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Moments before disaster.

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This commit is contained in:
lwark
2025-01-16 08:36:15 -06:00
parent 5cded949ed
commit bf711369c6
21 changed files with 541 additions and 368 deletions
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80
src/submissions/backend/validators/pydant.py
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@@ -73,7 +73,7 @@ class PydReagent(BaseModel):
if value is not None:
match value:
case int():
return datetime.fromordinal(datetime(1900, 1, 1).toordinal() + value - 2).date()
return datetime.fromordinal(datetime(1900, 1, 1).toordinal() + value - 2)
case 'NA':
return value
case str():
@@ -117,7 +117,8 @@ 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, Report]:
@report_result
def to_sql(self, submission: BasicSubmission | str = None) -> Tuple[Reagent, Report]:
"""
Converts this instance into a backend.db.models.kit.Reagent instance
@@ -128,6 +129,7 @@ class PydReagent(BaseModel):
if self.model_extra is not None:
self.__dict__.update(self.model_extra)
reagent = Reagent.query(lot=self.lot, name=self.name)
logger.debug(f"Reagent: {reagent}")
if reagent is None:
reagent = Reagent()
for key, value in self.__dict__.items():
@@ -140,7 +142,6 @@ class PydReagent(BaseModel):
assoc.comments = self.comment
else:
assoc = None
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:
submission.update_reagentassoc(reagent=reagent, role=self.role)
@@ -160,7 +161,7 @@ class PydSample(BaseModel, extra='allow'):
def validate_model(cls, data):
model = BasicSample.find_polymorphic_subclass(polymorphic_identity=data.sample_type)
for k, v in data.model_extra.items():
if k in model.timestamps():
if k in model.timestamps:
if isinstance(v, str):
v = datetime.strptime(v, "%Y-%m-%d")
data.__setattr__(k, v)
@@ -202,7 +203,7 @@ class PydSample(BaseModel, extra='allow'):
fields = list(self.model_fields.keys()) + list(self.model_extra.keys())
return {k: getattr(self, k) for k in fields}
def toSQL(self, submission: BasicSubmission | str = None) -> Tuple[
def to_sql(self, submission: BasicSubmission | str = None) -> Tuple[
BasicSample, List[SubmissionSampleAssociation], Result | None]:
"""
Converts this instance into a backend.db.models.submissions.Sample object
@@ -271,7 +272,7 @@ class PydTips(BaseModel):
def to_sql(self, submission: BasicSubmission) -> SubmissionTipsAssociation:
"""
Con
Convert this object to the SQL version for database storage.
Args:
submission (BasicSubmission): A submission object to associate tips represented here.
@@ -280,10 +281,10 @@ class PydTips(BaseModel):
SubmissionTipsAssociation: Association between queried tips and submission
"""
tips = Tips.query(name=self.name, limit=1)
logger.debug(f"Tips query has yielded: {tips}")
assoc = SubmissionTipsAssociation.query(tip_id=tips.id, submission_id=submission.id, role=self.role, limit=1)
if assoc is None:
assoc = SubmissionTipsAssociation(submission=submission, tips=tips, role_name=self.role)
# logger.debug(f"Tips query has yielded: {tips}")
assoc = SubmissionTipsAssociation.query_or_create(tips=tips, submission=submission, role=self.role, limit=1)
# if assoc is None:
# assoc = SubmissionTipsAssociation(submission=submission, tips=tips, role_name=self.role)
return assoc
@@ -316,7 +317,7 @@ class PydEquipment(BaseModel, extra='ignore'):
pass
return value
def toSQL(self, submission: BasicSubmission | str = None) -> Tuple[Equipment, SubmissionEquipmentAssociation]:
def to_sql(self, submission: BasicSubmission | str = None, extraction_kit: KitType | str = None) -> Tuple[Equipment, SubmissionEquipmentAssociation]:
"""
Creates Equipment and SubmssionEquipmentAssociations for this PydEquipment
@@ -328,6 +329,8 @@ class PydEquipment(BaseModel, extra='ignore'):
"""
if isinstance(submission, str):
submission = BasicSubmission.query(rsl_plate_num=submission)
if isinstance(extraction_kit, str):
extraction_kit = KitType.query(name=extraction_kit)
equipment = Equipment.query(asset_number=self.asset_number)
if equipment is None:
logger.error("No equipment found. Returning None.")
@@ -343,7 +346,12 @@ class PydEquipment(BaseModel, extra='ignore'):
if assoc is None:
assoc = SubmissionEquipmentAssociation(submission=submission, equipment=equipment)
# TODO: This seems precarious. What if there is more than one process?
process = Process.query(name=self.processes[0])
# NOTE: It looks like the way fetching the processes is done in the SQL model, this shouldn't be a problem, but I'll include a failsafe.
# NOTE: I need to find a way to filter this by the kit involved.
if len(self.processes) > 1:
process = Process.query(submission_type=submission.get_submission_type(), extraction_kit=extraction_kit, equipment_role=self.role)
else:
process = Process.query(name=self.processes[0])
if process is None:
logger.error(f"Found unknown process: {process}.")
assoc.process = process
@@ -405,10 +413,12 @@ class PydSubmission(BaseModel, extra='allow'):
@field_validator('equipment', mode='before')
@classmethod
def convert_equipment_dict(cls, value):
if isinstance(value, Generator):
return [PydEquipment(**equipment) for equipment in value]
if isinstance(value, dict):
return value['value']
if isinstance(value, Generator):
return [PydEquipment(**equipment) for equipment in value]
if not value:
return []
return value
@field_validator('comment', mode='before')
@@ -443,12 +453,11 @@ class PydSubmission(BaseModel, extra='allow'):
def strip_datetime_string(cls, value):
match value['value']:
case date():
return value
output = datetime.combine(value['value'], datetime.min.time())
case datetime():
return value.date()
pass
case int():
return dict(value=datetime.fromordinal(datetime(1900, 1, 1).toordinal() + value['value'] - 2).date(),
missing=True)
output = datetime.fromordinal(datetime(1900, 1, 1).toordinal() + value['value'] - 2)
case str():
string = re.sub(r"(_|-)\d(R\d)?$", "", value['value'])
try:
@@ -456,12 +465,15 @@ class PydSubmission(BaseModel, extra='allow'):
except ParserError as e:
logger.error(f"Problem parsing date: {e}")
try:
output = dict(value=parse(string.replace("-", "")).date(), missing=True)
output = parse(string.replace("-", "")).date()
except Exception as e:
logger.error(f"Problem with parse fallback: {e}")
return output
return value
case _:
raise ValueError(f"Could not get datetime from {value['value']}")
value['value'] = output.replace(tzinfo=timezone)
return value
@field_validator("submitting_lab", mode="before")
@classmethod
@@ -511,7 +523,7 @@ class PydSubmission(BaseModel, extra='allow'):
if "pytest" in sys.modules and sub_type.replace(" ", "") == "BasicSubmission":
output = "RSL-BS-Test001"
else:
output = RSLNamer(filename=values.data['filepath'].__str__(), sub_type=sub_type,
output = RSLNamer(filename=values.data['filepath'].__str__(), submission_type=sub_type,
data=values.data).parsed_name
return dict(value=output, missing=True)
@@ -653,9 +665,9 @@ class PydSubmission(BaseModel, extra='allow'):
return value
if isinstance(contact, tuple):
contact = contact[0]
value = dict(value=f"Defaulted to: {contact}", missing=True)
value = dict(value=f"Defaulted to: {contact}", missing=False)
logger.debug(f"Value after query: {value}")
return
return value
else:
logger.debug(f"Value after bypass check: {value}")
return value
@@ -665,7 +677,7 @@ class PydSubmission(BaseModel, extra='allow'):
# NOTE: this could also be done with default_factory
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'])
self.namer = RSLNamer(self.rsl_plate_num['value'], submission_type=self.submission_type['value'])
if run_custom:
self.submission_object.custom_validation(pyd=self)
@@ -777,10 +789,10 @@ class PydSubmission(BaseModel, extra='allow'):
match key:
case "reagents":
for reagent in self.reagents:
reagent, _ = reagent.toSQL(submission=instance)
reagent = reagent.to_sql(submission=instance)
case "samples":
for sample in self.samples:
sample, associations, _ = sample.toSQL(submission=instance)
sample, associations, _ = sample.to_sql(submission=instance)
for assoc in associations:
if assoc is not None:
if assoc not in instance.submission_sample_associations:
@@ -791,7 +803,7 @@ class PydSubmission(BaseModel, extra='allow'):
for equip in self.equipment:
if equip is None:
continue
equip, association = equip.toSQL(submission=instance)
equip, association = equip.to_sql(submission=instance, extraction_kit=self.extraction_kit)
if association is not None:
instance.submission_equipment_associations.append(association)
case "tips":
@@ -807,7 +819,7 @@ class PydSubmission(BaseModel, extra='allow'):
instance.submission_tips_associations.append(association)
else:
logger.warning(f"Tips association {association} is already present in {instance}")
case item if item in instance.timestamps():
case item if item in instance.timestamps:
logger.warning(f"Incoming timestamp key: {item}, with value: {value}")
if isinstance(value, date):
value = datetime.combine(value, datetime.now().time())
@@ -818,7 +830,7 @@ class PydSubmission(BaseModel, extra='allow'):
else:
value = value
instance.set_attribute(key=key, value=value)
case item if item in instance.jsons():
case item if item in instance.jsons:
try:
ii = value.items()
except AttributeError:
@@ -989,7 +1001,7 @@ class PydContact(BaseModel):
logger.debug(f"Output phone: {value}")
return value
def toSQL(self) -> Tuple[Contact, Report]:
def to_sql(self) -> Tuple[Contact, Report]:
"""
Converts this instance into a backend.db.models.organization. Contact instance.
Does not query for existing contacts.
@@ -1024,7 +1036,7 @@ class PydOrganization(BaseModel):
cost_centre: str
contacts: List[PydContact] | None
def toSQL(self) -> Organization:
def to_sql(self) -> Organization:
"""
Converts this instance into a backend.db.models.organization.Organization instance.
@@ -1055,7 +1067,7 @@ class PydReagentRole(BaseModel):
return timedelta(days=value)
return value
def toSQL(self, kit: KitType) -> ReagentRole:
def to_sql(self, kit: KitType) -> ReagentRole:
"""
Converts this instance into a backend.db.models.ReagentType instance
@@ -1082,7 +1094,7 @@ class PydKit(BaseModel):
name: str
reagent_roles: List[PydReagentRole] = []
def toSQL(self) -> Tuple[KitType, Report]:
def to_sql(self) -> Tuple[KitType, Report]:
"""
Converts this instance into a backend.db.models.kits.KitType instance
@@ -1093,7 +1105,7 @@ class PydKit(BaseModel):
instance = KitType.query(name=self.name)
if instance is None:
instance = KitType(name=self.name)
[item.toSQL(instance) for item in self.reagent_roles]
[item.to_sql(instance) for item in self.reagent_roles]
return instance, report