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Overhauling database.

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This commit is contained in:
lwark
2025-05-13 13:20:01 -05:00
parent 0dbb4ae77a
commit 75c665ea05
21 changed files with 729 additions and 1727 deletions
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68
src/submissions/backend/validators/pydant.py
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@@ -121,7 +121,7 @@ class PydReagent(BaseModel):
return {k: getattr(self, k) for k in fields}
@report_result
def to_sql(self, submission: BasicSubmission | str = None) -> Tuple[Reagent, Report]:
def to_sql(self, submission: BasicRun | str = None) -> Tuple[Reagent, Report]:
"""
Converts this instance into a backend.db.models.kit.Reagent instance
@@ -141,7 +141,7 @@ class PydReagent(BaseModel):
# NOTE: reagent method sets fields based on keys in dictionary
reagent.set_attribute(key, value)
if submission is not None and reagent not in submission.reagents:
assoc = SubmissionReagentAssociation(reagent=reagent, submission=submission)
assoc = RunReagentAssociation(reagent=reagent, submission=submission)
assoc.comments = self.comment
else:
assoc = None
@@ -198,13 +198,13 @@ class PydSample(BaseModel, extra='allow'):
return value
@report_result
def to_sql(self, submission: BasicSubmission | str = None) -> Tuple[
def to_sql(self, run: BasicRun | str = None) -> Tuple[
BasicSample, List[SubmissionSampleAssociation], Result | None]:
"""
Converts this instance into a backend.db.models.submissions.Sample object
Args:
submission (BasicSubmission | str, optional): Submission joined to this sample. Defaults to None.
run (BasicRun | str, optional): Submission joined to this sample. Defaults to None.
Returns:
Tuple[BasicSample, Result]: Sample object and result object.
@@ -220,13 +220,13 @@ class PydSample(BaseModel, extra='allow'):
case _:
instance.__setattr__(key, value)
out_associations = []
if submission is not None:
if isinstance(submission, str):
submission = BasicSubmission.query(rsl_plate_num=submission)
assoc_type = submission.submission_type_name
if run is not None:
if isinstance(run, str):
run = BasicRun.query(rsl_plate_num=run)
assoc_type = run.submission_type_name
for row, column, aid, submission_rank in zip(self.row, self.column, self.assoc_id, self.submission_rank):
association = SubmissionSampleAssociation.query_or_create(association_type=f"{assoc_type} Association",
submission=submission,
submission=run,
sample=instance,
row=row, column=column, id=aid,
submission_rank=submission_rank,
@@ -234,7 +234,7 @@ class PydSample(BaseModel, extra='allow'):
try:
out_associations.append(association)
except IntegrityError as e:
logger.error(f"Could not attach submission sample association due to: {e}")
logger.error(f"Could not attach run sample association due to: {e}")
instance.metadata.session.rollback()
return instance, out_associations, report
@@ -267,20 +267,20 @@ class PydTips(BaseModel):
return value
@report_result
def to_sql(self, submission: BasicSubmission) -> SubmissionTipsAssociation:
def to_sql(self, submission: BasicRun) -> SubmissionTipsAssociation:
"""
Convert this object to the SQL version for database storage.
Args:
submission (BasicSubmission): A submission object to associate tips represented here.
submission (BasicRun): A run object to associate tips represented here.
Returns:
SubmissionTipsAssociation: Association between queried tips and submission
SubmissionTipsAssociation: Association between queried tips and run
"""
report = Report()
tips = Tips.query(name=self.name, limit=1)
# logger.debug(f"Tips query has yielded: {tips}")
assoc = SubmissionTipsAssociation.query_or_create(tips=tips, submission=submission, role=self.role, limit=1)
assoc = SubmissionTipsAssociation.query_or_create(tips=tips, run=submission, role=self.role, limit=1)
return assoc, report
@@ -315,19 +315,19 @@ class PydEquipment(BaseModel, extra='ignore'):
return value
@report_result
def to_sql(self, submission: BasicSubmission | str = None, extraction_kit: KitType | str = None) -> Tuple[Equipment, SubmissionEquipmentAssociation]:
def to_sql(self, submission: BasicRun | str = None, extraction_kit: KitType | str = None) -> Tuple[Equipment, RunEquipmentAssociation]:
"""
Creates Equipment and SubmssionEquipmentAssociations for this PydEquipment
Args:
submission ( BasicSubmission | str ): BasicSubmission of interest
submission ( BasicRun | str ): BasicRun of interest
Returns:
Tuple[Equipment, SubmissionEquipmentAssociation]: SQL objects
Tuple[Equipment, RunEquipmentAssociation]: SQL objects
"""
report = Report()
if isinstance(submission, str):
submission = BasicSubmission.query(rsl_plate_num=submission)
submission = BasicRun.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)
@@ -335,15 +335,15 @@ class PydEquipment(BaseModel, extra='ignore'):
logger.error("No equipment found. Returning None.")
return
if submission is not None:
# NOTE: Need to make sure the same association is not added to the submission
# NOTE: Need to make sure the same association is not added to the run
try:
assoc = SubmissionEquipmentAssociation.query(equipment_id=equipment.id, submission_id=submission.id,
role=self.role, limit=1)
assoc = RunEquipmentAssociation.query(equipment_id=equipment.id, submission_id=submission.id,
role=self.role, limit=1)
except TypeError as e:
logger.error(f"Couldn't get association due to {e}, returning...")
assoc = None
if assoc is None:
assoc = SubmissionEquipmentAssociation(submission=submission, equipment=equipment)
assoc = RunEquipmentAssociation(submission=submission, equipment=equipment)
# TODO: This seems precarious. What if there is more than one process?
# 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.
@@ -360,7 +360,7 @@ class PydEquipment(BaseModel, extra='ignore'):
logger.warning(f"Found already existing association: {assoc}")
assoc = None
else:
logger.warning(f"No submission found")
logger.warning(f"No run found")
assoc = None
return equipment, assoc, report
@@ -519,7 +519,7 @@ class PydSubmission(BaseModel, extra='allow'):
value['value'] = value['value'].strip()
return value
else:
if "pytest" in sys.modules and sub_type.replace(" ", "") == "BasicSubmission":
if "pytest" in sys.modules and sub_type.replace(" ", "") == "BasicRun":
output = "RSL-BS-Test001"
else:
output = RSLNamer(filename=values.data['filepath'].__str__(), submission_type=sub_type,
@@ -674,7 +674,7 @@ 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
self.submission_object = BasicSubmission.find_polymorphic_subclass(
self.submission_object = BasicRun.find_polymorphic_subclass(
polymorphic_identity=self.submission_type['value'])
self.namer = RSLNamer(self.rsl_plate_num['value'], submission_type=self.submission_type['value'])
if run_custom:
@@ -771,18 +771,18 @@ class PydSubmission(BaseModel, extra='allow'):
return missing_info, missing_reagents
@report_result
def to_sql(self) -> Tuple[BasicSubmission | None, Report]:
def to_sql(self) -> Tuple[BasicRun | None, Report]:
"""
Converts this instance into a backend.db.models.submissions.BasicSubmission instance
Converts this instance into a backend.db.models.submissions.BasicRun instance
Returns:
Tuple[BasicSubmission, Result]: BasicSubmission instance, result object
Tuple[BasicRun, Result]: BasicRun instance, result object
"""
report = Report()
dicto = self.improved_dict()
# logger.debug(f"Pydantic submission type: {self.submission_type['value']}")
# logger.debug(f"Pydantic run type: {self.submission_type['value']}")
# logger.debug(f"Pydantic improved_dict: {pformat(dicto)}")
instance, result = BasicSubmission.query_or_create(submission_type=self.submission_type['value'],
instance, result = BasicRun.query_or_create(submission_type=self.submission_type['value'],
rsl_plate_num=self.rsl_plate_num['value'])
# logger.debug(f"Created or queried instance: {instance}")
if instance is None:
@@ -808,7 +808,7 @@ class PydSubmission(BaseModel, extra='allow'):
reagent = reagent.to_sql(submission=instance)
case "samples":
for sample in self.samples:
sample, associations, _ = sample.to_sql(submission=instance)
sample, associations, _ = sample.to_sql(run=instance)
for assoc in associations:
if assoc is not None:
if assoc not in instance.submission_sample_associations:
@@ -1186,7 +1186,7 @@ class PydEquipmentRole(BaseModel):
Args:
parent (_type_): parent widget
used (list): list of equipment already added to submission
used (list): list of equipment already added to run
Returns:
RoleComboBox: widget
@@ -1203,7 +1203,7 @@ class PydPCRControl(BaseModel):
ct: float
reagent_lot: str
submitted_date: datetime #: Date submitted to Robotics
submission_id: int
run_id: int
controltype_name: str
@report_result
@@ -1231,7 +1231,7 @@ class PydIridaControl(BaseModel, extra='ignore'):
kraken2_db_version: str
sample_id: int
submitted_date: datetime #: Date submitted to Robotics
submission_id: int
run_id: int
controltype_name: str
@field_validator("refseq_version", "kraken2_version", "kraken2_db_version", mode='before')