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Large scale refactor to improve db efficiency

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This commit is contained in:
Landon Wark
2023-09-27 14:16:28 -05:00
parent 82ab06efad
commit e484eabb22
37 changed files with 1782 additions and 1697 deletions
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67
src/submissions/frontend/custom_widgets/misc.py
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@@ -12,8 +12,8 @@ from PyQt6.QtWidgets import (
from PyQt6.QtCore import Qt, QDate, QSize
from tools import check_not_nan, jinja_template_loading, Settings
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_last_used_reagenttype_lot, lookup_all_reagent_names_by_role
from backend.db import construct_kit_from_yaml, \
lookup_reagent_types, lookup_reagents, lookup_submission_type, lookup_reagenttype_kittype_association
import logging
import numpy as np
from .pop_ups import AlertPop
@@ -27,7 +27,7 @@ class AddReagentForm(QDialog):
"""
dialog to add gather info about new reagent
"""
def __init__(self, ctx:dict, reagent_lot:str|None, reagent_type:str|None, expiry:date|None=None, reagent_name:str|None=None) -> None:
def __init__(self, ctx:dict, reagent_lot:str|None=None, reagent_type:str|None=None, expiry:date|None=None, reagent_name:str|None=None) -> None:
super().__init__()
self.ctx = ctx
if reagent_lot == None:
@@ -60,7 +60,7 @@ class AddReagentForm(QDialog):
# widget to get reagent type info
self.type_input = QComboBox()
self.type_input.setObjectName('type')
self.type_input.addItems([item for item in get_all_reagenttype_names(ctx=ctx)])
self.type_input.addItems([item.name for item in lookup_reagent_types(ctx=ctx)])
logger.debug(f"Trying to find index of {reagent_type}")
# convert input to user friendly string?
try:
@@ -85,9 +85,13 @@ class AddReagentForm(QDialog):
self.type_input.currentTextChanged.connect(self.update_names)
def update_names(self):
"""
Updates reagent names form field with examples from reagent type
"""
logger.debug(self.type_input.currentText())
self.name_input.clear()
self.name_input.addItems(item for item in lookup_all_reagent_names_by_role(ctx=self.ctx, role_name=self.type_input.currentText().replace(" ", "_").lower()))
lookup = lookup_reagents(ctx=self.ctx, reagent_type=self.type_input.currentText())
self.name_input.addItems(list(set([item.name for item in lookup])))
class ReportDatePicker(QDialog):
"""
@@ -103,17 +107,17 @@ class ReportDatePicker(QDialog):
self.buttonBox.accepted.connect(self.accept)
self.buttonBox.rejected.connect(self.reject)
# widgets to ask for dates
start_date = QDateEdit(calendarPopup=True)
start_date.setObjectName("start_date")
start_date.setDate(QDate.currentDate())
end_date = QDateEdit(calendarPopup=True)
end_date.setObjectName("end_date")
end_date.setDate(QDate.currentDate())
self.start_date = QDateEdit(calendarPopup=True)
self.start_date.setObjectName("start_date")
self.start_date.setDate(QDate.currentDate())
self.end_date = QDateEdit(calendarPopup=True)
self.end_date.setObjectName("end_date")
self.end_date.setDate(QDate.currentDate())
self.layout = QVBoxLayout()
self.layout.addWidget(QLabel("Start Date"))
self.layout.addWidget(start_date)
self.layout.addWidget(self.start_date)
self.layout.addWidget(QLabel("End Date"))
self.layout.addWidget(end_date)
self.layout.addWidget(self.end_date)
self.layout.addWidget(self.buttonBox)
self.setLayout(self.layout)
@@ -139,7 +143,8 @@ class KitAdder(QWidget):
used_for = QComboBox()
used_for.setObjectName("used_for")
# Insert all existing sample types
used_for.addItems(lookup_all_sample_types(ctx=parent_ctx))
# used_for.addItems(lookup_all_sample_types(ctx=parent_ctx))
used_for.addItems([item.name for item in lookup_submission_type(ctx=parent_ctx)])
used_for.setEditable(True)
self.grid.addWidget(used_for,3,1)
# set cost per run
@@ -203,7 +208,7 @@ class KitAdder(QWidget):
yml_type[used]['kits'][info['kit_name']]['reagenttypes'] = reagents
logger.debug(yml_type)
# send to kit constructor
result = create_kit_from_yaml(ctx=self.ctx, exp=yml_type)
result = construct_kit_from_yaml(ctx=self.ctx, exp=yml_type)
msg = AlertPop(message=result['message'], status=result['status'])
msg.exec()
self.__init__(self.ctx)
@@ -212,20 +217,22 @@ class ReagentTypeForm(QWidget):
"""
custom widget to add information about a new reagenttype
"""
def __init__(self, parent_ctx:dict) -> None:
def __init__(self, ctx:dict) -> None:
super().__init__()
grid = QGridLayout()
self.setLayout(grid)
grid.addWidget(QLabel("Name (*Exactly* as it appears in the excel submission form):"),0,0)
# Widget to get reagent info
reagent_getter = QComboBox()
reagent_getter.setObjectName("name")
self.reagent_getter = QComboBox()
self.reagent_getter.setObjectName("name")
# lookup all reagent type names from db
reagent_getter.addItems(get_all_reagenttype_names(ctx=parent_ctx))
reagent_getter.setEditable(True)
grid.addWidget(reagent_getter,0,1)
lookup = lookup_reagent_types(ctx=ctx)
logger.debug(f"Looked up ReagentType names: {lookup}")
self.reagent_getter.addItems([item.__str__() for item in lookup])
self.reagent_getter.setEditable(True)
grid.addWidget(self.reagent_getter,0,1)
grid.addWidget(QLabel("Extension of Life (months):"),0,2)
# widget toget extension of life
# widget to get extension of life
eol = QSpinBox()
eol.setObjectName('eol')
eol.setMinimum(0)
@@ -257,12 +264,14 @@ class ControlsDatePicker(QWidget):
class ImportReagent(QComboBox):
def __init__(self, ctx:dict, reagent:PydReagent, extraction_kit:str):
def __init__(self, ctx:Settings, reagent:dict|PydReagent, extraction_kit:str):
super().__init__()
self.setEditable(True)
if isinstance(reagent, dict):
reagent = PydReagent(**reagent)
# Ensure that all reagenttypes have a name that matches the items in the excel parser
query_var = reagent.type
logger.debug(f"Import Reagent is looking at: {reagent.lot} for {reagent.type}")
logger.debug(f"Import Reagent is looking at: {reagent.lot} for {query_var}")
if isinstance(reagent.lot, np.float64):
logger.debug(f"{reagent.lot} is a numpy float!")
try:
@@ -272,7 +281,8 @@ class ImportReagent(QComboBox):
# 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)]
lookup = lookup_reagents(ctx=ctx, reagent_type=query_var)
relevant_reagents = [item.__str__() for item in lookup]
output_reg = []
for rel_reagent in relevant_reagents:
# extract strings from any sets.
@@ -289,7 +299,8 @@ class ImportReagent(QComboBox):
relevant_reagents.insert(0, str(reagent.lot))
else:
# TODO: look up the last used reagent of this type in the database
looked_up_reg = lookup_last_used_reagenttype_lot(ctx=ctx, type_name=reagent.type, extraction_kit=extraction_kit)
looked_up_rt = lookup_reagenttype_kittype_association(ctx=ctx, reagent_type=reagent.type, kit_type=extraction_kit)
looked_up_reg = lookup_reagents(ctx=ctx, lot_number=looked_up_rt.last_used)
logger.debug(f"Because there was no reagent listed for {reagent}, we will insert the last lot used: {looked_up_reg}")
if looked_up_reg != None:
relevant_reagents.remove(str(looked_up_reg.lot))
@@ -309,12 +320,14 @@ class ImportReagent(QComboBox):
class ParsedQLabel(QLabel):
def __init__(self, input_object, field_name, title:bool=True):
def __init__(self, input_object, field_name, title:bool=True, label_name:str|None=None):
super().__init__()
try:
check = input_object['parsed']
except:
return
if label_name != None:
self.setObjectName(label_name)
if title:
output = field_name.replace('_', ' ').title()
else: