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Pre-frontend refactor.

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This commit is contained in:
Landon Wark
2023-11-09 09:55:51 -06:00
parent 5570d87b7c
commit bf4149b1b3
25 changed files with 1002 additions and 784 deletions
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36
src/submissions/backend/validators/__init__.py
View File

@@ -1,8 +1,7 @@
import logging, re
from pathlib import Path
from openpyxl import load_workbook
from backend.db.models import BasicSubmission
from tools import Settings
from backend.db import BasicSubmission, SubmissionType
logger = logging.getLogger(f"submissions.{__name__}")
@@ -10,14 +9,12 @@ logger = logging.getLogger(f"submissions.{__name__}")
class RSLNamer(object):
"""
Object that will enforce proper formatting on RSL plate names.
NOTE: Depreciated in favour of object based methods in 'submissions.py'
"""
def __init__(self, ctx, instr:str, sub_type:str|None=None):
self.ctx = ctx
def __init__(self, instr:str, sub_type:str|None=None):
self.submission_type = sub_type
if self.submission_type == None:
self.submission_type = self.retrieve_submission_type(ctx=self.ctx, instr=instr)
self.submission_type = self.retrieve_submission_type(instr=instr)
logger.debug(f"got submission type: {self.submission_type}")
if self.submission_type != None:
enforcer = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type)
@@ -25,25 +22,30 @@ class RSLNamer(object):
self.parsed_name = enforcer.enforce_name(instr=self.parsed_name)
@classmethod
def retrieve_submission_type(cls, ctx:Settings, instr:str|Path) -> str:
def retrieve_submission_type(cls, instr:str|Path) -> str:
match instr:
case Path():
logger.debug(f"Using path method.")
logger.debug(f"Using path method for {instr}.")
if instr.exists():
wb = load_workbook(instr)
try:
submission_type = [item.strip().title() for item in wb.properties.category.split(";")][0]
except AttributeError:
try:
for type in ctx.submission_types:
sts = {item.name:item.info_map['all_sheets'] for item in SubmissionType.query(key="all_sheets")}
for k,v in sts.items():
# This gets the *first* submission type that matches the sheet names in the workbook
if wb.sheetnames == ctx.submission_types[type]['excel_map']:
submission_type = type.title()
if wb.sheetnames == v:
submission_type = k.title()
break
except:
submission_type = cls.retrieve_submission_type(ctx=ctx, instr=instr.stem.__str__())
# On failure recurse using filename as string for string method
submission_type = cls.retrieve_submission_type(instr=instr.stem.__str__())
else:
submission_type = cls.retrieve_submission_type(instr=instr.stem.__str__())
case str():
regex = BasicSubmission.construct_regex()
logger.debug(f"Using string method.")
logger.debug(f"Using string method for {instr}.")
m = regex.search(instr)
try:
submission_type = m.lastgroup
@@ -51,9 +53,13 @@ class RSLNamer(object):
logger.critical("No RSL plate number found or submission type found!")
case _:
submission_type = None
if submission_type == None:
try:
check = submission_type == None
except UnboundLocalError:
check = True
if check:
from frontend.custom_widgets import SubmissionTypeSelector
dlg = SubmissionTypeSelector(ctx, title="Couldn't parse submission type.", message="Please select submission type from list below.")
dlg = SubmissionTypeSelector(title="Couldn't parse submission type.", message="Please select submission type from list below.")
if dlg.exec():
submission_type = dlg.parse_form()
submission_type = submission_type.replace("_", " ")

130
src/submissions/backend/validators/pydant.py
View File

@@ -6,14 +6,14 @@ from pydantic import BaseModel, field_validator, Field
from datetime import date, datetime, timedelta
from dateutil.parser import parse
from dateutil.parser._parser import ParserError
from typing import List, Any, Tuple
from typing import List, Any, Tuple, Literal
from . import RSLNamer
from pathlib import Path
import re
import logging
from tools import check_not_nan, convert_nans_to_nones, Settings, jinja_template_loading
from tools import check_not_nan, convert_nans_to_nones, jinja_template_loading
from backend.db.models import *
from sqlalchemy.exc import InvalidRequestError, StatementError
from sqlalchemy.exc import StatementError
from PyQt6.QtWidgets import QComboBox, QWidget
from pprint import pformat
from openpyxl import load_workbook
@@ -21,7 +21,6 @@ from openpyxl import load_workbook
logger = logging.getLogger(f"submissions.{__name__}")
class PydReagent(BaseModel):
ctx: Settings
lot: str|None
type: str|None
expiry: date|None
@@ -139,15 +138,17 @@ class PydSample(BaseModel, extra='allow'):
def int_to_str(cls, value):
return str(value)
def toSQL(self, ctx:Settings, submission):
def toSQL(self, submission=None):
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 = 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)()
# 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)()
# instance = BasicSample.query_or_create(**{k:v for k,v in self.__dict__.items() if k not in ['row', 'column']})
instance = BasicSample.query_or_create(sample_type=self.sample_type, submitter_id=self.submitter_id)
for key, value in self.__dict__.items():
# logger.debug(f"Setting sample field {key} to {value}")
match key:
@@ -155,20 +156,26 @@ class PydSample(BaseModel, extra='allow'):
continue
case _:
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 = 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.")
association = SubmissionSampleAssociation.find_polymorphic_subclass(polymorphic_identity=f"{submission.submission_type_name} Association")
association = association(submission=submission, sample=instance, row=row, column=column)
if submission != None:
assoc_type = self.sample_type.replace("Sample", "").strip()
for row, column in zip(self.row, self.column):
# logger.debug(f"Looking up association with identity: ({submission.submission_type_name} Association)")
logger.debug(f"Looking up association with identity: ({assoc_type} Association)")
# 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.")
# association = SubmissionSampleAssociation.find_polymorphic_subclass(polymorphic_identity=f"{submission.submission_type_name} Association")
# association = association(submission=submission, sample=instance, row=row, column=column)
association = SubmissionSampleAssociation.query_or_create(association_type=f"{assoc_type} Association",
submission=submission,
sample=instance,
row=row, column=column)
instance.sample_submission_associations.append(association)
return instance, result
class PydSubmission(BaseModel, extra='allow'):
ctx: Settings
filepath: Path
submission_type: dict|None
# For defaults
@@ -240,15 +247,16 @@ class PydSubmission(BaseModel, extra='allow'):
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 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")
# output = RSLNamer(ctx=values.data['ctx'], instr=values.data['filepath'].__str__(), sub_type=sub_type).parsed_name
output = RSLNamer(ctx=values.data['ctx'], instr=values.data['filepath'].__str__(), sub_type=sub_type).parsed_name
return dict(value=output, missing=True)
# 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")
# # output = RSLNamer(ctx=values.data['ctx'], instr=values.data['filepath'].__str__(), sub_type=sub_type).parsed_name
# output = RSLNamer(instr=values.data['filepath'].__str__(), sub_type=sub_type).parsed_name
# return dict(value=output, missing=True)
return value
else:
output = RSLNamer(ctx=values.data['ctx'], instr=values.data['filepath'].__str__(), sub_type=sub_type).parsed_name
output = RSLNamer(instr=values.data['filepath'].__str__(), sub_type=sub_type).parsed_name
return dict(value=output, missing=True)
@field_validator("technician", mode="before")
@@ -298,10 +306,8 @@ class PydSubmission(BaseModel, extra='allow'):
if check_not_nan(value['value']):
value = value['value'].title()
return dict(value=value, missing=False)
# else:
# return dict(value="RSL Name not found.")
else:
return dict(value=RSLNamer(ctx=values.data['ctx'], instr=values.data['filepath'].__str__()).submission_type.title(), missing=True)
return dict(value=RSLNamer(instr=values.data['filepath'].__str__()).submission_type.title(), missing=True)
@field_validator("submission_category")
@classmethod
@@ -345,58 +351,15 @@ 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 = BasicSubmission.query(rsl_number=self.rsl_plate_num['value'])
if instance == None:
instance = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type)()
else:
code = 1
msg = "This submission already exists.\nWould you like to overwrite?"
instance, code, msg = BasicSubmission.query_or_create(submission_type=self.submission_type['value'], rsl_plate_num=self.rsl_plate_num['value'])
self.handle_duplicate_samples()
logger.debug(f"Here's our list of duplicate removed samples: {self.samples}")
for key, value in self.__dict__.items():
if isinstance(value, dict):
value = value['value']
logger.debug(f"Setting {key} to {value}")
# set fields based on keys in dictionary
match key:
case "extraction_kit":
logger.debug(f"Looking up kit {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 = Organization.query(name=value)
logger.debug(f"Got {field_value} for organization {value}")
case "submitter_plate_num":
logger.debug(f"Submitter plate id: {value}")
field_value = value
case "samples":
# instance = construct_samples(ctx=ctx, instance=instance, samples=value)
for sample in value:
# logger.debug(f"Parsing {sample} to sql.")
sample, _ = sample.toSQL(ctx=self.ctx, submission=instance)
# instance.samples.append(sample)
continue
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 = SubmissionType.query(name=value)
case "sample_count":
if value == None:
field_value = len(self.samples)
else:
field_value = value
case "ctx" | "csv" | "filepath":
continue
case _:
field_value = value
# insert into field
try:
setattr(instance, key, field_value)
instance.set_attribute(key=key, value=value)
except AttributeError as e:
logger.debug(f"Could not set attribute: {key} to {value} due to: \n\n {e}")
continue
@@ -412,7 +375,6 @@ 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 Discount.query(kit_type=instance.extraction_kit, organization=instance.submitting_lab)]
logger.debug(f"We got discounts: {discounts}")
if len(discounts) > 0:
@@ -513,7 +475,9 @@ class PydSubmission(BaseModel, extra='allow'):
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))
render = template.render(**self.improved_dict(dictionaries=False)).replace("/", "")
logger.debug(f"Template rendered as: {render}")
return render
class PydContact(BaseModel):
@@ -521,7 +485,7 @@ class PydContact(BaseModel):
phone: str|None
email: str|None
def toSQL(self, ctx):
def toSQL(self):
return Contact(name=self.name, phone=self.phone, email=self.email)
class PydOrganization(BaseModel):
@@ -530,12 +494,12 @@ class PydOrganization(BaseModel):
cost_centre: str
contacts: List[PydContact]|None
def toSQL(self, ctx):
def toSQL(self):
instance = Organization()
for field in self.model_fields:
match field:
case "contacts":
value = [item.toSQL(ctx) for item in getattr(self, field)]
value = [item.toSQL() for item in getattr(self, field)]
case _:
value = getattr(self, field)
instance.set_attribute(name=field, value=value)
@@ -555,7 +519,7 @@ class PydReagentType(BaseModel):
return timedelta(days=value)
return value
def toSQL(self, ctx:Settings, kit:KitType):
def toSQL(self, kit:KitType):
# instance: ReagentType = lookup_reagent_types(ctx=ctx, name=self.name)
instance: ReagentType = ReagentType.query(name=self.name)
if instance == None:
@@ -576,14 +540,14 @@ class PydKit(BaseModel):
name: str
reagent_types: List[PydReagentType] = []
def toSQL(self, ctx):
def toSQL(self):
result = dict(message=None, status='Information')
# 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]
[item.toSQL(ctx, instance) for item in self.reagent_types]
[item.toSQL(instance) for item in self.reagent_types]
return instance, result