1525 lines
58 KiB
Python
1525 lines
58 KiB
Python
"""
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Contains pydantic models and accompanying validators
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"""
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from __future__ import annotations
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import uuid, re, logging, csv, sys, string
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from pydantic import BaseModel, field_validator, Field, model_validator, PrivateAttr
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from datetime import date, datetime, timedelta
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from dateutil.parser import parse
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from dateutil.parser import ParserError
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from typing import List, Tuple, Literal
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from types import GeneratorType
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from . import RSLNamer
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from pathlib import Path
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from tools import check_not_nan, convert_nans_to_nones, Report, Result, timezone
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from backend.db import models
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from backend.db.models import *
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from sqlalchemy.exc import StatementError, IntegrityError
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from sqlalchemy.orm.properties import ColumnProperty
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from sqlalchemy.orm.relationships import _RelationshipDeclared
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from sqlalchemy.orm.attributes import InstrumentedAttribute
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from PyQt6.QtWidgets import QWidget
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logger = logging.getLogger(f"procedure.{__name__}")
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class PydBaseClass(BaseModel, extra='allow', validate_assignment=True):
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_sql_object: ClassVar = None
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@model_validator(mode="before")
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@classmethod
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def prevalidate(cls, data):
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sql_fields = [k for k, v in cls._sql_object.__dict__.items() if isinstance(v, InstrumentedAttribute)]
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output = {}
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for key, value in data.items():
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new_key = key.replace("_", "")
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if new_key in sql_fields:
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output[new_key] = value
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else:
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output[key] = value
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return output
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@model_validator(mode='after')
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@classmethod
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def validate_model(cls, data):
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# _sql_object = getattr(models, cls.__name__.replace("Pyd", ""))
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# total_dict = data.model_fields.update(data.model_extra)
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for key, value in data.model_extra.items():
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if key in cls._sql_object.timestamps:
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if isinstance(value, str):
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data.__setattr__(key, datetime.strptime(value, "%Y-%m-%d"))
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if key == "row" and isinstance(value, str):
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if value.lower() in string.ascii_lowercase[0:8]:
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try:
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value = row_keys[value]
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except KeyError:
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value = value
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data.__setattr__(key, value)
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return data
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def __init__(self, **data):
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# NOTE: Grab the sql model for validation purposes.
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self.__class__._sql_object = getattr(models, self.__class__.__name__.replace("Pyd", ""))
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super().__init__(**data)
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def filter_field(self, key: str) -> Any:
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"""
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Attempts to get value from field dictionary
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Args:
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key (str): name of the field of interest
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Returns:
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Any (): Value found.
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"""
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item = getattr(self, key)
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match item:
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case dict():
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try:
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item = item['value']
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except KeyError:
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logger.error(f"Couldn't get dict value: {item}")
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case _:
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pass
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return item
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def improved_dict(self, dictionaries: bool = True) -> dict:
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"""
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Adds model_extra to fields.
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Args:
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dictionaries (bool, optional): Are dictionaries expected as input? i.e. Should key['value'] be retrieved. Defaults to True.
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Returns:
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dict: This instance as a dictionary
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"""
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fields = list(self.model_fields.keys()) + list(self.model_extra.keys())
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if dictionaries:
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output = {k: getattr(self, k) for k in fields}
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else:
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output = {k: self.filter_field(k) for k in fields}
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return output
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def to_sql(self):
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dicto = self.improved_dict(dictionaries=False)
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logger.debug(f"Dicto: {dicto}")
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sql, _ = self._sql_object().query_or_create(**dicto)
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return sql
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class PydReagent(BaseModel):
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lot: str | None
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reagentrole: str | None
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expiry: date | datetime | Literal['NA'] | None = Field(default=None, validate_default=True)
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name: str | None = Field(default=None, validate_default=True)
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missing: bool = Field(default=True)
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comment: str | None = Field(default="", validate_default=True)
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@field_validator('comment', mode='before')
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@classmethod
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def create_comment(cls, value):
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if value is None:
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return ""
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return value
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@field_validator("reagentrole", mode='before')
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@classmethod
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def remove_undesired_types(cls, value):
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match value:
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case "atcc":
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return None
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case _:
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return value
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@field_validator("reagentrole")
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@classmethod
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def rescue_type_with_lookup(cls, value, values):
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if value is None and values.data['lot'] is not None:
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try:
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return Reagent.query(lot=values.data['lot']).name
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except AttributeError:
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return value
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return value
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@field_validator("lot", mode='before')
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@classmethod
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def rescue_lot_string(cls, value):
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if value is not None:
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return convert_nans_to_nones(str(value).strip())
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return value
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@field_validator("lot")
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@classmethod
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def enforce_lot_string(cls, value):
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if value is not None:
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return value.upper().strip()
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return value
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@field_validator("expiry", mode="before")
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@classmethod
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def enforce_date(cls, value):
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if value is not None:
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match value:
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case int():
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return datetime.fromordinal(datetime(1900, 1, 1).toordinal() + value - 2)
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case 'NA':
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return value
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case str():
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return parse(value)
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case date():
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return datetime.combine(value, datetime.max.time())
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case datetime():
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return value
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case _:
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return convert_nans_to_nones(str(value))
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if value is None:
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value = date.today()
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return value
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@field_validator("expiry")
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@classmethod
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def date_na(cls, value):
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if isinstance(value, date) and value.year == 1970:
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value = "NA"
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return value
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@field_validator("name", mode="before")
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@classmethod
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def enforce_name(cls, value, values):
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if value is not None:
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return convert_nans_to_nones(str(value).strip())
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else:
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return values.data['reagentrole'].strip()
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def improved_dict(self) -> dict:
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"""
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Constructs a dictionary consisting of model.fields and model.extras
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Returns:
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dict: Information dictionary
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"""
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try:
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extras = list(self.model_extra.keys())
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except AttributeError:
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extras = []
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fields = list(self.model_fields.keys()) + extras
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return {k: getattr(self, k) for k in fields}
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@report_result
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def to_sql(self, procedure: Procedure | str = None) -> Tuple[Reagent, Report]:
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"""
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Converts this instance into a backend.db.models.kittype.Reagent instance
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Returns:
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Tuple[Reagent, Report]: Reagent instance and result of function
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"""
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report = Report()
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if self.model_extra is not None:
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self.__dict__.update(self.model_extra)
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reagent = Reagent.query(lot=self.lot, name=self.name)
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# logger.debug(f"Reagent: {reagent}")
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if reagent is None:
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reagent = Reagent()
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for key, value in self.__dict__.items():
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if isinstance(value, dict):
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value = value['value']
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# NOTE: reagent method sets fields based on keys in dictionary
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reagent.set_attribute(key, value)
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if procedure is not None and reagent not in procedure.reagents:
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assoc = ProcedureReagentAssociation(reagent=reagent, procedure=procedure)
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assoc.comments = self.comment
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else:
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assoc = None
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else:
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if submission is not None and reagent not in submission.reagents:
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submission.update_reagentassoc(reagent=reagent, role=self.role)
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return reagent, report
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class PydSample(PydBaseClass):
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sample_id: str
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sampletype: str | None = Field(default=None)
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submission_rank: int | List[int] | None = Field(default=0, validate_default=True)
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enabled: bool = Field(default=True)
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row: int = Field(default=0)
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column: int = Field(default=0)
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@field_validator("sample_id", mode="before")
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@classmethod
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def int_to_str(cls, value):
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return str(value)
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@field_validator("sample_id")
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@classmethod
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def strip_sub_id(cls, value):
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match value:
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case dict():
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value['value'] = value['value'].strip().upper()
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case str():
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value = value.strip().upper()
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case _:
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pass
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return value
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class PydTips(BaseModel):
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name: str
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lot: str | None = Field(default=None)
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tiprole: str
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@field_validator('tiprole', mode='before')
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@classmethod
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def get_role_name(cls, value):
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if isinstance(value, TipRole):
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value = value.name
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return value
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@report_result
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def to_sql(self, procedure: Run) -> ProcedureTipsAssociation:
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"""
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Convert this object to the SQL version for database storage.
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Args:
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procedure (BasicRun): A procedure object to associate tips represented here.
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Returns:
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SubmissionTipsAssociation: Association between queried tips and procedure
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"""
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report = Report()
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tips = Tips.query(name=self.name, limit=1)
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# logger.debug(f"Tips query has yielded: {tips}")
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assoc = ProcedureTipsAssociation.query_or_create(tips=tips, procedure=procedure, role=self.role, limit=1)
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return assoc, report
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class PydEquipment(BaseModel, extra='ignore'):
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asset_number: str
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name: str
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nickname: str | None
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process: List[str] | None
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equipmentrole: str | None
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tips: List[PydTips] | None = Field(default=None)
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@field_validator('equipmentrole', mode='before')
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@classmethod
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def get_role_name(cls, value):
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if isinstance(value, EquipmentRole):
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value = value.name
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return value
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@field_validator('process', mode='before')
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@classmethod
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def make_empty_list(cls, value):
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if isinstance(value, GeneratorType):
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value = [item.name for item in value]
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value = convert_nans_to_nones(value)
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if not value:
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value = ['']
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try:
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value = [item.strip() for item in value]
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except AttributeError:
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pass
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return value
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@report_result
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def to_sql(self, procedure: Procedure | str = None, kittype: KitType | str = None) -> Tuple[
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Equipment, ProcedureEquipmentAssociation]:
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"""
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Creates Equipment and SubmssionEquipmentAssociations for this PydEquipment
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Args:
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procedure ( BasicRun | str ): BasicRun of interest
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Returns:
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Tuple[Equipment, RunEquipmentAssociation]: SQL objects
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"""
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report = Report()
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if isinstance(procedure, str):
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procedure = Procedure.query(name=procedure)
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if isinstance(kittype, str):
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kittype = KitType.query(name=kittype)
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equipment = Equipment.query(asset_number=self.asset_number)
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if equipment is None:
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logger.error("No equipment found. Returning None.")
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return
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if procedure is not None:
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# NOTE: Need to make sure the same association is not added to the procedure
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try:
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assoc = ProcedureEquipmentAssociation.query(equipment_id=equipment.id, submission_id=procedure.id,
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equipmentrole=self.equipmentrole, limit=1)
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except TypeError as e:
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logger.error(f"Couldn't get association due to {e}, returning...")
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assoc = None
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if assoc is None:
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assoc = ProcedureEquipmentAssociation(submission=procedure, equipment=equipment)
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# TODO: This seems precarious. What if there is more than one process?
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# NOTE: It looks like the way fetching the process is done in the SQL model, this shouldn't be a problem, but I'll include a failsafe.
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# NOTE: I need to find a way to filter this by the kittype involved.
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if len(self.processes) > 1:
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process = Process.query(proceduretype=procedure.get_submission_type(), kittype=kittype,
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equipmentrole=self.role)
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else:
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process = Process.query(name=self.processes[0])
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if process is None:
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logger.error(f"Found unknown process: {process}.")
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# logger.debug(f"Using process: {process}")
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assoc.process = process
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assoc.equipmentrole = self.role
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else:
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logger.warning(f"Found already existing association: {assoc}")
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assoc = None
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else:
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logger.warning(f"No procedure found")
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assoc = None
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return equipment, assoc, report
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def improved_dict(self) -> dict:
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"""
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Constructs a dictionary consisting of model.fields and model.extras
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Returns:
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dict: Information dictionary
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"""
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try:
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extras = list(self.model_extra.keys())
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except AttributeError:
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extras = []
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fields = list(self.model_fields.keys()) + extras
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return {k: getattr(self, k) for k in fields}
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class PydSubmission(BaseModel, extra='allow'):
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filepath: Path
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submissiontype: dict | None
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submitter_plate_id: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
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rsl_plate_num: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
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submitted_date: dict | None = Field(default=dict(value=date.today(), missing=True), validate_default=True)
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clientlab: dict | None
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sample_count: dict | None
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kittype: dict | None
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technician: dict | None
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submission_category: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
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comment: dict | None = Field(default=dict(value="", missing=True), validate_default=True)
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reagent: List[dict] | List[PydReagent] = []
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sample: List[PydSample] | Generator
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equipment: List[PydEquipment] | None = []
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cost_centre: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
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contact: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
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tips: List[PydTips] | None = []
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@field_validator("tips", mode="before")
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@classmethod
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def expand_tips(cls, value):
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if isinstance(value, dict):
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value = value['value']
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if isinstance(value, Generator):
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return [PydTips(**tips) for tips in value]
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if not value:
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return []
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return value
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@field_validator('equipment', mode='before')
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@classmethod
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def convert_equipment_dict(cls, value):
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if isinstance(value, dict):
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return value['value']
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if isinstance(value, Generator):
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return [PydEquipment(**equipment) for equipment in value]
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if not value:
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return []
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return value
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|
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@field_validator('comment', mode='before')
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@classmethod
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def create_comment(cls, value):
|
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if value is None:
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return ""
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return value
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|
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@field_validator("submitter_plate_id")
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@classmethod
|
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def enforce_with_uuid(cls, value):
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if value['value'] in [None, "None"]:
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return dict(value=uuid.uuid4().hex.upper(), missing=True)
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else:
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value['value'] = value['value'].strip()
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return value
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|
|
@field_validator("submitted_date", mode="before")
|
|
@classmethod
|
|
def rescue_date(cls, value):
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try:
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check = value['value'] is None
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except TypeError:
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check = True
|
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if check:
|
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return dict(value=date.today(), missing=True)
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return value
|
|
|
|
@field_validator("submitted_date")
|
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@classmethod
|
|
def strip_datetime_string(cls, value):
|
|
match value['value']:
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|
case date():
|
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output = datetime.combine(value['value'], datetime.min.time())
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case datetime():
|
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pass
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case int():
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output = datetime.fromordinal(datetime(1900, 1, 1).toordinal() + value['value'] - 2)
|
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case str():
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string = re.sub(r"(_|-)\d(R\d)?$", "", value['value'])
|
|
try:
|
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output = dict(value=parse(string).date(), missing=True)
|
|
except ParserError as e:
|
|
logger.error(f"Problem parsing date: {e}")
|
|
try:
|
|
output = parse(string.replace("-", "")).date()
|
|
except Exception as e:
|
|
logger.error(f"Problem with parse fallback: {e}")
|
|
return value
|
|
case _:
|
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raise ValueError(f"Could not get datetime from {value['value']}")
|
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value['value'] = output.replace(tzinfo=timezone)
|
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return value
|
|
|
|
@field_validator("clientlab", mode="before")
|
|
@classmethod
|
|
def rescue_submitting_lab(cls, value):
|
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if value is None:
|
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return dict(value=None, missing=True)
|
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return value
|
|
|
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@field_validator("clientlab")
|
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@classmethod
|
|
def lookup_submitting_lab(cls, value):
|
|
if isinstance(value['value'], str):
|
|
try:
|
|
value['value'] = ClientLab.query(name=value['value']).name
|
|
except AttributeError:
|
|
value['value'] = None
|
|
if value['value'] is None:
|
|
value['missing'] = True
|
|
if "pytest" in sys.modules:
|
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value['value'] = "Nosocomial"
|
|
return value
|
|
from frontend.widgets.pop_ups import ObjectSelector
|
|
dlg = ObjectSelector(title="Missing Submitting Lab",
|
|
message="We need a submitting lab. Please select from the list.",
|
|
obj_type=ClientLab)
|
|
if dlg.exec():
|
|
value['value'] = dlg.parse_form()
|
|
else:
|
|
value['value'] = None
|
|
return value
|
|
|
|
@field_validator("rsl_plate_num", mode='before')
|
|
@classmethod
|
|
def rescue_rsl_number(cls, value):
|
|
if value is None:
|
|
return dict(value=None, missing=True)
|
|
return value
|
|
|
|
@field_validator("rsl_plate_num")
|
|
@classmethod
|
|
def rsl_from_file(cls, value, values):
|
|
sub_type = values.data['proceduretype']['value']
|
|
if check_not_nan(value['value']):
|
|
value['value'] = value['value'].strip()
|
|
return value
|
|
else:
|
|
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,
|
|
data=values.data).parsed_name
|
|
return dict(value=output, missing=True)
|
|
|
|
@field_validator("technician", mode="before")
|
|
@classmethod
|
|
def rescue_tech(cls, value):
|
|
if value is None:
|
|
return dict(value=None, missing=True)
|
|
return value
|
|
|
|
@field_validator("technician")
|
|
@classmethod
|
|
def enforce_tech(cls, value):
|
|
if check_not_nan(value['value']):
|
|
value['value'] = re.sub(r"\: \d", "", value['value'])
|
|
return value
|
|
else:
|
|
return dict(value=convert_nans_to_nones(value['value']), missing=True)
|
|
|
|
@field_validator("sample_count", mode='before')
|
|
@classmethod
|
|
def rescue_sample_count(cls, value):
|
|
if value is None:
|
|
return dict(value=None, missing=True)
|
|
return value
|
|
|
|
@field_validator("kittype", mode='before')
|
|
@classmethod
|
|
def rescue_kit(cls, value):
|
|
if check_not_nan(value):
|
|
if isinstance(value, str):
|
|
return dict(value=value, missing=False)
|
|
elif isinstance(value, dict):
|
|
return value
|
|
else:
|
|
raise ValueError(f"No extraction kittype found.")
|
|
if value is None:
|
|
# NOTE: Kit selection is done in the clientsubmissionparser, so should not be necessary here.
|
|
return dict(value=None, missing=True)
|
|
return value
|
|
|
|
@field_validator("submissiontype", mode='before')
|
|
@classmethod
|
|
def make_submission_type(cls, value, values):
|
|
if not isinstance(value, dict):
|
|
value = dict(value=value)
|
|
if check_not_nan(value['value']):
|
|
value = value['value'].title()
|
|
return dict(value=value, missing=False)
|
|
else:
|
|
return dict(value=RSLNamer.retrieve_submission_type(filename=values.data['filepath']).title(), missing=True)
|
|
|
|
@field_validator("submission_category", mode="before")
|
|
@classmethod
|
|
def create_category(cls, value):
|
|
if not isinstance(value, dict):
|
|
return dict(value=value, missing=True)
|
|
return value
|
|
|
|
@field_validator("submission_category")
|
|
@classmethod
|
|
def rescue_category(cls, value, values):
|
|
if isinstance(value['value'], str):
|
|
value['value'] = value['value'].title()
|
|
if value['value'] not in ["Research", "Diagnostic", "Surveillance", "Validation"]:
|
|
value['value'] = values.data['proceduretype']['value']
|
|
return value
|
|
|
|
@field_validator("reagent", mode="before")
|
|
@classmethod
|
|
def expand_reagents(cls, value):
|
|
if isinstance(value, Generator):
|
|
return [PydReagent(**reagent) for reagent in value]
|
|
return value
|
|
|
|
@field_validator("sample", mode="before")
|
|
@classmethod
|
|
def expand_samples(cls, value):
|
|
if isinstance(value, Generator):
|
|
return [PydSample(**sample) for sample in value]
|
|
return value
|
|
|
|
@field_validator("sample")
|
|
@classmethod
|
|
def assign_ids(cls, value):
|
|
starting_id = ClientSubmissionSampleAssociation.autoincrement_id()
|
|
for iii, sample in enumerate(value, start=starting_id):
|
|
# NOTE: Why is this a list? Answer: to zip with the lists of rows and columns in case of multiple of the same sample.
|
|
sample.assoc_id = [iii]
|
|
return value
|
|
|
|
@field_validator("cost_centre", mode="before")
|
|
@classmethod
|
|
def rescue_cost_centre(cls, value):
|
|
match value:
|
|
case dict():
|
|
return value
|
|
case _:
|
|
return dict(value=value, missing=True)
|
|
|
|
@field_validator("cost_centre")
|
|
@classmethod
|
|
def get_cost_centre(cls, value, values):
|
|
match value['value']:
|
|
case None:
|
|
from backend.db.models import Organization
|
|
org = Organization.query(name=values.data['clientlab']['value'])
|
|
try:
|
|
return dict(value=org.cost_centre, missing=True)
|
|
except AttributeError:
|
|
return dict(value="xxx", missing=True)
|
|
case _:
|
|
return value
|
|
|
|
@field_validator("contact")
|
|
@classmethod
|
|
def get_contact_from_org(cls, value, values):
|
|
# logger.debug(f"Value coming in: {value}")
|
|
match value:
|
|
case dict():
|
|
if isinstance(value['value'], tuple):
|
|
value['value'] = value['value'][0]
|
|
case tuple():
|
|
value = dict(value=value[0], missing=False)
|
|
case _:
|
|
value = dict(value=value, missing=False)
|
|
# logger.debug(f"Value after match: {value}")
|
|
check = Contact.query(name=value['value'])
|
|
# logger.debug(f"Check came back with {check}")
|
|
if not isinstance(check, Contact):
|
|
org = values.data['clientlab']['value']
|
|
# logger.debug(f"Checking organization: {org}")
|
|
if isinstance(org, str):
|
|
org = ClientLab.query(name=values.data['clientlab']['value'], limit=1)
|
|
if isinstance(org, ClientLab):
|
|
contact = org.contact[0].name
|
|
else:
|
|
logger.warning(f"All attempts at defaulting Contact failed, returning: {value}")
|
|
return value
|
|
if isinstance(contact, tuple):
|
|
contact = contact[0]
|
|
value = dict(value=f"Defaulted to: {contact}", missing=False)
|
|
# logger.debug(f"Value after query: {value}")
|
|
return value
|
|
else:
|
|
# logger.debug(f"Value after bypass check: {value}")
|
|
return value
|
|
|
|
def __init__(self, run_custom: bool = False, **data):
|
|
super().__init__(**data)
|
|
# NOTE: this could also be done with default_factory
|
|
self.submission_object = Run.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:
|
|
self.submission_object.custom_validation(pyd=self)
|
|
|
|
def set_attribute(self, key: str, value):
|
|
"""
|
|
Better handling of attribute setting.
|
|
|
|
Args:
|
|
key (str): Name of field to set
|
|
value (_type_): Value to set field to.
|
|
"""
|
|
self.__setattr__(name=key, value=value)
|
|
|
|
def handle_duplicate_samples(self):
|
|
"""
|
|
Collapses multiple sample with same submitter id into one with lists for rows, columns.
|
|
Necessary to prevent trying to create duplicate sample in SQL creation.
|
|
"""
|
|
submitter_ids = list(set([sample.sample_id for sample in self.samples]))
|
|
output = []
|
|
for id in submitter_ids:
|
|
relevants = [item for item in self.samples if item.sample_id == id]
|
|
if len(relevants) <= 1:
|
|
output += relevants
|
|
else:
|
|
rows = [item.row[0] for item in relevants]
|
|
columns = [item.column[0] for item in relevants]
|
|
ids = [item.assoc_id[0] for item in relevants]
|
|
ranks = [item.submission_rank[0] for item in relevants]
|
|
dummy = relevants[0]
|
|
dummy.assoc_id = ids
|
|
dummy.row = rows
|
|
dummy.column = columns
|
|
dummy.submission_rank = ranks
|
|
output.append(dummy)
|
|
self.samples = output
|
|
|
|
def improved_dict(self, dictionaries: bool = True) -> dict:
|
|
"""
|
|
Adds model_extra to fields.
|
|
|
|
Args:
|
|
dictionaries (bool, optional): Are dictionaries expected as input? i.e. Should key['value'] be retrieved. Defaults to True.
|
|
|
|
Returns:
|
|
dict: This instance as a dictionary
|
|
"""
|
|
fields = list(self.model_fields.keys()) + list(self.model_extra.keys())
|
|
if dictionaries:
|
|
output = {k: getattr(self, k) for k in fields}
|
|
output['reagents'] = [item.improved_dict() for item in self.reagents]
|
|
output['sample'] = [item.improved_dict() for item in self.samples]
|
|
try:
|
|
output['equipment'] = [item.improved_dict() for item in self.equipment]
|
|
except TypeError:
|
|
pass
|
|
else:
|
|
output = {k: self.filter_field(k) for k in fields}
|
|
return output
|
|
|
|
def filter_field(self, key: str) -> Any:
|
|
"""
|
|
Attempts to get value from field dictionary
|
|
|
|
Args:
|
|
key (str): name of the field of interest
|
|
|
|
Returns:
|
|
Any (): Value found.
|
|
"""
|
|
item = getattr(self, key)
|
|
match item:
|
|
case dict():
|
|
try:
|
|
item = item['value']
|
|
except KeyError:
|
|
logger.error(f"Couldn't get dict value: {item}")
|
|
case _:
|
|
pass
|
|
return item
|
|
|
|
def find_missing(self) -> Tuple[dict, dict]:
|
|
"""
|
|
Retrieves info and reagents marked as missing.
|
|
|
|
Returns:
|
|
Tuple[dict, dict]: Dict for missing info, dict for missing reagents.
|
|
"""
|
|
info = {k: v for k, v in self.improved_dict().items() if isinstance(v, dict)}
|
|
missing_info = {k: v for k, v in info.items() if v['missing']}
|
|
missing_reagents = [reagent for reagent in self.reagents if reagent.missing]
|
|
return missing_info, missing_reagents
|
|
|
|
@report_result
|
|
def to_sql(self) -> Tuple[BasicRun | None, Report]:
|
|
"""
|
|
Converts this instance into a backend.db.models.procedure.BasicRun instance
|
|
|
|
Returns:
|
|
Tuple[BasicRun, Result]: BasicRun instance, result object
|
|
"""
|
|
report = Report()
|
|
dicto = self.improved_dict()
|
|
# logger.debug(f"Pydantic procedure type: {self.proceduretype['value']}")
|
|
# logger.debug(f"Pydantic improved_dict: {pformat(dicto)}")
|
|
instance, result = BasicRun.query_or_create(submissiontype=self.submission_type['value'],
|
|
rsl_plate_num=self.rsl_plate_num['value'])
|
|
# logger.debug(f"Created or queried instance: {instance}")
|
|
if instance is None:
|
|
report.add_result(Result(msg="Overwrite Cancelled."))
|
|
return None, report
|
|
report.add_result(result)
|
|
self.handle_duplicate_samples()
|
|
for key, value in dicto.items():
|
|
# logger.debug(f"Checking key {key}, value {value}")
|
|
if isinstance(value, dict):
|
|
try:
|
|
value = value['value']
|
|
except KeyError:
|
|
if key == "custom":
|
|
pass
|
|
else:
|
|
continue
|
|
if value is None:
|
|
continue
|
|
match key:
|
|
case "reagents":
|
|
for reagent in self.reagents:
|
|
reagent = reagent.to_sql(submission=instance)
|
|
case "sample":
|
|
for sample in self.samples:
|
|
sample, associations, _ = sample.to_sql(run=instance)
|
|
for assoc in associations:
|
|
if assoc is not None:
|
|
if assoc not in instance.clientsubmissionsampleassociation:
|
|
instance.clientsubmissionsampleassociation.append(assoc)
|
|
else:
|
|
logger.warning(f"Sample association {assoc} is already present in {instance}")
|
|
case "equipment":
|
|
for equip in self.equipment:
|
|
if equip is None:
|
|
continue
|
|
equip, association = equip.to_sql(procedure=instance, kittype=self.extraction_kit)
|
|
if association is not None:
|
|
instance.submission_equipment_associations.append(association)
|
|
case "tips":
|
|
for tips in self.tips:
|
|
if tips is None:
|
|
continue
|
|
try:
|
|
association = tips.to_sql(procedure=instance)
|
|
except AttributeError:
|
|
continue
|
|
if association is not None:
|
|
if association not in instance.submission_tips_associations:
|
|
instance.submission_tips_associations.append(association)
|
|
else:
|
|
logger.warning(f"Tips association {association} is already present in {instance}")
|
|
case item if item in instance.timestamps:
|
|
logger.warning(f"Incoming timestamp key: {item}, with value: {value}")
|
|
if isinstance(value, date):
|
|
value = datetime.combine(value, datetime.now().time())
|
|
value = value.replace(tzinfo=timezone)
|
|
elif isinstance(value, str):
|
|
value: datetime = datetime.strptime(value, "%Y-%m-%d")
|
|
value = value.replace(tzinfo=timezone)
|
|
else:
|
|
value = value
|
|
instance.set_attribute(key=key, value=value)
|
|
case item if item in instance.jsons:
|
|
# logger.debug(f"Validating json value: {item} to value:{pformat(value)}")
|
|
try:
|
|
ii = value.items()
|
|
except AttributeError:
|
|
ii = {}
|
|
for k, v in ii:
|
|
if isinstance(v, datetime):
|
|
value[k] = v.strftime("%Y-%m-%d %H:%M:%S")
|
|
else:
|
|
pass
|
|
# logger.debug(f"Setting json value: {item} to value:{pformat(value)}")
|
|
instance.set_attribute(key=key, value=value)
|
|
case _:
|
|
try:
|
|
check = instance.__getattribute__(key) != value
|
|
except AttributeError:
|
|
continue
|
|
if check:
|
|
try:
|
|
instance.set_attribute(key=key, value=value)
|
|
except AttributeError as e:
|
|
logger.error(f"Could not set attribute: {key} to {value} due to: \n\n {e}")
|
|
continue
|
|
except KeyError:
|
|
continue
|
|
else:
|
|
logger.warning(f"{key} already == {value} so no updating.")
|
|
try:
|
|
instance.calculate_base_cost()
|
|
except (TypeError, AttributeError) as e:
|
|
logger.error(f"Looks like that kittype doesn't have cost breakdown yet due to: {e}, using 0.")
|
|
try:
|
|
instance.run_cost = instance.extraction_kit.cost_per_run
|
|
except AttributeError:
|
|
instance.run_cost = 0
|
|
# NOTE: Apply any discounts that are applicable for client and kittype.
|
|
try:
|
|
discounts = [item.amount for item in
|
|
Discount.query(kittype=instance.extraction_kit, organization=instance.clientlab)]
|
|
if len(discounts) > 0:
|
|
instance.run_cost = instance.run_cost - sum(discounts)
|
|
except Exception as e:
|
|
logger.error(f"An unknown exception occurred when calculating discounts: {e}")
|
|
return instance, report
|
|
|
|
def to_form(self, parent: QWidget, disable: list | None = None):
|
|
"""
|
|
Converts this instance into a frontend.widgets.submission_widget.SubmissionFormWidget
|
|
|
|
Args:
|
|
disable (list, optional): a list of widgets to be disabled in the form. Defaults to None.
|
|
parent (QWidget): parent widget of the constructed object
|
|
|
|
Returns:
|
|
SubmissionFormWidget: Submission form widget
|
|
"""
|
|
from frontend.widgets.submission_widget import SubmissionFormWidget
|
|
try:
|
|
logger.debug(f"PCR info: {self.pcr_info}")
|
|
except AttributeError:
|
|
pass
|
|
return SubmissionFormWidget(parent=parent, pyd=self, disable=disable)
|
|
|
|
def to_writer(self) -> "SheetWriter":
|
|
"""
|
|
Sends data here to the sheet writer.
|
|
|
|
Returns:
|
|
SheetWriter: Sheetwriter object that will perform writing.
|
|
"""
|
|
from backend.excel.writer import SheetWriter
|
|
return SheetWriter(self)
|
|
|
|
def construct_filename(self) -> str:
|
|
"""
|
|
Creates filename for this instance
|
|
|
|
Returns:
|
|
str: Output filename
|
|
"""
|
|
template = self.submission_object.filename_template()
|
|
render = self.namer.construct_export_name(template=template, **self.improved_dict(dictionaries=False)).replace(
|
|
"/", "")
|
|
return render
|
|
|
|
def check_kit_integrity(self, extraction_kit: str | dict | None = None, exempt: List[PydReagent] = []) -> Tuple[
|
|
List[PydReagent], Report, List[PydReagent]]:
|
|
"""
|
|
Ensures all reagents expected in kittype are listed in Submission
|
|
|
|
Args:
|
|
extraction_kit (str | dict | None, optional): kittype to be checked. Defaults to None.
|
|
exempt (List[PydReagent], optional): List of reagents that don't need to be checked. Defaults to []
|
|
|
|
Returns:
|
|
Tuple[List[PydReagent], Report]: List of reagents and Result object containing a message and any missing components.
|
|
"""
|
|
report = Report()
|
|
# logger.debug(f"The following reagents are exempt from the kittype integrity check:\n{exempt}")
|
|
if isinstance(extraction_kit, str):
|
|
extraction_kit = dict(value=extraction_kit)
|
|
if extraction_kit is not None and extraction_kit != self.extraction_kit['value']:
|
|
self.extraction_kit['value'] = extraction_kit['value']
|
|
ext_kit = KitType.query(name=self.extraction_kit['value'])
|
|
ext_kit_rtypes = [item.to_pydantic() for item in
|
|
ext_kit.get_reagents(required_only=True, proceduretype=self.submission_type['value'])]
|
|
# NOTE: Exclude any reagenttype found in this pydclientsubmission not expected in kittype.
|
|
expected_check = [item.equipmentrole for item in ext_kit_rtypes]
|
|
output_reagents = [rt for rt in self.reagents if rt.role in expected_check]
|
|
missing_check = [item.role for item in output_reagents]
|
|
missing_reagents = [rt for rt in ext_kit_rtypes if
|
|
rt.equipmentrole not in missing_check and rt.equipmentrole not in exempt]
|
|
# logger.debug(f"Missing reagents: {missing_reagents}")
|
|
missing_reagents += [rt for rt in output_reagents if rt.missing]
|
|
output_reagents += [rt for rt in missing_reagents if rt not in output_reagents]
|
|
# NOTE: if lists are equal return no problem
|
|
if len(missing_reagents) == 0:
|
|
result = None
|
|
else:
|
|
result = Result(
|
|
msg=f"The excel sheet you are importing is missing some reagents expected by the kittype.\n\nIt looks like you are missing: {[item.equipmentrole.upper() for item in missing_reagents]}\n\nAlternatively, you may have set the wrong extraction kittype.\n\nThe program will populate lists using existing reagents.\n\nPlease make sure you check the lots carefully!",
|
|
status="Warning")
|
|
report.add_result(result)
|
|
return output_reagents, report, missing_reagents
|
|
|
|
def check_reagent_expiries(self, exempt: List[PydReagent] = []):
|
|
report = Report()
|
|
expired = []
|
|
for reagent in self.reagents:
|
|
if reagent not in exempt:
|
|
role_eol = ReagentRole.query(name=reagent.role).eol_ext
|
|
try:
|
|
dt = datetime.combine(reagent.expiry, datetime.max.time())
|
|
except TypeError:
|
|
continue
|
|
if datetime.now() > dt + role_eol:
|
|
expired.append(f"{reagent.role}, {reagent.lot}: {reagent.expiry.date()} + {role_eol.days}")
|
|
if expired:
|
|
output = '\n'.join(expired)
|
|
result = Result(status="Warning",
|
|
msg=f"The following reagents are expired:\n\n{output}"
|
|
)
|
|
report.add_result(result)
|
|
return report
|
|
|
|
def export_csv(self, filename: Path | str):
|
|
try:
|
|
worksheet = self.csv
|
|
except AttributeError:
|
|
logger.error("No csv found.")
|
|
return
|
|
if isinstance(filename, str):
|
|
filename = Path(filename)
|
|
with open(filename, 'w', newline="") as f:
|
|
c = csv.writer(f)
|
|
for r in worksheet.rows:
|
|
c.writerow([cell.value for cell in r])
|
|
|
|
@property
|
|
def sample_list(self) -> List[dict]:
|
|
samples = []
|
|
for sample in self.samples:
|
|
sample = sample.improved_dict()
|
|
sample['row'] = sample['row'][0]
|
|
sample['column'] = sample['column'][0]
|
|
sample['submission_rank'] = sample['submission_rank'][0]
|
|
samples.append(sample)
|
|
samples = sorted(samples, key=itemgetter("submission_rank"))
|
|
return samples
|
|
|
|
|
|
class PydContact(BaseModel):
|
|
name: str
|
|
phone: str | None
|
|
email: str | None
|
|
|
|
@field_validator("phone")
|
|
@classmethod
|
|
def enforce_phone_number(cls, value):
|
|
area_regex = re.compile(r"^\(?(\d{3})\)?(-| )?")
|
|
if len(value) > 8:
|
|
match = area_regex.match(value)
|
|
# logger.debug(f"Match: {match.group(1)}")
|
|
value = area_regex.sub(f"({match.group(1).strip()}) ", value)
|
|
# logger.debug(f"Output phone: {value}")
|
|
return value
|
|
|
|
@report_result
|
|
def to_sql(self) -> Tuple[Contact, Report]:
|
|
"""
|
|
Converts this instance into a backend.db.models.organization. Contact instance.
|
|
Does not query for existing contact.
|
|
|
|
Returns:
|
|
Contact: Contact instance
|
|
"""
|
|
report = Report()
|
|
instance = Contact.query(name=self.name, phone=self.phone, email=self.email)
|
|
if not instance or isinstance(instance, list):
|
|
instance = Contact()
|
|
try:
|
|
all_fields = self.model_fields + self.model_extra
|
|
except TypeError:
|
|
all_fields = self.model_fields
|
|
for field in all_fields:
|
|
value = getattr(self, field)
|
|
match field:
|
|
case "organization":
|
|
value = [Organization.query(name=value)]
|
|
case _:
|
|
pass
|
|
try:
|
|
instance.__setattr__(field, value)
|
|
except AttributeError as e:
|
|
logger.error(f"Could not set {instance} {field} to {value} due to {e}")
|
|
return instance, report
|
|
|
|
|
|
class PydOrganization(BaseModel):
|
|
name: str
|
|
cost_centre: str
|
|
contact: List[PydContact] | None
|
|
|
|
@field_validator("contact", mode="before")
|
|
@classmethod
|
|
def string_to_list(cls, value):
|
|
if isinstance(value, str):
|
|
value = Contact.query(name=value)
|
|
try:
|
|
value = [value.to_pydantic()]
|
|
except AttributeError:
|
|
return None
|
|
return value
|
|
|
|
@report_result
|
|
def to_sql(self) -> ClientLab:
|
|
"""
|
|
Converts this instance into a backend.db.models.organization.Organization instance.
|
|
|
|
Returns:
|
|
Organization: Organization instance
|
|
"""
|
|
report = Report()
|
|
instance = ClientLab()
|
|
for field in self.model_fields:
|
|
match field:
|
|
case "contact":
|
|
value = getattr(self, field)
|
|
if value:
|
|
value = [item.to_sql() for item in value if item]
|
|
case _:
|
|
value = getattr(self, field)
|
|
logger.debug(f"Setting {field} to {value}")
|
|
if value:
|
|
setattr(instance, field, value)
|
|
return instance, report
|
|
|
|
|
|
class PydReagentRole(BaseModel):
|
|
name: str
|
|
eol_ext: timedelta | int | None
|
|
uses: dict | None
|
|
required: int | None = Field(default=1)
|
|
|
|
@field_validator("eol_ext")
|
|
@classmethod
|
|
def int_to_timedelta(cls, value):
|
|
if isinstance(value, int):
|
|
return timedelta(days=value)
|
|
return value
|
|
|
|
@report_result
|
|
def to_sql(self, kit: KitType) -> ReagentRole:
|
|
"""
|
|
Converts this instance into a backend.db.models.ReagentType instance
|
|
|
|
Args:
|
|
kit (KitType): KitType joined to the reagentrole
|
|
|
|
Returns:
|
|
ReagentRole: ReagentType instance
|
|
"""
|
|
report = Report()
|
|
instance: ReagentRole = ReagentRole.query(name=self.name)
|
|
if instance is None:
|
|
instance = ReagentRole(name=self.name, eol_ext=self.eol_ext)
|
|
try:
|
|
assoc = KitTypeReagentRoleAssociation.query(reagentrole=instance, kittype=kit)
|
|
except StatementError:
|
|
assoc = None
|
|
if assoc is None:
|
|
assoc = KitTypeReagentRoleAssociation(kittype=kit, reagentrole=instance, uses=self.uses,
|
|
required=self.required)
|
|
return instance, report
|
|
|
|
|
|
class PydKitType(BaseModel):
|
|
name: str
|
|
reagent_roles: List[PydReagent] = []
|
|
|
|
@report_result
|
|
def to_sql(self) -> Tuple[KitType, Report]:
|
|
"""
|
|
Converts this instance into a backend.db.models.kits.KitType instance
|
|
|
|
Returns:
|
|
Tuple[KitType, Report]: KitType instance and report of results.
|
|
"""
|
|
report = Report()
|
|
instance = KitType.query(name=self.name)
|
|
if instance is None:
|
|
instance = KitType(name=self.name)
|
|
for role in self.reagent_roles:
|
|
role.to_sql(instance)
|
|
return instance, report
|
|
|
|
|
|
class PydEquipmentRole(BaseModel):
|
|
name: str
|
|
equipment: List[PydEquipment]
|
|
process: List[str] | None
|
|
|
|
@field_validator("process", mode="before")
|
|
@classmethod
|
|
def expand_processes(cls, value):
|
|
if isinstance(value, GeneratorType):
|
|
value = [item for item in value]
|
|
return value
|
|
|
|
def to_form(self, parent, used: list) -> "RoleComboBox":
|
|
"""
|
|
Creates a widget for user input into this class.
|
|
|
|
Args:
|
|
parent (_type_): parent widget
|
|
used (list): list of equipment already added to procedure
|
|
|
|
Returns:
|
|
RoleComboBox: widget
|
|
"""
|
|
from frontend.widgets.equipment_usage import RoleComboBox
|
|
return RoleComboBox(parent=parent, role=self, used=used)
|
|
|
|
|
|
# class PydPCRControl(BaseModel):
|
|
#
|
|
# name: str
|
|
# subtype: str
|
|
# target: str
|
|
# ct: float
|
|
# reagent_lot: str
|
|
# submitted_date: datetime #: Date submitted to Robotics
|
|
# procedure_id: int
|
|
# controltype_name: str
|
|
#
|
|
# @report_result
|
|
# def to_sql(self):
|
|
# report = Report
|
|
# instance = PCRControl.query(name=self.name)
|
|
# if not instance:
|
|
# instance = PCRControl()
|
|
# for key in self.model_fields:
|
|
# field_value = self.__getattribute__(key)
|
|
# if instance.__getattribute__(key) != field_value:
|
|
# instance.__setattr__(key, field_value)
|
|
# return instance, report
|
|
#
|
|
#
|
|
# class PydIridaControl(BaseModel, extra='ignore'):
|
|
#
|
|
# name: str
|
|
# contains: list | dict #: unstructured hashes in contains.tsv for each organism
|
|
# matches: list | dict #: unstructured hashes in matches.tsv for each organism
|
|
# kraken: list | dict #: unstructured output from kraken_report
|
|
# subtype: Literal["ATCC49226", "ATCC49619", "EN-NOS", "EN-SSTI", "MCS-NOS", "MCS-SSTI", "SN-NOS", "SN-SSTI"]
|
|
# refseq_version: str #: version of refseq used in fastq parsing
|
|
# kraken2_version: str
|
|
# kraken2_db_version: str
|
|
# sample_id: int
|
|
# submitted_date: datetime #: Date submitted to Robotics
|
|
# procedure_id: int
|
|
# controltype_name: str
|
|
#
|
|
# @field_validator("refseq_version", "kraken2_version", "kraken2_db_version", mode='before')
|
|
# @classmethod
|
|
# def enforce_string(cls, value):
|
|
# if not value:
|
|
# value = ""
|
|
# return value
|
|
#
|
|
# @report_result
|
|
# def to_sql(self):
|
|
# report = Report()
|
|
# instance = IridaControl.query(name=self.name)
|
|
# if not instance:
|
|
# instance = IridaControl()
|
|
# for key in self.model_fields:
|
|
# field_value = self.__getattribute__(key)
|
|
# if instance.__getattribute__(key) != field_value:
|
|
# instance.__setattr__(key, field_value)
|
|
# return instance, report
|
|
|
|
|
|
class PydProcess(BaseModel, extra="allow"):
|
|
name: str
|
|
version: str = Field(default="1")
|
|
submissiontype: List[str]
|
|
equipment: List[str]
|
|
equipmentrole: List[str]
|
|
kittype: List[str]
|
|
tiprole: List[str]
|
|
|
|
@field_validator("submissiontype", "equipment", "equipmentrole", "kittype", "tiprole", mode="before")
|
|
@classmethod
|
|
def enforce_list(cls, value):
|
|
if not isinstance(value, list):
|
|
return [value]
|
|
return value
|
|
|
|
@report_result
|
|
def to_sql(self):
|
|
report = Report()
|
|
instance = Process.query(name=self.name)
|
|
if not instance:
|
|
instance = Process()
|
|
fields = [item for item in self.model_fields]
|
|
for field in fields:
|
|
logger.debug(f"Field: {field}")
|
|
try:
|
|
field_type = getattr(instance.__class__, field).property
|
|
except AttributeError:
|
|
logger.error(f"No attribute: {field} in {instance.__class__}")
|
|
continue
|
|
match field_type:
|
|
case _RelationshipDeclared():
|
|
logger.debug(f"{field} is a relationship with {field_type.entity.class_}")
|
|
query_str = getattr(self, field)
|
|
if isinstance(query_str, list):
|
|
query_str = query_str[0]
|
|
if query_str in ["", " ", None]:
|
|
continue
|
|
logger.debug(f"Querying {field_type.entity.class_} with name {query_str}")
|
|
field_value = field_type.entity.class_.query(name=query_str)
|
|
logger.debug(f"{field} query result: {field_value}")
|
|
case ColumnProperty():
|
|
logger.debug(f"{field} is a property.")
|
|
field_value = getattr(self, field)
|
|
instance.set_attribute(key=field, value=field_value)
|
|
return instance, report
|
|
|
|
|
|
class PydElastic(BaseModel, extra="allow", arbitrary_types_allowed=True):
|
|
"""Allows for creation of arbitrary pydantic models"""
|
|
instance: BaseClass
|
|
|
|
@report_result
|
|
def to_sql(self):
|
|
# print(self.instance)
|
|
fields = [item for item in self.model_extra]
|
|
for field in fields:
|
|
try:
|
|
field_type = getattr(self.instance.__class__, field).property
|
|
except AttributeError:
|
|
logger.error(f"No attribute: {field} in {self.instance.__class__}")
|
|
continue
|
|
match field_type:
|
|
case _RelationshipDeclared():
|
|
# logger.debug(f"{field} is a relationship with {field_type.entity.class_}")
|
|
field_value = field_type.entity.class_.argument.query(name=getattr(self, field))
|
|
# logger.debug(f"{field} query result: {field_value}")
|
|
case ColumnProperty():
|
|
# logger.debug(f"{field} is a property.")
|
|
field_value = getattr(self, field)
|
|
self.instance.__setattr__(field, field_value)
|
|
return self.instance
|
|
|
|
|
|
# NOTE: Generified objects below:
|
|
|
|
class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
|
|
proceduretype: ProcedureType | None = Field(default=None)
|
|
run: Run | None = Field(default=None)
|
|
name: dict = Field(default=dict(value="NA", missing=True), validate_default=True)
|
|
technician: dict = Field(default=dict(value="NA", missing=True))
|
|
repeat: bool = Field(default=False)
|
|
kittype: dict = Field(default=dict(value="NA", missing=True))
|
|
possible_kits: list | None = Field(default=[], validate_default=True)
|
|
plate_map: str | None = Field(default=None)
|
|
reagent: list | None = Field(default=[])
|
|
reagentrole: dict | None = Field(default={}, validate_default=True)
|
|
samples: List[PydSample] = Field(default=[])
|
|
|
|
@field_validator("name")
|
|
@classmethod
|
|
def rescue_name(cls, value, values):
|
|
if value['value'] == cls.model_fields['name'].default['value']:
|
|
if values.data['proceduretype']:
|
|
value['value'] = values.data['proceduretype'].name
|
|
return value
|
|
|
|
@field_validator("possible_kits")
|
|
@classmethod
|
|
def rescue_possible_kits(cls, value, values):
|
|
if not value:
|
|
if values.data['proceduretype']:
|
|
value = [kittype.name for kittype in values.data['proceduretype'].kittype]
|
|
return value
|
|
|
|
@field_validator("name", "technician", "kittype")
|
|
@classmethod
|
|
def set_colour(cls, value):
|
|
if value["missing"]:
|
|
value["colour"] = "FE441D"
|
|
else:
|
|
value["colour"] = "6ffe1d"
|
|
return value
|
|
|
|
@field_validator("reagentrole")
|
|
@classmethod
|
|
def rescue_reagentrole(cls, value, values):
|
|
if not value:
|
|
if values.data['kittype']['value'] != cls.model_fields['kittype'].default['value']:
|
|
kittype = KitType.query(name=values.data['kittype']['value'])
|
|
value = {item.name: item.reagents for item in kittype.reagentrole}
|
|
return value
|
|
|
|
def update_kittype_reagentroles(self, kittype: str | KitType):
|
|
if kittype == self.__class__.model_fields['kittype'].default['value']:
|
|
return
|
|
if isinstance(kittype, str):
|
|
kittype_obj = KitType.query(name=kittype)
|
|
try:
|
|
self.reagentrole = {item.name: item.get_reagents(kittype=kittype_obj) for item in
|
|
kittype_obj.get_reagents(proceduretype=self.proceduretype)}
|
|
except AttributeError:
|
|
self.reagentrole = {}
|
|
self.kittype['value'] = kittype
|
|
self.possible_kits.insert(0, self.possible_kits.pop(self.possible_kits.index(kittype)))
|
|
|
|
def update_samples(self, sample_list: List[dict]):
|
|
logger.debug(f"Incoming sample_list:\n{pformat(sample_list)}")
|
|
for sample_dict in sample_list:
|
|
if sample_dict['sample_id'].startswith("blank_"):
|
|
continue
|
|
row, column = self.proceduretype.ranked_plate[sample_dict['index']]
|
|
logger.debug(f"Row: {row}, Column: {column}")
|
|
try:
|
|
sample = next(
|
|
(item for item in self.samples if item.sample_id.upper() == sample_dict['sample_id'].upper()))
|
|
except StopIteration:
|
|
# NOTE: Code to check for added controls.
|
|
logger.debug(f"Sample not found by name: {sample_dict['sample_id']}, checking row {row} column {column}")
|
|
try:
|
|
sample = next(
|
|
(item for item in self.samples if item.row == row and item.column == column))
|
|
except StopIteration:
|
|
logger.error(f"Couldn't find sample: {pformat(sample_dict)}")
|
|
continue
|
|
logger.debug(f"Sample of interest: {sample.improved_dict()}")
|
|
sample.sample_id = sample_dict['sample_id']
|
|
sample.well_id = sample_dict['sample_id']
|
|
sample.row = row
|
|
sample.column = column
|
|
logger.debug(f"Updated samples:\n{pformat(self.samples)}")
|
|
|
|
def to_sql(self):
|
|
from backend.db.models import RunSampleAssociation, ProcedureSampleAssociation
|
|
sql = super().to_sql()
|
|
if self.run:
|
|
sql.run = self.run
|
|
if self.proceduretype:
|
|
sql.proceduretype = self.proceduretype
|
|
for sample in self.samples:
|
|
if sample.sample_id.startswith("blank_") or sample.sample_id == "":
|
|
continue
|
|
sample_sql = sample.to_sql()
|
|
if sql.run:
|
|
if sample_sql not in sql.run.sample:
|
|
logger.debug(f"sample {sample_sql} not found in {sql.run.sample}")
|
|
run_assoc = RunSampleAssociation(sample=sample_sql, run=self.run, row=sample.row, column=sample.column)
|
|
else:
|
|
logger.debug(f"sample {sample_sql} found in {sql.run.sample}")
|
|
proc_assoc = ProcedureSampleAssociation(procedure=sql, sample=sample_sql, row=sample.row, column=sample.column)
|
|
if self.kittype['value'] not in ["NA", None, ""]:
|
|
kittype = KitType.query(name=self.kittype['value'], limit=1)
|
|
if kittype:
|
|
sql.kittype = kittype
|
|
return sql, None
|
|
|
|
|
|
|
|
class PydClientSubmission(PydBaseClass):
|
|
# sql_object: ClassVar = ClientSubmission
|
|
|
|
filepath: Path
|
|
submissiontype: dict | None
|
|
submitted_date: dict | None = Field(default=dict(value=date.today(), missing=True), validate_default=True)
|
|
clientlab: dict | None
|
|
sample_count: dict | None
|
|
submission_category: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
|
|
comment: dict | None = Field(default=dict(value="", missing=True), validate_default=True)
|
|
cost_centre: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
|
|
contact: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
|
|
submitter_plate_id: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
|
|
|
|
@field_validator("sample_count")
|
|
@classmethod
|
|
def enforce_integer(cls, value):
|
|
try:
|
|
value['value'] = int(value['value'])
|
|
except ValueError:
|
|
raise f"sample count value must be an integer"
|
|
return value
|
|
|
|
@field_validator("submitter_plate_id")
|
|
@classmethod
|
|
def create_submitter_plate_num(cls, value, values):
|
|
if value['value'] in [None, "None"]:
|
|
val = f"{values.data['submissiontype']['value']}-{values.data['submission_category']['value']}-{values.data['submitted_date']['value']}"
|
|
return dict(value=val, missing=True)
|
|
else:
|
|
value['value'] = value['value'].strip()
|
|
return value
|
|
|
|
@field_validator("submitted_date")
|
|
@classmethod
|
|
def rescue_date(cls, value):
|
|
try:
|
|
check = value['value'] is None
|
|
except TypeError:
|
|
check = True
|
|
if check:
|
|
return dict(value=date.today(), missing=True)
|
|
else:
|
|
match value['value']:
|
|
case str():
|
|
value['value'] = datetime.strptime(value['value'], "%Y-%m-%d")
|
|
value['value'] = datetime.combine(value['value'], datetime.now().time())
|
|
case _:
|
|
pass
|
|
return value
|
|
|
|
@field_validator("submission_category")
|
|
@classmethod
|
|
def enforce_typing(cls, value, values):
|
|
if not value['value'] in ["Research", "Diagnostic", "Surveillance", "Validation"]:
|
|
try:
|
|
value['value'] = values.data['submissiontype']['value']
|
|
except AttributeError:
|
|
value['value'] = "NA"
|
|
return value
|
|
|
|
def to_form(self, parent: QWidget, samples: List = [], disable: list | None = None):
|
|
"""
|
|
Converts this instance into a frontend.widgets.submission_widget.SubmissionFormWidget
|
|
|
|
Args:
|
|
samples ():
|
|
disable (list, optional): a list of widgets to be disabled in the form. Defaults to None.
|
|
parent (QWidget): parent widget of the constructed object
|
|
|
|
Returns:
|
|
SubmissionFormWidget: Submission form widget
|
|
"""
|
|
from frontend.widgets.submission_widget import ClientSubmissionFormWidget
|
|
return ClientSubmissionFormWidget(parent=parent, clientsubmission=self, samples=samples, disable=disable)
|