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Pre-major refactor

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This commit is contained in:
Landon Wark
2023-11-03 10:49:37 -05:00
parent 22a23b7838
commit 5570d87b7c
19 changed files with 1078 additions and 1045 deletions
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2
src/submissions/backend/validators/__init__.py
View File

@@ -22,7 +22,7 @@ class RSLNamer(object):
if self.submission_type != None:
enforcer = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type)
self.parsed_name = self.retrieve_rsl_number(instr=instr, regex=enforcer.get_regex())
self.parsed_name = enforcer.enforce_name(ctx=ctx, instr=self.parsed_name)
self.parsed_name = enforcer.enforce_name(instr=self.parsed_name)
@classmethod
def retrieve_submission_type(cls, ctx:Settings, instr:str|Path) -> str:

68
src/submissions/backend/validators/pydant.py
View File

@@ -2,7 +2,6 @@
Contains pydantic models and accompanying validators
'''
import uuid
from PyQt6 import QtCore
from pydantic import BaseModel, field_validator, Field
from datetime import date, datetime, timedelta
from dateutil.parser import parse
@@ -12,14 +11,10 @@ from . import RSLNamer
from pathlib import Path
import re
import logging
from tools import check_not_nan, convert_nans_to_nones, Settings
from backend.db.functions import (lookup_submissions, lookup_reagent_types, lookup_reagents, lookup_kit_types,
lookup_organizations, lookup_submission_type, lookup_discounts, lookup_samples, lookup_submission_sample_association,
lookup_reagenttype_kittype_association
)
from tools import check_not_nan, convert_nans_to_nones, Settings, jinja_template_loading
from backend.db.models import *
from sqlalchemy.exc import InvalidRequestError, StatementError
from PyQt6.QtWidgets import QComboBox, QWidget, QLabel, QVBoxLayout
from PyQt6.QtWidgets import QComboBox, QWidget
from pprint import pformat
from openpyxl import load_workbook
@@ -47,7 +42,8 @@ class PydReagent(BaseModel):
def rescue_type_with_lookup(cls, value, values):
if value == None and values.data['lot'] != None:
try:
return lookup_reagents(ctx=values.data['ctx'], lot_number=values.data['lot']).name
# return lookup_reagents(ctx=values.data['ctx'], lot_number=values.data['lot']).name
return Reagent.query(lot_number=values.data['lot'].name)
except AttributeError:
return value
return value
@@ -94,7 +90,8 @@ class PydReagent(BaseModel):
def toSQL(self) -> Tuple[Reagent, dict]:
result = None
logger.debug(f"Reagent SQL constructor is looking up type: {self.type}, lot: {self.lot}")
reagent = lookup_reagents(ctx=self.ctx, lot_number=self.lot)
# reagent = lookup_reagents(ctx=self.ctx, lot_number=self.lot)
reagent = Reagent.query(lot_number=self.lot)
logger.debug(f"Result: {reagent}")
if reagent == None:
reagent = Reagent()
@@ -109,7 +106,8 @@ class PydReagent(BaseModel):
case "expiry":
reagent.expiry = value
case "type":
reagent_type = lookup_reagent_types(ctx=self.ctx, name=value)
# reagent_type = lookup_reagent_types(ctx=self.ctx, name=value)
reagent_type = ReagentType.query(name=value)
if reagent_type != None:
reagent.type.append(reagent_type)
case "name":
@@ -145,7 +143,8 @@ class PydSample(BaseModel, extra='allow'):
result = None
self.__dict__.update(self.model_extra)
logger.debug(f"Here is the incoming sample dict: \n{self.__dict__}")
instance = lookup_samples(ctx=ctx, submitter_id=self.submitter_id)
# instance = lookup_samples(ctx=ctx, submitter_id=self.submitter_id)
instance = BasicSample.query(submitter_id=self.submitter_id)
if instance == None:
logger.debug(f"Sample {self.submitter_id} doesn't exist yet. Looking up sample object with polymorphic identity: {self.sample_type}")
instance = BasicSample.find_polymorphic_subclass(polymorphic_identity=self.sample_type)()
@@ -158,7 +157,8 @@ class PydSample(BaseModel, extra='allow'):
instance.set_attribute(name=key, value=value)
for row, column in zip(self.row, self.column):
logger.debug(f"Looking up association with identity: ({submission.submission_type_name} Association)")
association = lookup_submission_sample_association(ctx=ctx, submission=submission, row=row, column=column)
# association = lookup_submission_sample_association(ctx=ctx, submission=submission, row=row, column=column)
association = SubmissionSampleAssociation.query(submission=submission, row=row, column=column)
logger.debug(f"Returned association: {association}")
if association == None or association == []:
logger.debug(f"Looked up association at row {row}, column {column} didn't exist, creating new association.")
@@ -239,7 +239,8 @@ class PydSubmission(BaseModel, extra='allow'):
logger.debug(f"RSL-plate initial value: {value['value']}")
sub_type = values.data['submission_type']['value']
if check_not_nan(value['value']):
if lookup_submissions(ctx=values.data['ctx'], rsl_number=value['value']) == None:
# if lookup_submissions(ctx=values.data['ctx'], rsl_number=value['value']) == None:
if BasicSubmission.query(rsl_number=value['value']) == None:
return dict(value=value['value'], missing=False)
else:
logger.warning(f"Submission number {value} already exists in DB, attempting salvage with filepath")
@@ -325,9 +326,12 @@ class PydSubmission(BaseModel, extra='allow'):
output.append(dummy)
self.samples = output
def improved_dict(self):
def improved_dict(self, dictionaries:bool=True):
fields = list(self.model_fields.keys()) + list(self.model_extra.keys())
output = {k:getattr(self, k) for k in fields}
if dictionaries:
output = {k:getattr(self, k) for k in fields}
else:
output = {k:(getattr(self, k) if not isinstance(getattr(self, k), dict) else getattr(self, k)['value']) for k in fields}
return output
def find_missing(self):
@@ -341,7 +345,8 @@ class PydSubmission(BaseModel, extra='allow'):
msg = None
status = None
self.__dict__.update(self.model_extra)
instance = lookup_submissions(ctx=self.ctx, rsl_number=self.rsl_plate_num['value'])
# instance = lookup_submissions(ctx=self.ctx, rsl_number=self.rsl_plate_num['value'])
instance = BasicSubmission.query(rsl_number=self.rsl_plate_num['value'])
if instance == None:
instance = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type)()
else:
@@ -357,11 +362,13 @@ class PydSubmission(BaseModel, extra='allow'):
match key:
case "extraction_kit":
logger.debug(f"Looking up kit {value}")
field_value = lookup_kit_types(ctx=self.ctx, name=value)
# field_value = lookup_kit_types(ctx=self.ctx, name=value)
field_value = KitType.query(name=value)
logger.debug(f"Got {field_value} for kit {value}")
case "submitting_lab":
logger.debug(f"Looking up organization: {value}")
field_value = lookup_organizations(ctx=self.ctx, name=value)
# field_value = lookup_organizations(ctx=self.ctx, name=value)
field_value = Organization.query(name=value)
logger.debug(f"Got {field_value} for organization {value}")
case "submitter_plate_num":
logger.debug(f"Submitter plate id: {value}")
@@ -376,7 +383,8 @@ class PydSubmission(BaseModel, extra='allow'):
case "reagents":
field_value = [reagent['value'].toSQL()[0] if isinstance(reagent, dict) else reagent.toSQL()[0] for reagent in value]
case "submission_type":
field_value = lookup_submission_type(ctx=self.ctx, name=value)
# field_value = lookup_submission_type(ctx=self.ctx, name=value)
field_value = SubmissionType.query(name=value)
case "sample_count":
if value == None:
field_value = len(self.samples)
@@ -404,7 +412,8 @@ class PydSubmission(BaseModel, extra='allow'):
# Apply any discounts that are applicable for client and kit.
try:
logger.debug("Checking and applying discounts...")
discounts = [item.amount for item in lookup_discounts(ctx=self.ctx, kit_type=instance.extraction_kit, organization=instance.submitting_lab)]
# discounts = [item.amount for item in lookup_discounts(ctx=self.ctx, kit_type=instance.extraction_kit, organization=instance.submitting_lab)]
discounts = [item.amount for item in Discount.query(kit_type=instance.extraction_kit, organization=instance.submitting_lab)]
logger.debug(f"We got discounts: {discounts}")
if len(discounts) > 0:
discounts = sum(discounts)
@@ -433,7 +442,8 @@ class PydSubmission(BaseModel, extra='allow'):
if len(reagents + list(info.keys())) == 0:
return None
logger.debug(f"We have blank info and/or reagents in the excel sheet.\n\tLet's try to fill them in.")
extraction_kit = lookup_kit_types(ctx=self.ctx, name=self.extraction_kit['value'])
# extraction_kit = lookup_kit_types(ctx=self.ctx, name=self.extraction_kit['value'])
extraction_kit = KitType.query(name=self.extraction_kit['value'])
logger.debug(f"We have the extraction kit: {extraction_kit.name}")
excel_map = extraction_kit.construct_xl_map_for_use(self.submission_type['value'])
logger.debug(f"Extraction kit map:\n\n{pformat(excel_map)}")
@@ -498,6 +508,13 @@ class PydSubmission(BaseModel, extra='allow'):
workbook = custom_parser.custom_autofill(workbook)
return workbook
def construct_filename(self):
env = jinja_template_loading()
template = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type).filename_template()
logger.debug(f"Using template string: {template}")
template = env.from_string(template)
return template.render(**self.improved_dict(dictionaries=False))
class PydContact(BaseModel):
name: str
@@ -539,12 +556,14 @@ class PydReagentType(BaseModel):
return value
def toSQL(self, ctx:Settings, kit:KitType):
instance: ReagentType = lookup_reagent_types(ctx=ctx, name=self.name)
# instance: ReagentType = lookup_reagent_types(ctx=ctx, name=self.name)
instance: ReagentType = ReagentType.query(name=self.name)
if instance == None:
instance = ReagentType(name=self.name, eol_ext=self.eol_ext)
logger.debug(f"This is the reagent type instance: {instance.__dict__}")
try:
assoc = lookup_reagenttype_kittype_association(ctx=ctx, reagent_type=instance, kit_type=kit)
# assoc = lookup_reagenttype_kittype_association(ctx=ctx, reagent_type=instance, kit_type=kit)
assoc = KitTypeReagentTypeAssociation.query(reagent_type=instance, kit_type=kit)
except StatementError:
assoc = None
if assoc == None:
@@ -559,7 +578,8 @@ class PydKit(BaseModel):
def toSQL(self, ctx):
result = dict(message=None, status='Information')
instance = lookup_kit_types(ctx=ctx, name=self.name)
# instance = lookup_kit_types(ctx=ctx, name=self.name)
instance = KitType.query(name=self.name)
if instance == None:
instance = KitType(name=self.name)
# instance.reagent_types = [item.toSQL(ctx, instance) for item in self.reagent_types]