670 lines
27 KiB
Python
670 lines
27 KiB
Python
'''
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All database related operations.
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'''
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from .functions import *
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# from . import models
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# from .models.kits import reagenttypes_kittypes
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# from .models.submissions import reagents_submissions
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# import pandas as pd
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# import sqlalchemy.exc
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# import sqlite3
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# import logging
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# from datetime import date, datetime, timedelta
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# from sqlalchemy import and_
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# import uuid
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# # import base64
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# from sqlalchemy import JSON, event
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# from sqlalchemy.engine import Engine
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# import json
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# # from dateutil.relativedelta import relativedelta
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# from getpass import getuser
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# import numpy as np
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# from tools import check_not_nan, check_is_power_user
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# import yaml
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# from pathlib import Path
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# logger = logging.getLogger(f"submissions.{__name__}")
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# # The below _should_ allow automatic creation of foreign keys in the database
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# @event.listens_for(Engine, "connect")
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# def set_sqlite_pragma(dbapi_connection, connection_record):
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# cursor = dbapi_connection.cursor()
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# cursor.execute("PRAGMA foreign_keys=ON")
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# cursor.close()
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# def store_submission(ctx:dict, base_submission:models.BasicSubmission) -> None|dict:
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# """
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# Upserts submissions into database
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# Args:
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# ctx (dict): settings passed down from gui
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# base_submission (models.BasicSubmission): submission to be add to db
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# Returns:
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# None|dict : object that indicates issue raised for reporting in gui
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# """
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# logger.debug(f"Hello from store_submission")
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# # Add all samples to sample table
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# for sample in base_submission.samples:
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# sample.rsl_plate = base_submission
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# logger.debug(f"Attempting to add sample: {sample.to_string()}")
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# try:
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# ctx['database_session'].add(sample)
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# except (sqlite3.IntegrityError, sqlalchemy.exc.IntegrityError) as e:
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# logger.debug(f"Hit an integrity error : {e}")
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# continue
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# # Add submission to submission table
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# ctx['database_session'].add(base_submission)
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# logger.debug(f"Attempting to add submission: {base_submission.rsl_plate_num}")
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# try:
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# ctx['database_session'].commit()
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# except (sqlite3.IntegrityError, sqlalchemy.exc.IntegrityError) as e:
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# logger.debug(f"Hit an integrity error : {e}")
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# ctx['database_session'].rollback()
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# return {"message":"This plate number already exists, so we can't add it."}
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# except (sqlite3.OperationalError, sqlalchemy.exc.IntegrityError) as e:
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# logger.debug(f"Hit an operational error: {e}")
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# ctx['database_session'].rollback()
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# return {"message":"The database is locked for editing."}
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# return None
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# def store_reagent(ctx:dict, reagent:models.Reagent) -> None|dict:
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# """
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# Inserts a reagent into the database.
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# Args:
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# ctx (dict): settings passed down from gui
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# reagent (models.Reagent): Reagent object to be added to db
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# Returns:
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# None|dict: object indicating issue to be reported in the gui
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# """
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# logger.debug(f"Reagent dictionary: {reagent.__dict__}")
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# ctx['database_session'].add(reagent)
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# try:
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# ctx['database_session'].commit()
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# except (sqlite3.OperationalError, sqlalchemy.exc.OperationalError):
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# return {"message":"The database is locked for editing."}
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# return None
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# def construct_submission_info(ctx:dict, info_dict:dict) -> models.BasicSubmission:
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# """
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# Construct submission object from dictionary
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# Args:
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# ctx (dict): settings passed down from gui
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# info_dict (dict): dictionary to be transformed
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# Returns:
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# models.BasicSubmission: Constructed submission object
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# """
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# # convert submission type into model name
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# query = info_dict['submission_type'].replace(" ", "")
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# # Ensure an rsl plate number exists for the plate
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# if info_dict["rsl_plate_num"] == 'nan' or info_dict["rsl_plate_num"] == None or not check_not_nan(info_dict["rsl_plate_num"]):
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# instance = None
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# msg = "A proper RSL plate number is required."
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# return instance, {'code': 2, 'message': "A proper RSL plate number is required."}
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# # check database for existing object
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# instance = ctx['database_session'].query(models.BasicSubmission).filter(models.BasicSubmission.rsl_plate_num==info_dict['rsl_plate_num']).first()
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# # get model based on submission type converted above
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# logger.debug(f"Looking at models for submission type: {query}")
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# model = getattr(models, query)
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# logger.debug(f"We've got the model: {type(model)}")
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# info_dict['submission_type'] = info_dict['submission_type'].replace(" ", "_").lower()
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# # if query return nothing, ie doesn't already exist in db
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# if instance == None:
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# instance = model()
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# logger.debug(f"Submission doesn't exist yet, creating new instance: {instance}")
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# msg = None
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# code = 0
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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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# for item in info_dict:
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# logger.debug(f"Setting {item} to {info_dict[item]}")
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# # set fields based on keys in dictionary
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# match item:
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# case "extraction_kit":
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# q_str = info_dict[item]
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# logger.debug(f"Looking up kit {q_str}")
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# try:
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# field_value = lookup_kittype_by_name(ctx=ctx, name=q_str)
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# except (sqlite3.IntegrityError, sqlalchemy.exc.IntegrityError) as e:
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# logger.error(f"Hit an integrity error: {e}")
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# logger.debug(f"Got {field_value} for kit {q_str}")
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# case "submitting_lab":
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# q_str = info_dict[item].replace(" ", "_").lower()
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# logger.debug(f"Looking up organization: {q_str}")
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# field_value = lookup_org_by_name(ctx=ctx, name=q_str)
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# logger.debug(f"Got {field_value} for organization {q_str}")
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# case "submitter_plate_num":
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# # Because of unique constraint, there will be problems with
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# # multiple submissions named 'None', so...
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# logger.debug(f"Submitter plate id: {info_dict[item]}")
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# if info_dict[item] == None or info_dict[item] == "None":
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# logger.debug(f"Got None as a submitter plate number, inserting random string to preserve database unique constraint.")
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# info_dict[item] = uuid.uuid4().hex.upper()
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# field_value = info_dict[item]
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# case _:
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# field_value = info_dict[item]
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# # insert into field
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# try:
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# setattr(instance, item, field_value)
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# except AttributeError:
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# logger.debug(f"Could not set attribute: {item} to {info_dict[item]}")
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# continue
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# # calculate cost of the run: immutable cost + mutable times number of columns
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# # This is now attached to submission upon creation to preserve at-run costs incase of cost increase in the future.
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# try:
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# instance.run_cost = instance.extraction_kit.immutable_cost + (instance.extraction_kit.mutable_cost * ((instance.sample_count / 8)/12))
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# except (TypeError, AttributeError):
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# logger.debug(f"Looks like that kit doesn't have cost breakdown yet, using full plate cost.")
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# instance.run_cost = instance.extraction_kit.cost_per_run
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# # We need to make sure there's a proper rsl plate number
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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 {info_dict['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 construct_reagent(ctx:dict, info_dict:dict) -> models.Reagent:
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# """
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# Construct reagent object from dictionary
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# Args:
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# ctx (dict): settings passed down from gui
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# info_dict (dict): dictionary to be converted
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# Returns:
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# models.Reagent: Constructed reagent object
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# """
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# reagent = models.Reagent()
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# for item in info_dict:
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# logger.debug(f"Reagent info item: {item}")
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# # set fields based on keys in dictionary
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# match item:
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# case "lot":
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# reagent.lot = info_dict[item].upper()
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# case "expiry":
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# reagent.expiry = info_dict[item]
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# case "type":
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# reagent.type = lookup_reagenttype_by_name(ctx=ctx, rt_name=info_dict[item].replace(" ", "_").lower())
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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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# # try:
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# # reagent.expiry = reagent.expiry + reagent.type.eol_ext
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# # except TypeError as e:
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# # logger.debug(f"We got a type error: {e}.")
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# # except AttributeError:
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# # pass
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# return reagent
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# def lookup_reagent(ctx:dict, reagent_lot:str) -> models.Reagent:
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# """
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# Query db for reagent based on lot number
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# Args:
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# ctx (dict): settings passed down from gui
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# reagent_lot (str): lot number to query
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# Returns:
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# models.Reagent: looked up reagent
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# """
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# lookedup = ctx['database_session'].query(models.Reagent).filter(models.Reagent.lot==reagent_lot).first()
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# return lookedup
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# def get_all_reagenttype_names(ctx:dict) -> list[str]:
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# """
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# Lookup all reagent types and get names
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# Args:
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# ctx (dict): settings passed from gui
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# Returns:
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# list[str]: reagent type names
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# """
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# lookedup = [item.__str__() for item in ctx['database_session'].query(models.ReagentType).all()]
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# return lookedup
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# def lookup_reagenttype_by_name(ctx:dict, rt_name:str) -> models.ReagentType:
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# """
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# Lookup a single reagent type by name
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# Args:
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# ctx (dict): settings passed from gui
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# rt_name (str): reagent type name to look up
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# Returns:
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# models.ReagentType: looked up reagent type
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# """
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# logger.debug(f"Looking up ReagentType by name: {rt_name}")
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# lookedup = ctx['database_session'].query(models.ReagentType).filter(models.ReagentType.name==rt_name).first()
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# logger.debug(f"Found ReagentType: {lookedup}")
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# return lookedup
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# def lookup_kittype_by_use(ctx:dict, used_by:str) -> list[models.KitType]:
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# """
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# Lookup kits by a sample type its used for
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# Args:
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# ctx (dict): settings passed from gui
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# used_by (str): sample type (should be string in D3 of excel sheet)
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# Returns:
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# list[models.KitType]: list of kittypes that have that sample type in their uses
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# """
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# return ctx['database_session'].query(models.KitType).filter(models.KitType.used_for.contains(used_by)).all()
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# def lookup_kittype_by_name(ctx:dict, name:str) -> models.KitType:
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# """
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# Lookup a kit type by name
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# Args:
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# ctx (dict): settings passed from bui
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# name (str): name of kit to query
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# Returns:
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# models.KitType: retrieved kittype
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# """
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# logger.debug(f"Querying kittype: {name}")
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# return ctx['database_session'].query(models.KitType).filter(models.KitType.name==name).first()
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# def lookup_regent_by_type_name(ctx:dict, type_name:str) -> list[models.Reagent]:
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# """
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# Lookup reagents by their type name
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# Args:
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# ctx (dict): settings passed from gui
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# type_name (str): reagent type name
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# Returns:
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# list[models.Reagent]: list of retrieved reagents
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# """
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# return ctx['database_session'].query(models.Reagent).join(models.Reagent.type, aliased=True).filter(models.ReagentType.name==type_name).all()
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# def lookup_regent_by_type_name_and_kit_name(ctx:dict, type_name:str, kit_name:str) -> list[models.Reagent]:
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# """
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# Lookup reagents by their type name and kits they belong to (Broken... maybe cursed, I'm not sure.)
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# Args:
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# ctx (dict): settings pass by gui
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# type_name (str): reagent type name
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# kit_name (str): kit name
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# Returns:
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# list[models.Reagent]: list of retrieved reagents
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# """
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# # What I want to do is get the reagent type by name
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# # Hang on, this is going to be a long one.
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# # by_type = ctx['database_session'].query(models.Reagent).join(models.Reagent.type, aliased=True).filter(models.ReagentType.name.endswith(type_name)).all()
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# rt_types = ctx['database_session'].query(models.ReagentType).filter(models.ReagentType.name.endswith(type_name))
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# # add filter for kit name...
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# try:
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# check = not np.isnan(kit_name)
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# except TypeError:
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# check = True
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# if check:
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# kit_type = lookup_kittype_by_name(ctx=ctx, name=kit_name)
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# logger.debug(f"reagenttypes: {[item.name for item in rt_types.all()]}, kit: {kit_type.name}")
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# # add in lookup for related kit_id
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# rt_types = rt_types.join(reagenttypes_kittypes).filter(reagenttypes_kittypes.c.kits_id==kit_type.id).first()
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# else:
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# rt_types = rt_types.first()
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# output = rt_types.instances
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# return output
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# def lookup_all_submissions_by_type(ctx:dict, sub_type:str|None=None) -> list[models.BasicSubmission]:
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# """
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# Get all submissions, filtering by type if given
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# Args:
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# ctx (dict): settings pass from gui
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# type (str | None, optional): submission type (should be string in D3 of excel sheet). Defaults to None.
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# Returns:
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# list[models.BasicSubmission]: list of retrieved submissions
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# """
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# if sub_type == None:
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# subs = ctx['database_session'].query(models.BasicSubmission).all()
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# else:
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# subs = ctx['database_session'].query(models.BasicSubmission).filter(models.BasicSubmission.submission_type==sub_type.lower().replace(" ", "_")).all()
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# return subs
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# def lookup_all_orgs(ctx:dict) -> list[models.Organization]:
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# """
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# Lookup all organizations (labs)
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# Args:
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# ctx (dict): settings passed from gui
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# Returns:
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# list[models.Organization]: list of retrieved organizations
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# """
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# return ctx['database_session'].query(models.Organization).all()
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# def lookup_org_by_name(ctx:dict, name:str|None) -> models.Organization:
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# """
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# Lookup organization (lab) by (startswith) name.
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# Args:
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# ctx (dict): settings passed from gui
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# name (str | None): name of organization
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# Returns:
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# models.Organization: retrieved organization
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# """
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# logger.debug(f"Querying organization: {name}")
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# return ctx['database_session'].query(models.Organization).filter(models.Organization.name.startswith(name)).first()
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# def submissions_to_df(ctx:dict, sub_type:str|None=None) -> pd.DataFrame:
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# """
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# Convert submissions looked up by type to dataframe
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# Args:
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# ctx (dict): settings passed by gui
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# type (str | None, optional): submission type (should be string in D3 of excel sheet) Defaults to None.
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# Returns:
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# pd.DataFrame: dataframe constructed from retrieved submissions
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# """
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# logger.debug(f"Type: {sub_type}")
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# # use lookup function to create list of dicts
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# subs = [item.to_dict() for item in lookup_all_submissions_by_type(ctx=ctx, sub_type=sub_type)]
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# # make df from dicts (records) in list
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# df = pd.DataFrame.from_records(subs)
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# # Exclude sub information
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# try:
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# df = df.drop("controls", axis=1)
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# except:
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# logger.warning(f"Couldn't drop 'controls' column from submissionsheet df.")
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# try:
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# df = df.drop("ext_info", axis=1)
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# except:
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# logger.warning(f"Couldn't drop 'controls' column from submissionsheet df.")
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# return df
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# def lookup_submission_by_id(ctx:dict, id:int) -> models.BasicSubmission:
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# """
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# Lookup submission by id number
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# Args:
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# ctx (dict): settings passed from gui
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# id (int): submission id number
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# Returns:
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# models.BasicSubmission: retrieved submission
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# """
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# return ctx['database_session'].query(models.BasicSubmission).filter(models.BasicSubmission.id==id).first()
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# def lookup_submissions_by_date_range(ctx:dict, start_date:datetime.date, end_date:datetime.date) -> list[models.BasicSubmission]:
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# """
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# Lookup submissions greater than start_date and less than end_date
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# Args:
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# ctx (dict): settings passed from gui
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# start_date (datetime.date): date to start looking
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# end_date (datetime.date): date to end looking
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# Returns:
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# list[models.BasicSubmission]: list of retrieved submissions
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# """
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# # return ctx['database_session'].query(models.BasicSubmission).filter(and_(models.BasicSubmission.submitted_date > start_date, models.BasicSubmission.submitted_date < end_date)).all()
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# start_date = start_date.strftime("%Y-%m-%d")
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# end_date = end_date.strftime("%Y-%m-%d")
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# return ctx['database_session'].query(models.BasicSubmission).filter(models.BasicSubmission.submitted_date.between(start_date, end_date)).all()
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# def get_all_Control_Types_names(ctx:dict) -> list[str]:
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# """
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# Grabs all control type names from db.
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# Args:
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# settings (dict): settings passed down from gui.
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# Returns:
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# list: list of controltype names
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# """
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# conTypes = ctx['database_session'].query(models.ControlType).all()
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# conTypes = [conType.name for conType in conTypes]
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# logger.debug(f"Control Types: {conTypes}")
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# return conTypes
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# def create_kit_from_yaml(ctx:dict, exp:dict) -> dict:
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# """
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# Create and store a new kit in the database based on a .yml file
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# TODO: split into create and store functions
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# Args:
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# ctx (dict): Context dictionary passed down from frontend
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# exp (dict): Experiment dictionary created from yaml file
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# Returns:
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# dict: a dictionary containing results of db addition
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# """
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# # Don't want just anyone adding kits
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# if not check_is_power_user(ctx=ctx):
|
|
# logger.debug(f"{getuser()} does not have permission to add kits.")
|
|
# return {'code':1, 'message':"This user does not have permission to add kits.", "status":"warning"}
|
|
# # iterate through keys in dict
|
|
# for type in exp:
|
|
# if type == "password":
|
|
# continue
|
|
# # A submission type may use multiple kits.
|
|
# for kt in exp[type]['kits']:
|
|
# kit = models.KitType(name=kt, used_for=[type.replace("_", " ").title()], constant_cost=exp[type]["kits"][kt]["constant_cost"], mutable_cost=exp[type]["kits"][kt]["mutable_cost"])
|
|
# # A kit contains multiple reagent types.
|
|
# for r in exp[type]['kits'][kt]['reagenttypes']:
|
|
# # check if reagent type already exists.
|
|
# look_up = ctx['database_session'].query(models.ReagentType).filter(models.ReagentType.name==r).first()
|
|
# if look_up == None:
|
|
# rt = models.ReagentType(name=r.replace(" ", "_").lower(), eol_ext=timedelta(30*exp[type]['kits'][kt]['reagenttypes'][r]['eol_ext']), kits=[kit])
|
|
# else:
|
|
# rt = look_up
|
|
# rt.kits.append(kit)
|
|
# # add this because I think it's necessary to get proper back population
|
|
# kit.reagent_types_id.append(rt.id)
|
|
# ctx['database_session'].add(rt)
|
|
# logger.debug(f"Kit construction reagent type: {rt.__dict__}")
|
|
# logger.debug(f"Kit construction kit: {kit.__dict__}")
|
|
# ctx['database_session'].add(kit)
|
|
# ctx['database_session'].commit()
|
|
# return {'code':0, 'message':'Kit has been added', 'status': 'information'}
|
|
|
|
|
|
# def create_org_from_yaml(ctx:dict, org:dict) -> dict:
|
|
# """
|
|
# Create and store a new organization based on a .yml file
|
|
|
|
# Args:
|
|
# ctx (dict): Context dictionary passed down from frontend
|
|
# org (dict): Dictionary containing organization info.
|
|
|
|
# Returns:
|
|
# dict: dictionary containing results of db addition
|
|
# """
|
|
# # Don't want just anyone adding in clients
|
|
# if not check_is_power_user(ctx=ctx):
|
|
# logger.debug(f"{getuser()} does not have permission to add kits.")
|
|
# return {'code':1, 'message':"This user does not have permission to add organizations."}
|
|
# # the yml can contain multiple clients
|
|
# for client in org:
|
|
# cli_org = models.Organization(name=client.replace(" ", "_").lower(), cost_centre=org[client]['cost centre'])
|
|
# # a client can contain multiple contacts
|
|
# for contact in org[client]['contacts']:
|
|
# cont_name = list(contact.keys())[0]
|
|
# # check if contact already exists
|
|
# look_up = ctx['database_session'].query(models.Contact).filter(models.Contact.name==cont_name).first()
|
|
# if look_up == None:
|
|
# cli_cont = models.Contact(name=cont_name, phone=contact[cont_name]['phone'], email=contact[cont_name]['email'], organization=[cli_org])
|
|
# else:
|
|
# cli_cont = look_up
|
|
# cli_cont.organization.append(cli_org)
|
|
# ctx['database_session'].add(cli_cont)
|
|
# logger.debug(f"Client creation contact: {cli_cont.__dict__}")
|
|
# logger.debug(f"Client creation client: {cli_org.__dict__}")
|
|
# ctx['database_session'].add(cli_org)
|
|
# ctx["database_session"].commit()
|
|
# return {"code":0, "message":"Organization has been added."}
|
|
|
|
|
|
# def lookup_all_sample_types(ctx:dict) -> list[str]:
|
|
# """
|
|
# Lookup all sample types and get names
|
|
|
|
# Args:
|
|
# ctx (dict): settings pass from gui
|
|
|
|
# Returns:
|
|
# list[str]: list of sample type names
|
|
# """
|
|
# uses = [item.used_for for item in ctx['database_session'].query(models.KitType).all()]
|
|
# # flattened list of lists
|
|
# uses = list(set([item for sublist in uses for item in sublist]))
|
|
# return uses
|
|
|
|
|
|
# def get_all_available_modes(ctx:dict) -> list[str]:
|
|
# """
|
|
# Get types of analysis for controls
|
|
|
|
# Args:
|
|
# ctx (dict): settings passed from gui
|
|
|
|
# Returns:
|
|
# list[str]: list of analysis types
|
|
# """
|
|
# # Only one control is necessary since they all share the same control types.
|
|
# rel = ctx['database_session'].query(models.Control).first()
|
|
# try:
|
|
# cols = [item.name for item in list(rel.__table__.columns) if isinstance(item.type, JSON)]
|
|
# except AttributeError as e:
|
|
# logger.debug(f"Failed to get available modes from db: {e}")
|
|
# cols = []
|
|
# return cols
|
|
|
|
|
|
# def get_all_controls_by_type(ctx:dict, con_type:str, start_date:date|None=None, end_date:date|None=None) -> list[models.Control]:
|
|
# """
|
|
# Returns a list of control objects that are instances of the input controltype.
|
|
# Between dates if supplied.
|
|
|
|
# Args:
|
|
# ctx (dict): Settings passed down from gui
|
|
# con_type (str): Name of control type.
|
|
# start_date (date | None, optional): Start date of query. Defaults to None.
|
|
# end_date (date | None, optional): End date of query. Defaults to None.
|
|
|
|
# Returns:
|
|
# list[models.Control]: list of control samples.
|
|
# """
|
|
# logger.debug(f"Using dates: {start_date} to {end_date}")
|
|
# if start_date != None and end_date != None:
|
|
# start_date = start_date.strftime("%Y-%m-%d")
|
|
# end_date = end_date.strftime("%Y-%m-%d")
|
|
# output = ctx['database_session'].query(models.Control).join(models.ControlType).filter_by(name=con_type).filter(models.Control.submitted_date.between(start_date, end_date)).all()
|
|
# else:
|
|
# output = ctx['database_session'].query(models.Control).join(models.ControlType).filter_by(name=con_type).all()
|
|
# logger.debug(f"Returned controls between dates: {output}")
|
|
# return output
|
|
|
|
|
|
# def get_control_subtypes(ctx:dict, type:str, mode:str) -> list[str]:
|
|
# """
|
|
# Get subtypes for a control analysis mode
|
|
|
|
# Args:
|
|
# ctx (dict): settings passed from gui
|
|
# type (str): control type name
|
|
# mode (str): analysis mode name
|
|
|
|
# Returns:
|
|
# list[str]: list of subtype names
|
|
# """
|
|
# # Only the first control of type is necessary since they all share subtypes
|
|
# try:
|
|
# outs = get_all_controls_by_type(ctx=ctx, con_type=type)[0]
|
|
# except TypeError:
|
|
# return []
|
|
# # Get analysis mode data as dict
|
|
# jsoner = json.loads(getattr(outs, mode))
|
|
# logger.debug(f"JSON out: {jsoner}")
|
|
# try:
|
|
# genera = list(jsoner.keys())[0]
|
|
# except IndexError:
|
|
# return []
|
|
# subtypes = [item for item in jsoner[genera] if "_hashes" not in item and "_ratio" not in item]
|
|
# return subtypes
|
|
|
|
|
|
# def get_all_controls(ctx:dict) -> list[models.Control]:
|
|
# """
|
|
# Retrieve a list of all controls from the database
|
|
|
|
# Args:
|
|
# ctx (dict): settings passed down from the gui.
|
|
|
|
# Returns:
|
|
# list[models.Control]: list of all control objects
|
|
# """
|
|
# return ctx['database_session'].query(models.Control).all()
|
|
|
|
|
|
# def lookup_submission_by_rsl_num(ctx:dict, rsl_num:str) -> models.BasicSubmission:
|
|
# """
|
|
# Retrieve a submission from the database based on rsl plate number
|
|
|
|
# Args:
|
|
# ctx (dict): settings passed down from gui
|
|
# rsl_num (str): rsl plate number
|
|
|
|
# Returns:
|
|
# models.BasicSubmission: Submissions object retrieved from database
|
|
# """
|
|
# return ctx['database_session'].query(models.BasicSubmission).filter(models.BasicSubmission.rsl_plate_num.startswith(rsl_num)).first()
|
|
|
|
|
|
# def lookup_submissions_using_reagent(ctx:dict, reagent:models.Reagent) -> list[models.BasicSubmission]:
|
|
# return ctx['database_session'].query(models.BasicSubmission).join(reagents_submissions).filter(reagents_submissions.c.reagent_id==reagent.id).all()
|
|
|
|
|
|
# def delete_submission_by_id(ctx:dict, id:int) -> None:
|
|
# """
|
|
# Deletes a submission and its associated samples from the database.
|
|
|
|
# Args:
|
|
# ctx (dict): settings passed down from gui
|
|
# id (int): id of submission to be deleted.
|
|
# """
|
|
# # In order to properly do this Im' going to have to delete all of the secondary table stuff as well.
|
|
# # Retrieve submission
|
|
# sub = ctx['database_session'].query(models.BasicSubmission).filter(models.BasicSubmission.id==id).first()
|
|
# # Convert to dict for storing backup as a yml
|
|
# backup = sub.to_dict()
|
|
# try:
|
|
# with open(Path(ctx['backup_path']).joinpath(f"{sub.rsl_plate_num}-backup({date.today().strftime('%Y%m%d')}).yml"), "w") as f:
|
|
# yaml.dump(backup, f)
|
|
# except KeyError:
|
|
# pass
|
|
# sub.reagents = []
|
|
# for sample in sub.samples:
|
|
# ctx['database_session'].delete(sample)
|
|
# ctx["database_session"].delete(sub)
|
|
# ctx["database_session"].commit() |