Pre-removal of constructors module.
This commit is contained in:
Landon Wark
@@ -3,22 +3,28 @@ Contains pydantic models and accompanying validators
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'''
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import uuid
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from pydantic import BaseModel, field_validator, Field
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from datetime import date, datetime
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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._parser import ParserError
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from typing import List, Any
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from typing import List, Any, Tuple
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from . import RSLNamer
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from pathlib import Path
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import re
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import logging
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from tools import check_not_nan, convert_nans_to_nones, Settings
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from backend.db.functions import lookup_submissions
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from backend.db.functions import (lookup_submissions, lookup_reagent_types, lookup_reagents, lookup_kit_types,
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lookup_organizations, lookup_submission_type, lookup_discounts, lookup_samples, lookup_submission_sample_association,
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lookup_reagenttype_kittype_association
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)
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from backend.db.models import *
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from sqlalchemy.exc import InvalidRequestError, StatementError
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logger = logging.getLogger(f"submissions.{__name__}")
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class PydSheetReagent(BaseModel):
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type: str|None
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class PydReagent(BaseModel):
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ctx: Settings
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lot: str|None
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type: str|None
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exp: date|None
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name: str|None
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@@ -30,6 +36,16 @@ class PydSheetReagent(BaseModel):
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return None
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case _:
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return value
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@field_validator("type")
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@classmethod
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def rescue_type_with_lookup(cls, value, values):
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if value == None and values.data['lot'] != None:
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try:
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return lookup_reagents(ctx=values.data['ctx'], lot_number=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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@@ -70,7 +86,81 @@ class PydSheetReagent(BaseModel):
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else:
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return values.data['type']
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class PydSheetSubmission(BaseModel, extra='allow'):
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def toSQL(self):# -> Tuple[Reagent, dict]:
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result = None
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logger.debug(f"Reagent SQL constructor is looking up type: {self.type}, lot: {self.lot}")
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reagent = lookup_reagents(ctx=self.ctx, lot_number=self.lot)
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logger.debug(f"Result: {reagent}")
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if reagent == 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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logger.debug(f"Reagent info item for {key}: {value}")
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# set fields based on keys in dictionary
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match key:
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case "lot":
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reagent.lot = value.upper()
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case "expiry":
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reagent.expiry = value
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case "type":
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reagent_type = lookup_reagent_types(ctx=self.ctx, name=value)
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if reagent_type != None:
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reagent.type.append(reagent_type)
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case "name":
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reagent.name = value
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# add end-of-life extension from reagent type to expiry date
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# NOTE: this will now be done only in the reporting phase to account for potential changes in end-of-life extensions
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return reagent, result
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class PydSample(BaseModel, extra='allow'):
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submitter_id: str
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sample_type: str
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row: int|List[int]|None
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column: int|List[int]|None
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@field_validator("row", "column")
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@classmethod
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def row_int_to_list(cls, value):
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if isinstance(value, int):
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return [value]
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return value
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# @field_validator(column)
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# @classmethod
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# def column_int_to_list(cls, value):
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# if isinstance(value, int):
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# return [value]
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# return value
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def toSQL(self, ctx:Settings, submission):
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result = None
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self.__dict__.update(self.model_extra)
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logger.debug(f"Here is the incoming sample dict: \n{self.__dict__}")
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instance = lookup_samples(ctx=ctx, submitter_id=self.submitter_id)
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if instance == None:
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logger.debug(f"Sample {self.submitter_id} doesn't exist yet. Looking up sample object with polymorphic identity: {self.sample_type}")
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instance = BasicSample.find_polymorphic_subclass(polymorphic_identity=self.sample_type)()
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for key, value in self.__dict__.items():
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# logger.debug(f"Setting sample field {key} to {value}")
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match key:
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case "row" | "column":
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continue
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case _:
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instance.set_attribute(name=key, value=value)
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for row, column in zip(self.row, self.column):
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logger.debug(f"Looking up association with identity: ({submission.submission_type_name} Association)")
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association = lookup_submission_sample_association(ctx=ctx, submission=submission, row=row, column=column)
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logger.debug(f"Returned association: {association}")
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if association == None or association == []:
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logger.debug(f"Looked up association at row {row}, column {column} didn't exist, creating new association.")
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association = SubmissionSampleAssociation.find_polymorphic_subclass(polymorphic_identity=f"{submission.submission_type_name} Association")
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association = association(submission=submission, sample=instance, row=row, column=column)
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instance.sample_submission_associations.append(association)
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return instance, result
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class PydSubmission(BaseModel, extra='allow'):
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ctx: Settings
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filepath: Path
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submission_type: dict|None
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@@ -83,7 +173,7 @@ class PydSheetSubmission(BaseModel, extra='allow'):
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extraction_kit: dict|None
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technician: dict|None
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submission_category: dict|None = Field(default=dict(value=None, parsed=False), validate_default=True)
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reagents: List[dict] = []
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reagents: List[dict]|List[PydReagent] = []
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samples: List[Any]
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@field_validator("submitter_plate_num")
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@@ -211,3 +301,165 @@ class PydSheetSubmission(BaseModel, extra='allow'):
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if value['value'] not in ["Research", "Diagnostic", "Surveillance"]:
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value['value'] = values.data['submission_type']['value']
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return value
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def toSQL(self):
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code = 0
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msg = None
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self.__dict__.update(self.model_extra)
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instance = lookup_submissions(ctx=self.ctx, rsl_number=self.rsl_plate_num['value'])
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if instance == None:
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instance = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type)()
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else:
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code = 1
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msg = "This submission already exists.\nWould you like to overwrite?"
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self.handle_duplicate_samples()
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logger.debug(f"Here's our list of duplicate removed samples: {self.samples}")
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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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logger.debug(f"Setting {key} to {value}")
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# set fields based on keys in dictionary
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match key:
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case "extraction_kit":
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logger.debug(f"Looking up kit {value}")
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field_value = lookup_kit_types(ctx=self.ctx, name=value)
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logger.debug(f"Got {field_value} for kit {value}")
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case "submitting_lab":
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logger.debug(f"Looking up organization: {value}")
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field_value = lookup_organizations(ctx=self.ctx, name=value)
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logger.debug(f"Got {field_value} for organization {value}")
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case "submitter_plate_num":
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logger.debug(f"Submitter plate id: {value}")
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field_value = value
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case "samples":
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# instance = construct_samples(ctx=ctx, instance=instance, samples=value)
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for sample in value:
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# logger.debug(f"Parsing {sample} to sql.")
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sample, _ = sample.toSQL(ctx=self.ctx, submission=instance)
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# instance.samples.append(sample)
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continue
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case "reagents":
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field_value = [reagent['value'].toSQL()[0] if isinstance(reagent, dict) else reagent.toSQL()[0] for reagent in value]
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case "submission_type":
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field_value = lookup_submission_type(ctx=self.ctx, name=value)
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case "ctx" | "csv" | "filepath":
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continue
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case _:
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field_value = value
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# insert into field
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try:
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setattr(instance, key, field_value)
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except AttributeError as e:
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logger.debug(f"Could not set attribute: {key} to {value} due to: \n\n {e}")
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continue
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except KeyError:
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continue
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try:
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logger.debug(f"Calculating costs for procedure...")
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instance.calculate_base_cost()
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except (TypeError, AttributeError) as e:
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logger.debug(f"Looks like that kit doesn't have cost breakdown yet due to: {e}, using full plate cost.")
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instance.run_cost = instance.extraction_kit.cost_per_run
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logger.debug(f"Calculated base run cost of: {instance.run_cost}")
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# Apply any discounts that are applicable for client and kit.
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try:
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logger.debug("Checking and applying discounts...")
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discounts = [item.amount for item in lookup_discounts(ctx=self.ctx, kit_type=instance.extraction_kit, organization=instance.submitting_lab)]
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logger.debug(f"We got discounts: {discounts}")
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if len(discounts) > 0:
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discounts = sum(discounts)
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instance.run_cost = instance.run_cost - discounts
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except Exception as e:
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logger.error(f"An unknown exception occurred when calculating discounts: {e}")
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# We need to make sure there's a proper rsl plate number
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logger.debug(f"We've got a total cost of {instance.run_cost}")
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try:
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logger.debug(f"Constructed instance: {instance.to_string()}")
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except AttributeError as e:
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logger.debug(f"Something went wrong constructing instance {self.rsl_plate_num}: {e}")
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logger.debug(f"Constructed submissions message: {msg}")
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return instance, {'code':code, 'message':msg}
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def handle_duplicate_samples(self):
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submitter_ids = list(set([sample.submitter_id for sample in self.samples]))
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output = []
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for id in submitter_ids:
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relevants = [item for item in self.samples if item.submitter_id==id]
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if len(relevants) <= 1:
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output += relevants
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else:
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rows = [item.row[0] for item in relevants]
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columns = [item.column[0] for item in relevants]
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dummy = relevants[0]
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dummy.row = rows
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dummy.column = columns
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output.append(dummy)
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self.samples = output
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class PydContact(BaseModel):
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name: str
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phone: str|None
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email: str|None
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def toSQL(self, ctx):
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return Contact(name=self.name, phone=self.phone, email=self.email)
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class PydOrganization(BaseModel):
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name: str
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cost_centre: str
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contacts: List[PydContact]|None
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def toSQL(self, ctx):
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instance = Organization()
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for field in self.model_fields:
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match field:
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case "contacts":
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value = [item.toSQL(ctx) for item in getattr(self, field)]
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case _:
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value = getattr(self, field)
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instance.set_attribute(name=field, value=value)
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return instance
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class PydReagentType(BaseModel):
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name: str
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eol_ext: timedelta|int|None
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uses: dict|None
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required: int|None = Field(default=1)
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@field_validator("eol_ext")
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@classmethod
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def int_to_timedelta(cls, value):
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if isinstance(value, int):
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return timedelta(days=value)
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return value
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def toSQL(self, ctx:Settings, kit:KitType):
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instance: ReagentType = lookup_reagent_types(ctx=ctx, name=self.name)
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if instance == None:
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instance = ReagentType(name=self.name, eol_ext=self.eol_ext)
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logger.debug(f"This is the reagent type instance: {instance.__dict__}")
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try:
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assoc = lookup_reagenttype_kittype_association(ctx=ctx, reagent_type=instance, kit_type=kit)
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except StatementError:
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assoc = None
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if assoc == None:
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assoc = KitTypeReagentTypeAssociation(kit_type=kit, reagent_type=instance, uses=self.uses, required=self.required)
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kit.kit_reagenttype_associations.append(assoc)
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return instance
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class PydKit(BaseModel):
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name: str
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reagent_types: List[PydReagentType]|None
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def toSQL(self, ctx):
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instance = lookup_kit_types(ctx=ctx, name=self.name)
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if instance == None:
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instance = KitType(name=self.name)
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instance.reagent_types = [item.toSQL(ctx, instance) for item in self.reagent_types]
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return instance
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