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Attempting fix of failure to update reagent on edit.

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This commit is contained in:
lwark
2024-12-02 14:52:39 -06:00
parent b45a125c51
commit 2c281166d4
10 changed files with 74 additions and 38 deletions
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45
src/submissions/backend/validators/pydant.py
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@@ -115,7 +115,7 @@ class PydReagent(BaseModel):
fields = list(self.model_fields.keys()) + extras
return {k: getattr(self, k) for k in fields}
def toSQL(self, submission: BasicSubmission | str = None) -> Tuple[Reagent, SubmissionReagentAssociation, Report]:
def toSQL(self, submission: BasicSubmission | str = None) -> Tuple[Reagent, Report]:
"""
Converts this instance into a backend.db.models.kit.Reagent instance
@@ -164,13 +164,14 @@ class PydReagent(BaseModel):
report.add_result(Result(owner=__name__, code=0, msg="New reagent created.", status="Information"))
else:
if submission is not None and reagent not in submission.reagents:
assoc = SubmissionReagentAssociation(reagent=reagent, submission=submission)
assoc.comments = self.comment
else:
assoc = None
# assoc = SubmissionReagentAssociation(reagent=reagent, submission=submission)
# assoc.comments = self.comment
submission.update_reagentassoc(reagent=reagent, role=self.role)
# else:
# assoc = None
# add end-of-life extension from reagent type to expiry date
# NOTE: this will now be done only in the reporting phase to account for potential changes in end-of-life extensions
return reagent, assoc, report
return reagent, report
class PydSample(BaseModel, extra='allow'):
@@ -299,6 +300,13 @@ class PydTips(BaseModel):
lot: str | None = Field(default=None)
role: str
@field_validator('role', mode='before')
@classmethod
def get_role_name(cls, value):
if isinstance(value, TipRole):
value = value.name
return value
def to_sql(self, submission: BasicSubmission) -> SubmissionTipsAssociation:
"""
Con
@@ -324,6 +332,13 @@ class PydEquipment(BaseModel, extra='ignore'):
role: str | None
tips: List[PydTips] | None = Field(default=None)
@field_validator('role', mode='before')
@classmethod
def get_role_name(cls, value):
if isinstance(value, EquipmentRole):
value = value.name
return value
@field_validator('processes', mode='before')
@classmethod
def make_empty_list(cls, value):
@@ -786,7 +801,7 @@ class PydSubmission(BaseModel, extra='allow'):
"""
report = Report()
dicto = self.improved_dict()
logger.warning(f"\n\nQuery or create: {self.submission_type['value']}, {self.rsl_plate_num['value']}")
# logger.warning(f"\n\nQuery or create: {self.submission_type['value']}, {self.rsl_plate_num['value']}")
instance, result = BasicSubmission.query_or_create(submission_type=self.submission_type['value'],
rsl_plate_num=self.rsl_plate_num['value'])
logger.debug(f"Result of query or create: {instance}")
@@ -807,17 +822,15 @@ class PydSubmission(BaseModel, extra='allow'):
# logger.debug(f"Setting {key} to {value}")
match key:
case "reagents":
# if report.results[0].code == 1:
# instance.submission_reagent_associations = []
# logger.debug(f"Looking through {self.reagents}")
for reagent in self.reagents:
reagent, assoc, _ = reagent.toSQL(submission=instance)
logger.debug(f"Checking reagent {reagent.lot}")
reagent, _ = reagent.toSQL(submission=instance)
# logger.debug(f"Association: {assoc}")
if assoc is not None: # and assoc not in instance.submission_reagent_associations:
if assoc not in instance.submission_reagent_associations:
instance.submission_reagent_associations.append(assoc)
else:
logger.warning(f"Reagent association {assoc} is already present in {instance}")
# if assoc is not None: # and assoc not in instance.submission_reagent_associations:
# if assoc not in instance.submission_reagent_associations:
# instance.submission_reagent_associations.append(assoc)
# else:
# logger.warning(f"Reagent association {assoc} is already present in {instance.submission_reagent_associations}")
case "samples":
for sample in self.samples:
sample, associations, _ = sample.toSQL(submission=instance)