for rt in ext_kit_rtypes if rt.type not in missing_check]
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missing_reagents += [rt for rt in output_reagents if rt.missing]
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output_reagents += [rt for rt in missing_reagents if rt not in output_reagents]
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logger.debug(f"Missing reagents types: {missing_reagents}")
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# logger.debug(f"Missing reagents types: {missing_reagents}")
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# if lists are equal return no problem
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if len(missing_reagents) == 0:
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result = None
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@@ -873,7 +873,7 @@ class PydReagentType(BaseModel):
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instance: ReagentType = ReagentType.query(name=self.name)
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if instance == None:
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instance = ReagentType(name=self.name, eol_ext=self.eol_ext)
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logger.debug(f"This is the reagent type instance: {instance.__dict__}")
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# logger.debug(f"This is the reagent type instance: {instance.__dict__}")
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try:
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assoc = KitTypeReagentTypeAssociation.query(reagent_type=instance, kit_type=kit)
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except StatementError:
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Reference in New Issue
Block a user