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Preparation for code cleanup

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This commit is contained in:
Landon Wark
2023-03-08 09:02:32 -06:00
parent 82d5378479
commit 285ccecd73
2 changed files with 50 additions and 40 deletions
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43
src/submissions/frontend/__init__.py
View File

@@ -30,7 +30,7 @@ from backend.db import (construct_submission_info, lookup_reagent,
)
from backend.db import lookup_kittype_by_name
from .functions import check_kit_integrity
from .functions import check_kit_integrity, insert_reagent_import
from tools import check_not_nan, create_reagent_list
from backend.excel.reports import make_report_xlsx, make_report_html
@@ -138,40 +138,7 @@ class App(QMainWindow):
about = AlertPop(message=output, status="information")
about.exec()
def insert_reagent_import(self, item:str, prsr:SheetParser|None=None) -> QComboBox:
add_widget = QComboBox()
add_widget.setEditable(True)
# Ensure that all reagenttypes have a name that matches the items in the excel parser
query_var = item.replace("lot_", "")
logger.debug(f"Query for: {query_var}")
if prsr != None:
if isinstance(prsr.sub[item], numpy.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=self.ctx, type_name=query_var)]#, kit_name=prsr.sub['extraction_kit'])]
output_reg = []
for reagent in relevant_reagents:
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 items
if prsr != None:
logger.debug(f"Relevant reagents for {prsr.sub[item]}: {relevant_reagents}")
if str(prsr.sub[item]['lot']) not in relevant_reagents and prsr.sub[item]['lot'] != 'nan':
if check_not_nan(prsr.sub[item]['lot']):
relevant_reagents.insert(0, str(prsr.sub[item]['lot']))
logger.debug(f"New relevant reagents: {relevant_reagents}")
add_widget.addItems(relevant_reagents)
return add_widget
def importSubmission(self):
"""
@@ -257,7 +224,7 @@ class App(QMainWindow):
except:
add_widget.setDate(date.today())
case 'reagent':
# TODO make this a function so I can add in missing reagents below when checking kit integrity.
# create label
self.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
# add_widget = QComboBox()
@@ -290,7 +257,7 @@ class App(QMainWindow):
# relevant_reagents.insert(0, str(prsr.sub[item]['lot']))
# logger.debug(f"New relevant reagents: {relevant_reagents}")
# add_widget.addItems(relevant_reagents)
add_widget = self.insert_reagent_import(item, prsr=prsr)
add_widget = insert_reagent_import(ctx=self.ctx, item=item, prsr=prsr)
self.reagents[item] = prsr.sub[item]
case 'samples':
# hold samples in 'self' until form submitted
@@ -311,7 +278,7 @@ class App(QMainWindow):
msg.exec()
for item in kit_integrity['missing']:
self.table_widget.formlayout.addWidget(QLabel(f"Lot {item.replace('_', ' ').title()}"))
add_widget =self.insert_reagent_import(item)
add_widget = insert_reagent_import(ctx=self.ctx, item=item)
self.table_widget.formlayout.addWidget(add_widget)
# create submission button
submit_btn = QPushButton("Submit")

47
src/submissions/frontend/functions.py
View File

@@ -1,8 +1,19 @@
# from ..models import *
from backend.db.models import *
from backend.db import lookup_regent_by_type_name
from tools import check_not_nan
# from backend.db import lookup_kittype_by_name
import logging
import numpy as np
from backend.excel.parser import SheetParser
from PyQt6.QtWidgets import (
QMainWindow, QLabel, QToolBar,
QTabWidget, QWidget, QVBoxLayout,
QPushButton, QFileDialog,
QLineEdit, QMessageBox, QComboBox, QDateEdit, QHBoxLayout,
QSpinBox, QScrollArea
)
logger = logging.getLogger(f"submissions.{__name__}")
@@ -28,6 +39,38 @@ def check_kit_integrity(sub:BasicSubmission|KitType, reagenttypes:list|None=None
return result
def insert_reagent_import(ctx:dict, item:str, prsr:SheetParser|None=None) -> QComboBox:
add_widget = QComboBox()
add_widget.setEditable(True)
# Ensure that all reagenttypes have a name that matches the items in the excel parser
query_var = item.replace("lot_", "")
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'])]
output_reg = []
for reagent in relevant_reagents:
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 items
if prsr != None:
logger.debug(f"Relevant reagents for {prsr.sub[item]}: {relevant_reagents}")
if str(prsr.sub[item]['lot']) not in relevant_reagents and prsr.sub[item]['lot'] != 'nan':
if check_not_nan(prsr.sub[item]['lot']):
relevant_reagents.insert(0, str(prsr.sub[item]['lot']))
logger.debug(f"New relevant reagents: {relevant_reagents}")
add_widget.addItems(relevant_reagents)
return add_widget