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WastewaterArcticAssociation completed.

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This commit is contained in:
lwark
2024-06-13 13:47:30 -05:00
parent f73a3e6c35
commit 4a7d0b0bd4
9 changed files with 449 additions and 24 deletions
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96
src/submissions/backend/db/models/submissions.py
View File

@@ -1789,28 +1789,28 @@ class WastewaterArtic(BasicSubmission):
"""
# logger.debug(f"Hello from {self.__class__.__name__} dictionary sample adjuster.")
output = []
set_plate = None
# set_plate = None
for assoc in self.submission_sample_associations:
dicto = assoc.to_sub_dict()
if self.source_plates is None:
output.append(dicto)
continue
for item in self.source_plates:
if assoc.sample.id is None:
old_plate = None
else:
old_plate = WastewaterAssociation.query(submission=item['plate'], sample=assoc.sample, limit=1)
if old_plate is not None:
set_plate = old_plate.submission.rsl_plate_num
# logger.debug(f"Dictionary: {pformat(dicto)}")
if dicto['ww_processing_num'].startswith("NTC"):
dicto['well'] = dicto['ww_processing_num']
else:
dicto['well'] = f"{row_map[old_plate.row]}{old_plate.column}"
break
elif dicto['ww_processing_num'].startswith("NTC"):
dicto['well'] = dicto['ww_processing_num']
dicto['plate_name'] = set_plate
# if self.source_plates is None:
# output.append(dicto)
# continue
# for item in self.source_plates:
# if assoc.sample.id is None:
# old_plate = None
# else:
# old_plate = WastewaterAssociation.query(submission=item['plate'], sample=assoc.sample, limit=1)
# if old_plate is not None:
# set_plate = old_plate.submission.rsl_plate_num
# # logger.debug(f"Dictionary: {pformat(dicto)}")
# if dicto['ww_processing_num'].startswith("NTC"):
# dicto['well'] = dicto['ww_processing_num']
# else:
# dicto['well'] = f"{row_map[old_plate.row]}{old_plate.column}"
# break
# elif dicto['ww_processing_num'].startswith("NTC"):
# dicto['well'] = dicto['ww_processing_num']
# dicto['plate_name'] = set_plate
# logger.debug(f"Here is our raw sample: {pformat(dicto)}")
output.append(dicto)
return output
@@ -2342,7 +2342,7 @@ class SubmissionSampleAssociation(BaseClass):
}
def __init__(self, submission: BasicSubmission = None, sample: BasicSample = None, row: int = 1, column: int = 1,
id: int | None = None, submission_rank: int = 0):
id: int | None = None, submission_rank: int = 0, **kwargs):
self.submission = submission
self.sample = sample
self.row = row
@@ -2352,6 +2352,12 @@ class SubmissionSampleAssociation(BaseClass):
self.id = id
else:
self.id = self.__class__.autoincrement_id()
logger.debug(f"Looking at kwargs: {pformat(kwargs)}")
for k,v in kwargs.items():
try:
self.__setattr__(k, v)
except AttributeError:
logger.error(f"Couldn't set {k} to {v}")
# logger.debug(f"Using submission sample association id: {self.id}")
def __repr__(self) -> str:
@@ -2532,7 +2538,7 @@ class SubmissionSampleAssociation(BaseClass):
Returns:
SubmissionSampleAssociation: Queried or new association.
"""
# logger.debug(f"Attempting create or query with {kwargs}")
logger.debug(f"Attempting create or query with {kwargs}")
match submission:
case BasicSubmission():
pass
@@ -2562,7 +2568,6 @@ class SubmissionSampleAssociation(BaseClass):
if instance is None:
# sanitized_kwargs = {k:v for k,v in kwargs.items() if k not in ['id']}
used_cls = cls.find_polymorphic_subclass(polymorphic_identity=association_type)
# instance = used_cls(submission=submission, sample=sample, id=id, **kwargs)
instance = used_cls(submission=submission, sample=sample, id=id, **kwargs)
return instance
@@ -2627,3 +2632,48 @@ class WastewaterAssociation(SubmissionSampleAssociation):
except ValueError as e:
logger.error(f"Problem incrementing id: {e}")
return 1
class WastewaterArticAssociation(SubmissionSampleAssociation):
id = Column(INTEGER, ForeignKey("_submissionsampleassociation.id"), primary_key=True)
source_plate = Column(String(16))
source_plate_number = Column(INTEGER)
source_well = Column(String(8))
ct = Column(String(8)) #: AKA ct for N1
__mapper_args__ = dict(polymorphic_identity="Wastewater Artic Association",
polymorphic_load="inline",
inherit_condition=(id == SubmissionSampleAssociation.id))
def to_sub_dict(self) -> dict:
"""
Returns a sample dictionary updated with instance information. Extends parent
Returns:
dict: Updated dictionary with row, column and well updated
"""
sample = super().to_sub_dict()
sample['ct'] = self.ct
sample['source_plate'] = self.source_plate
sample['source_plate_number'] = self.source_plate_number
sample['source_well'] = self.source_well
return sample
@classmethod
def autoincrement_id(cls) -> int:
"""
Increments the association id automatically. Overrides parent
Returns:
int: incremented id
"""
try:
parent = [base for base in cls.__bases__ if base.__name__ == "SubmissionSampleAssociation"][0]
return max([item.id for item in parent.query()]) + 1
except ValueError as e:
logger.error(f"Problem incrementing id: {e}")
return 1

5
src/submissions/backend/validators/pydant.py
View File

@@ -256,7 +256,7 @@ class PydSample(BaseModel, extra='allow'):
submission=submission,
sample=instance,
row=row, column=column, id=aid,
submission_rank=submission_rank)
submission_rank=submission_rank, **self.model_extra)
logger.debug(f"Using submission_sample_association: {association}")
try:
# instance.sample_submission_associations.append(association)
@@ -375,6 +375,7 @@ class PydSubmission(BaseModel, extra='allow'):
@classmethod
def convert_equipment_dict(cls, value):
# logger.debug(f"Equipment: {value}")
if isinstance(value, dict):
return value['value']
return value
@@ -697,6 +698,8 @@ class PydSubmission(BaseModel, extra='allow'):
for key, value in dicto.items():
if isinstance(value, dict):
value = value['value']
if value is None:
continue
# logger.debug(f"Setting {key} to {value}")
match key:
case "reagents":