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Pydantic switchover debugging.

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This commit is contained in:
lwark
2025-03-07 10:19:12 -06:00
parent abcdbac5b8
commit 919376c1ce
7 changed files with 1327 additions and 9 deletions
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15
src/submissions/backend/db/models/__init__.py
View File

@@ -397,8 +397,8 @@ class BaseClass(Base):
"""
Custom dunder method to handle potential list relationship issues.
"""
if key != "_sa_instance_state":
logger.debug(f"Attempting to set {key} to {pformat(value)}")
# if key != "_sa_instance_state":
# logger.debug(f"Attempting to set {key} to {pformat(value)}")
try:
field_type = getattr(self.__class__, key)
except AttributeError:
@@ -407,21 +407,25 @@ class BaseClass(Base):
logger.debug(f"{key} is an InstrumentedAttribute.")
match field_type.property:
case ColumnProperty():
logger.debug(f"Setting ColumnProperty to {value}")
# logger.debug(f"Setting ColumnProperty to {value}")
return super().__setattr__(key, value)
case _RelationshipDeclared():
logger.debug(f"Setting _RelationshipDeclared to {value}")
logger.debug(f"{self.__class__.__name__} Setting _RelationshipDeclared for {key} to {value}")
if field_type.property.uselist:
logger.debug(f"Setting with uselist")
existing = self.__getattribute__(key)
# NOTE: This is causing problems with removal of items from lists. Have to overhaul it.
if existing is not None:
logger.debug(f"{key} Existing: {existing}, incoming: {value}")
if isinstance(value, list):
value = existing + value
# value = existing + value
value = value
else:
value = existing + [value]
else:
value = [value]
value = list(set(value))
logger.debug(f"Final value for {key}: {value}")
return super().__setattr__(key, value)
else:
if isinstance(value, list):
@@ -429,6 +433,7 @@ class BaseClass(Base):
value = value[0]
else:
raise ValueError("Object is too long to parse a single value.")
# value = value
return super().__setattr__(key, value)
case _:
return super().__setattr__(key, value)

47
src/submissions/backend/db/models/kits.py
View File

@@ -3,6 +3,7 @@ All kit and reagent related models
"""
from __future__ import annotations
import json, zipfile, yaml, logging, re
import sys
from pprint import pformat
from sqlalchemy import Column, String, TIMESTAMP, JSON, INTEGER, ForeignKey, Interval, Table, FLOAT, BLOB
from sqlalchemy.orm import relationship, validates, Query
@@ -231,6 +232,7 @@ class KitType(BaseClass):
@classmethod
def query_or_create(cls, **kwargs) -> Tuple[KitType, bool]:
from backend.validators.pydant import PydKitType
from backend.validators.omni_gui_objects import BaseOmni
new = False
disallowed = ['expiry']
sanitized_kwargs = {k: v for k, v in kwargs.items() if k not in disallowed}
@@ -1074,7 +1076,7 @@ class SubmissionType(BaseClass):
new = True
for k, v in sanitized_kwargs.items():
setattr(instance, k, v)
logger.info(f"Instance from query or create: {instance}")
logger.info(f"Instance from submissiontype query or create: {instance}")
return instance, new
@classmethod
@@ -1298,7 +1300,7 @@ class SubmissionTypeKitTypeAssociation(BaseClass):
new = True
for k, v in sanitized_kwargs.items():
setattr(instance, k, v)
logger.info(f"Instance from query or create: {instance}")
logger.info(f"Instance from SubmissionTypeKitTypeAssociation query or create: {instance}")
return instance, new
@classmethod
@@ -1428,6 +1430,22 @@ class KitTypeReagentRoleAssociation(BaseClass):
except AttributeError:
return "Blank KitTypeReagentRole"
@hybrid_property
def submissiontype(self):
return self.submission_type
@submissiontype.setter
def submissiontype(self, value):
self.submission_type = value
@hybrid_property
def kittype(self):
return self.kit_type
@kittype.setter
def kittype(self, value):
self.kit_type = value
@validates('required')
def validate_required(self, key, value):
"""
@@ -1478,8 +1496,31 @@ class KitTypeReagentRoleAssociation(BaseClass):
instance = cls()
new = True
for k, v in sanitized_kwargs.items():
logger.debug(f"Key: {k} has value: {v}")
match k:
case "kittype" | "kit_type":
k = "kit_type"
if isinstance(v, str):
v = KitType.query(name=v)
else:
v = v.instance_object
case "submissiontype" | "submission_type":
k = "submission_type"
if isinstance(v, str):
v = SubmissionType.query(name=v)
else:
v = v.instance_object
case "reagentrole" | "reagent_role":
k = "reagent_role"
if isinstance(v, str):
v = ReagentRole.query(name=v)
else:
v = v.instance_object
case _:
pass
setattr(instance, k, v)
logger.info(f"Instance from query or create: {instance}")
logger.info(f"Instance from query or create: {instance.__dict__}")
# sys.exit()
return instance, new
@classmethod

2
src/submissions/backend/db/models/submissions.py
View File

@@ -460,6 +460,7 @@ class BasicSubmission(BaseClass, LogMixin):
"""
rows = range(1, plate_rows + 1)
columns = range(1, plate_columns + 1)
logger.debug(f"sample list for plate map: {pformat(sample_list)}")
# NOTE: An overly complicated list comprehension create a list of sample locations
# NOTE: next will return a blank cell if no value found for row/column
output_samples = [next((item for item in sample_list if item['row'] == row and item['column'] == column),
@@ -1536,6 +1537,7 @@ class Wastewater(BasicSubmission):
continue
thing['tooltip'] = f"Sample Name: {thing['name']}\nWell: {thing['sample_location']}"
dummy_samples.append(thing)
logger.debug(f"Dummy samples for 24 well: {pformat(dummy_samples)}")
output['origin_plate'] = self.__class__.make_plate_map(sample_list=dummy_samples, plate_rows=4,
plate_columns=6)
# logger.debug(f"PCR info: {output['pcr_info']}")