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Pydantic added for validation.

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Landon Wark
2023-07-07 14:27:26 -05:00
parent 0c81c74f70
commit 1c804bfc6a
12 changed files with 497 additions and 141 deletions
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127
src/submissions/frontend/custom_widgets/misc.py
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@@ -2,20 +2,23 @@
Contains miscellaneous widgets for frontend functions
'''
from datetime import date
import typing
import difflib
from typing import Tuple
from PyQt6.QtWidgets import (
QLabel, QVBoxLayout,
QLineEdit, QComboBox, QDialog,
QDialogButtonBox, QDateEdit, QSizePolicy, QWidget,
QGridLayout, QPushButton, QSpinBox, QDoubleSpinBox,
QHBoxLayout,
QHBoxLayout, QMainWindow
)
from PyQt6.QtCore import Qt, QDate, QSize
# from submissions.backend.db.functions import lookup_kittype_by_use
# from submissions.backend.db import lookup_regent_by_type_name_and_kit_name
from tools import check_not_nan
from ..all_window_functions import extract_form_info
from backend.db import get_all_reagenttype_names, lookup_all_sample_types, create_kit_from_yaml, lookup_regent_by_type_name, lookup_kittype_by_use#, lookup_regent_by_type_name_and_kit_name
from backend.db import get_all_reagenttype_names, lookup_all_sample_types, create_kit_from_yaml, \
lookup_regent_by_type_name, lookup_kittype_by_use, lookup_all_orgs
#, lookup_regent_by_type_name_and_kit_name
from backend.excel.parser import SheetParser
from jinja2 import Environment, FileSystemLoader
import sys
@@ -297,55 +300,103 @@ class ControlsDatePicker(QWidget):
return QSize(80,20)
# class ImportReagent(QComboBox):
# def __init__(self, ctx:dict, item:str, prsr:SheetParser|None=None):
# super().__init__()
# self.setEditable(True)
# # Ensure that all reagenttypes have a name that matches the items in the excel parser
# query_var = item.replace("lot_", "")
# if prsr != None:
# logger.debug(f"Import Reagent is looking at: {prsr.sub[item]} for {item}")
# else:
# logger.debug(f"Import Reagent is going to retrieve all reagents for {item}")
# logger.debug(f"Query for: {query_var}")
# if prsr != None:
# if isinstance(prsr.sub[item], np.float64):
# logger.debug(f"{prsr.sub[item]['lot']} is a numpy float!")
# try:
# prsr.sub[item] = int(prsr.sub[item]['lot'])
# except ValueError:
# pass
# # query for reagents using type name from sheet and kit from sheet
# logger.debug(f"Attempting lookup of reagents by type: {query_var}")
# # below was lookup_reagent_by_type_name_and_kit_name, but I couldn't get it to work.
# relevant_reagents = [item.__str__() for item in lookup_regent_by_type_name(ctx=ctx, type_name=query_var)]#, kit_name=prsr.sub['extraction_kit'])]
# # relevant_reagents = [item.__str__() for item in lookup_regent_by_type_name_and_kit_name(ctx=ctx, type_name=query_var, kit_name=prsr.sub['extraction_kit'])]
# output_reg = []
# for reagent in relevant_reagents:
# # extract strings from any sets.
# if isinstance(reagent, set):
# for thing in reagent:
# output_reg.append(thing)
# elif isinstance(reagent, str):
# output_reg.append(reagent)
# relevant_reagents = output_reg
# # if reagent in sheet is not found insert it into the front of relevant reagents so it shows
# if prsr != None:
# logger.debug(f"Relevant reagents for {prsr.sub[item]}: {relevant_reagents}")
# if str(prsr.sub[item]['lot']) not in relevant_reagents:
# if check_not_nan(prsr.sub[item]['lot']):
# relevant_reagents.insert(0, str(prsr.sub[item]['lot']))
# else:
# if len(relevant_reagents) > 1:
# logger.debug(f"Found {prsr.sub[item]['lot']} in relevant reagents: {relevant_reagents}. Moving to front of list.")
# idx = relevant_reagents.index(str(prsr.sub[item]['lot']))
# logger.debug(f"The index we got for {prsr.sub[item]['lot']} in {relevant_reagents} was {idx}")
# moved_reag = relevant_reagents.pop(idx)
# relevant_reagents.insert(0, moved_reag)
# else:
# logger.debug(f"Found {prsr.sub[item]['lot']} in relevant reagents: {relevant_reagents}. But no need to move due to short list.")
# logger.debug(f"New relevant reagents: {relevant_reagents}")
# self.setObjectName(f"lot_{item}")
# self.addItems(relevant_reagents)
class ImportReagent(QComboBox):
def __init__(self, ctx:dict, item:str, prsr:SheetParser|None=None):
def __init__(self, ctx:dict, reagent:dict):
super().__init__()
self.setEditable(True)
# Ensure that all reagenttypes have a name that matches the items in the excel parser
query_var = item.replace("lot_", "")
if prsr != None:
logger.debug(f"Import Reagent is looking at: {prsr.sub[item]} for {item}")
else:
logger.debug(f"Import Reagent is going to retrieve all reagents for {item}")
logger.debug(f"Query for: {query_var}")
if prsr != None:
if isinstance(prsr.sub[item], np.float64):
logger.debug(f"{prsr.sub[item]['lot']} is a numpy float!")
try:
prsr.sub[item] = int(prsr.sub[item]['lot'])
except ValueError:
pass
query_var = reagent['type']
logger.debug(f"Import Reagent is looking at: {reagent['lot']} for {reagent['type']}")
if isinstance(reagent['lot'], np.float64):
logger.debug(f"{reagent['lot']} is a numpy float!")
try:
reagent['lot'] = int(reagent['lot'])
except ValueError:
pass
# query for reagents using type name from sheet and kit from sheet
logger.debug(f"Attempting lookup of reagents by type: {query_var}")
# below was lookup_reagent_by_type_name_and_kit_name, but I couldn't get it to work.
relevant_reagents = [item.__str__() for item in lookup_regent_by_type_name(ctx=ctx, type_name=query_var)]#, kit_name=prsr.sub['extraction_kit'])]
# relevant_reagents = [item.__str__() for item in lookup_regent_by_type_name_and_kit_name(ctx=ctx, type_name=query_var, kit_name=prsr.sub['extraction_kit'])]
output_reg = []
for reagent in relevant_reagents:
for rel_reagent in relevant_reagents:
# extract strings from any sets.
if isinstance(reagent, set):
for thing in reagent:
if isinstance(rel_reagent, set):
for thing in rel_reagent:
output_reg.append(thing)
elif isinstance(reagent, str):
output_reg.append(reagent)
elif isinstance(rel_reagent, str):
output_reg.append(rel_reagent)
relevant_reagents = output_reg
# if reagent in sheet is not found insert it into the front of relevant reagents so it shows
if prsr != None:
logger.debug(f"Relevant reagents for {prsr.sub[item]}: {relevant_reagents}")
if str(prsr.sub[item]['lot']) not in relevant_reagents:
if check_not_nan(prsr.sub[item]['lot']):
relevant_reagents.insert(0, str(prsr.sub[item]['lot']))
# if prsr != None:
logger.debug(f"Relevant reagents for {reagent['lot']}: {relevant_reagents}")
if str(reagent['lot']) not in relevant_reagents:
if check_not_nan(reagent['lot']):
relevant_reagents.insert(0, str(reagent['lot']))
else:
if len(relevant_reagents) > 1:
logger.debug(f"Found {reagent['lot']} in relevant reagents: {relevant_reagents}. Moving to front of list.")
idx = relevant_reagents.index(str(reagent['lot']))
logger.debug(f"The index we got for {reagent['lot']} in {relevant_reagents} was {idx}")
moved_reag = relevant_reagents.pop(idx)
relevant_reagents.insert(0, moved_reag)
else:
if len(relevant_reagents) > 1:
logger.debug(f"Found {prsr.sub[item]['lot']} in relevant reagents: {relevant_reagents}. Moving to front of list.")
idx = relevant_reagents.index(str(prsr.sub[item]['lot']))
logger.debug(f"The index we got for {prsr.sub[item]['lot']} in {relevant_reagents} was {idx}")
moved_reag = relevant_reagents.pop(idx)
relevant_reagents.insert(0, moved_reag)
else:
logger.debug(f"Found {prsr.sub[item]['lot']} in relevant reagents: {relevant_reagents}. But no need to move due to short list.")
logger.debug(f"Found {reagent['lot']} in relevant reagents: {relevant_reagents}. But no need to move due to short list.")
logger.debug(f"New relevant reagents: {relevant_reagents}")
self.setObjectName(f"lot_{item}")
self.addItems(relevant_reagents)
self.setObjectName(f"lot_{reagent['type']}")
self.addItems(relevant_reagents)