Post code clean-up, before attempt to upgrade controls to FigureWidgets
This commit is contained in:
lwark
@@ -23,15 +23,15 @@ class RSLNamer(object):
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# NOTE: Preferred method is path retrieval, but might also need validation for just string.
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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 self.submission_type is None:
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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 is not None:
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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 data is None:
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if not data:
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data = dict(submission_type=self.submission_type)
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if "submission_type" not in data.keys():
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data['submission_type'] = self.submission_type
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@@ -45,6 +45,9 @@ class RSLNamer(object):
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Args:
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filename (str | Path): filename
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Raises:
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TypeError: Raised if unsupported variable type for filename given.
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Returns:
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str: parsed submission type
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"""
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@@ -84,6 +87,7 @@ class RSLNamer(object):
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case str():
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submission_type = st_from_str(filename=filename)
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case _:
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raise TypeError(f"Unsupported filename type: {type(filename)}.")
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submission_type = None
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try:
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check = submission_type is None
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@@ -157,7 +157,6 @@ class PydReagent(BaseModel):
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if submission is not None and reagent not in submission.reagents:
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assoc = SubmissionReagentAssociation(reagent=reagent, submission=submission)
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assoc.comments = self.comment
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# reagent.reagent_submission_associations.append(assoc)
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else:
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assoc = None
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report.add_result(Result(owner=__name__, code=0, msg="New reagent created.", status="Information"))
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@@ -165,7 +164,6 @@ class PydReagent(BaseModel):
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if submission is not None and reagent not in submission.reagents:
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assoc = SubmissionReagentAssociation(reagent=reagent, submission=submission)
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assoc.comments = self.comment
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# reagent.reagent_submission_associations.append(assoc)
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else:
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assoc = None
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# add end-of-life extension from reagent type to expiry date
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@@ -187,12 +185,10 @@ class PydSample(BaseModel, extra='allow'):
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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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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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# print(dir(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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@@ -329,8 +325,6 @@ class PydEquipment(BaseModel, extra='ignore'):
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value = convert_nans_to_nones(value)
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if not value:
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value = ['']
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# if len(value) == 0:
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# value = ['']
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try:
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value = [item.strip() for item in value]
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except AttributeError:
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@@ -416,7 +410,6 @@ class PydSubmission(BaseModel, extra='allow'):
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@field_validator("tips", mode="before")
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@classmethod
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def expand_tips(cls, value):
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# print(f"\n{type(value)}\n")
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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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@@ -594,7 +587,6 @@ class PydSubmission(BaseModel, extra='allow'):
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value = value['value'].title()
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return dict(value=value, missing=False)
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else:
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# return dict(value=RSLNamer(instr=values.data['filepath'].__str__()).submission_type.title(), missing=True)
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return dict(value=RSLNamer.retrieve_submission_type(filename=values.data['filepath']).title(), missing=True)
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@field_validator("submission_category", mode="before")
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@@ -688,7 +680,6 @@ class PydSubmission(BaseModel, extra='allow'):
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def __init__(self, run_custom: bool = False, **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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logger.debug(data)
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self.submission_object = BasicSubmission.find_polymorphic_subclass(
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polymorphic_identity=self.submission_type['value'])
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self.namer = RSLNamer(self.rsl_plate_num['value'], sub_type=self.submission_type['value'])
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@@ -729,7 +720,6 @@ class PydSubmission(BaseModel, extra='allow'):
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output.append(dummy)
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self.samples = output
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# TODO: Return samples, reagents, etc to dictionaries as well.
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def improved_dict(self, dictionaries: bool = True) -> dict:
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"""
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Adds model_extra to fields.
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@@ -786,7 +776,6 @@ class PydSubmission(BaseModel, extra='allow'):
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Returns:
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Tuple[BasicSubmission, Result]: BasicSubmission instance, result object
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"""
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# self.__dict__.update(self.model_extra)
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report = Report()
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dicto = self.improved_dict()
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instance, result = BasicSubmission.query_or_create(submission_type=self.submission_type['value'],
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@@ -817,7 +806,6 @@ class PydSubmission(BaseModel, extra='allow'):
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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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