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Post code clean-up, before attempt to upgrade controls to FigureWidgets

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lwark
2024-10-21 08:17:43 -05:00
parent 495d1a5a7f
commit 1f83b61c81
29 changed files with 441 additions and 1089 deletions
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12
src/submissions/backend/validators/pydant.py
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@@ -157,7 +157,6 @@ class PydReagent(BaseModel):
if submission is not None and reagent not in submission.reagents:
assoc = SubmissionReagentAssociation(reagent=reagent, submission=submission)
assoc.comments = self.comment
# reagent.reagent_submission_associations.append(assoc)
else:
assoc = None
report.add_result(Result(owner=__name__, code=0, msg="New reagent created.", status="Information"))
@@ -165,7 +164,6 @@ class PydReagent(BaseModel):
if submission is not None and reagent not in submission.reagents:
assoc = SubmissionReagentAssociation(reagent=reagent, submission=submission)
assoc.comments = self.comment
# reagent.reagent_submission_associations.append(assoc)
else:
assoc = None
# add end-of-life extension from reagent type to expiry date
@@ -187,12 +185,10 @@ class PydSample(BaseModel, extra='allow'):
# logger.debug(f"Data for pydsample: {data}")
model = BasicSample.find_polymorphic_subclass(polymorphic_identity=data.sample_type)
for k, v in data.model_extra.items():
# print(k, v)
if k in model.timestamps():
if isinstance(v, str):
v = datetime.strptime(v, "%Y-%m-%d")
data.__setattr__(k, v)
# print(dir(data))
# logger.debug(f"Data coming out of validation: {pformat(data)}")
return data
@@ -329,8 +325,6 @@ class PydEquipment(BaseModel, extra='ignore'):
value = convert_nans_to_nones(value)
if not value:
value = ['']
# if len(value) == 0:
# value = ['']
try:
value = [item.strip() for item in value]
except AttributeError:
@@ -416,7 +410,6 @@ class PydSubmission(BaseModel, extra='allow'):
@field_validator("tips", mode="before")
@classmethod
def expand_tips(cls, value):
# print(f"\n{type(value)}\n")
if isinstance(value, dict):
value = value['value']
if isinstance(value, Generator):
@@ -594,7 +587,6 @@ class PydSubmission(BaseModel, extra='allow'):
value = value['value'].title()
return dict(value=value, missing=False)
else:
# return dict(value=RSLNamer(instr=values.data['filepath'].__str__()).submission_type.title(), missing=True)
return dict(value=RSLNamer.retrieve_submission_type(filename=values.data['filepath']).title(), missing=True)
@field_validator("submission_category", mode="before")
@@ -688,7 +680,6 @@ class PydSubmission(BaseModel, extra='allow'):
def __init__(self, run_custom: bool = False, **data):
super().__init__(**data)
# NOTE: this could also be done with default_factory
logger.debug(data)
self.submission_object = BasicSubmission.find_polymorphic_subclass(
polymorphic_identity=self.submission_type['value'])
self.namer = RSLNamer(self.rsl_plate_num['value'], sub_type=self.submission_type['value'])
@@ -729,7 +720,6 @@ class PydSubmission(BaseModel, extra='allow'):
output.append(dummy)
self.samples = output
# TODO: Return samples, reagents, etc to dictionaries as well.
def improved_dict(self, dictionaries: bool = True) -> dict:
"""
Adds model_extra to fields.
@@ -786,7 +776,6 @@ class PydSubmission(BaseModel, extra='allow'):
Returns:
Tuple[BasicSubmission, Result]: BasicSubmission instance, result object
"""
# self.__dict__.update(self.model_extra)
report = Report()
dicto = self.improved_dict()
instance, result = BasicSubmission.query_or_create(submission_type=self.submission_type['value'],
@@ -817,7 +806,6 @@ class PydSubmission(BaseModel, extra='allow'):
# logger.debug(f"Association: {assoc}")
if assoc is not None: # and assoc not in instance.submission_reagent_associations:
instance.submission_reagent_associations.append(assoc)
# instance.reagents.append(reagent)
case "samples":
for sample in self.samples:
sample, associations, _ = sample.toSQL(submission=instance)