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Major refactor for improved documentation and readability

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This commit is contained in:
Landon Wark
2023-03-17 15:23:22 -05:00
parent c645d3a9cf
commit 9c9c373830
29 changed files with 1828 additions and 1236 deletions
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19
src/submissions/frontend/__init__.py
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@@ -1,3 +1,6 @@
'''
Operations for all user interactions.
'''
import json
import re
from PyQt6.QtWidgets import (
@@ -19,8 +22,7 @@ from xhtml2pdf import pisa
# import plotly.express as px
import yaml
import pprint
from backend.excel.parser import SheetParser
from backend.excel.reports import convert_data_list_to_df
from backend.excel import convert_data_list_to_df, make_report_xlsx, make_report_html, SheetParser
from backend.db import (construct_submission_info, lookup_reagent,
construct_reagent, store_submission, lookup_kittype_by_use,
lookup_regent_by_type_name, lookup_all_orgs, lookup_submissions_by_date_range,
@@ -29,18 +31,15 @@ from backend.db import (construct_submission_info, lookup_reagent,
create_org_from_yaml, store_reagent
)
from backend.db import lookup_kittype_by_name
from .functions import check_kit_integrity
from tools import check_not_nan, extract_form_info
from backend.excel.reports import make_report_xlsx, make_report_html
from frontend.custom_widgets.sub_details import SubmissionsSheet
from frontend.custom_widgets.pop_ups import AlertPop, QuestionAsker
from frontend.custom_widgets import AddReagentForm, ReportDatePicker, KitAdder, ControlsDatePicker, ImportReagent
from .functions import extract_form_info
from tools import check_not_nan, check_kit_integrity
# from backend.excel.reports import
from frontend.custom_widgets import SubmissionsSheet, AlertPop, QuestionAsker, AddReagentForm, ReportDatePicker, KitAdder, ControlsDatePicker, ImportReagent
import logging
import difflib
from getpass import getuser
from datetime import date
from frontend.visualizations.charts import create_charts
from frontend.visualizations import create_charts
logger = logging.getLogger(f'submissions.{__name__}')
logger.info("Hello, I am a logger")

328
src/submissions/frontend/custom_widgets/__init__.py
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@@ -1,323 +1,7 @@
from datetime import date
from PyQt6.QtWidgets import (
QLabel, QVBoxLayout,
QLineEdit, QComboBox, QDialog,
QDialogButtonBox, QDateEdit, QSizePolicy, QWidget,
QGridLayout, QPushButton, QSpinBox,
QScrollBar, QHBoxLayout,
)
from PyQt6.QtCore import Qt, QDate, QSize
# from submissions.backend.db import lookup_regent_by_type_name_and_kit_name
from tools import check_not_nan, 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_regent_by_type_name_and_kit_name
from backend.excel.parser import SheetParser
from jinja2 import Environment, FileSystemLoader
import sys
from pathlib import Path
import logging
import numpy as np
from .pop_ups import AlertPop
'''
Contains all custom generated PyQT6 derivative widgets.
'''
logger = logging.getLogger(f"submissions.{__name__}")
if getattr(sys, 'frozen', False):
loader_path = Path(sys._MEIPASS).joinpath("files", "templates")
else:
loader_path = Path(__file__).parents[2].joinpath('templates').absolute().__str__()
loader = FileSystemLoader(loader_path)
env = Environment(loader=loader)
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) -> None:
super().__init__()
if reagent_lot == None:
reagent_lot = ""
self.setWindowTitle("Add Reagent")
QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
self.buttonBox = QDialogButtonBox(QBtn)
self.buttonBox.accepted.connect(self.accept)
self.buttonBox.rejected.connect(self.reject)
# widget to get lot info
lot_input = QLineEdit()
lot_input.setObjectName("lot")
lot_input.setText(reagent_lot)
# widget to get expiry info
exp_input = QDateEdit(calendarPopup=True)
exp_input.setObjectName('expiry')
# if expiry is not passed in from gui, use today
if expiry == None:
exp_input.setDate(QDate.currentDate())
else:
exp_input.setDate(expiry)
# widget to get reagent type info
type_input = QComboBox()
type_input.setObjectName('type')
type_input.addItems([item.replace("_", " ").title() for item in get_all_reagenttype_names(ctx=ctx)])
logger.debug(f"Trying to find index of {reagent_type}")
# convert input to user friendly string?
try:
reagent_type = reagent_type.replace("_", " ").title()
except AttributeError:
reagent_type = None
# set parsed reagent type to top of list
index = type_input.findText(reagent_type, Qt.MatchFlag.MatchEndsWith)
if index >= 0:
type_input.setCurrentIndex(index)
self.layout = QVBoxLayout()
self.layout.addWidget(QLabel("Lot"))
self.layout.addWidget(lot_input)
self.layout.addWidget(QLabel("Expiry"))
self.layout.addWidget(exp_input)
self.layout.addWidget(QLabel("Type"))
self.layout.addWidget(type_input)
self.layout.addWidget(self.buttonBox)
self.setLayout(self.layout)
class ReportDatePicker(QDialog):
"""
custom dialog to ask for report start/stop dates
"""
def __init__(self) -> None:
super().__init__()
self.setWindowTitle("Select Report Date Range")
# make confirm/reject buttons
QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
self.buttonBox = QDialogButtonBox(QBtn)
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.layout = QVBoxLayout()
self.layout.addWidget(QLabel("Start Date"))
self.layout.addWidget(start_date)
self.layout.addWidget(QLabel("End Date"))
self.layout.addWidget(end_date)
self.layout.addWidget(self.buttonBox)
self.setLayout(self.layout)
class KitAdder(QWidget):
"""
dialog to get information to add kit
"""
def __init__(self, parent_ctx:dict) -> None:
super().__init__()
self.ctx = parent_ctx
self.grid = QGridLayout()
self.setLayout(self.grid)
# insert submit button at top
self.submit_btn = QPushButton("Submit")
self.grid.addWidget(self.submit_btn,0,0,1,1)
self.grid.addWidget(QLabel("Kit Name:"),2,0)
# widget to get kit name
kit_name = QLineEdit()
kit_name.setObjectName("kit_name")
self.grid.addWidget(kit_name,2,1)
self.grid.addWidget(QLabel("Used For Sample Type:"),3,0)
# widget to get uses of kit
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.setEditable(True)
self.grid.addWidget(used_for,3,1)
# set cost per run
self.grid.addWidget(QLabel("Constant cost per full plate (plates, work hours, etc.):"),4,0)
# widget to get constant cost
const_cost = QSpinBox()
const_cost.setObjectName("const_cost")
const_cost.setMinimum(0)
const_cost.setMaximum(9999)
self.grid.addWidget(const_cost,4,1)
self.grid.addWidget(QLabel("Mutable cost per full plate (tips, reagents, etc.):"),5,0)
# widget to get mutable costs
mut_cost = QSpinBox()
mut_cost.setObjectName("mut_cost")
mut_cost.setMinimum(0)
mut_cost.setMaximum(9999)
self.grid.addWidget(mut_cost,5,1)
# button to add additional reagent types
self.add_RT_btn = QPushButton("Add Reagent Type")
self.grid.addWidget(self.add_RT_btn)
self.add_RT_btn.clicked.connect(self.add_RT)
self.submit_btn.clicked.connect(self.submit)
def add_RT(self) -> None:
"""
insert new reagent type row
"""
# get bottommost row
maxrow = self.grid.rowCount()
reg_form = ReagentTypeForm(parent_ctx=self.ctx)
reg_form.setObjectName(f"ReagentForm_{maxrow}")
self.grid.addWidget(reg_form, maxrow + 1,0,1,2)
def submit(self) -> None:
"""
send kit to database
"""
# get form info
info, reagents = extract_form_info(self)
logger.debug(f"kit info: {info}")
yml_type = {}
try:
yml_type['password'] = info['password']
except KeyError:
pass
used = info['used_for'].replace(" ", "_").lower()
yml_type[used] = {}
yml_type[used]['kits'] = {}
yml_type[used]['kits'][info['kit_name']] = {}
yml_type[used]['kits'][info['kit_name']]['constant_cost'] = info["const_cost"]
yml_type[used]['kits'][info['kit_name']]['mutable_cost'] = info["mut_cost"]
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)
msg = AlertPop(message=result['message'], status=result['status'])
msg.exec()
# def extract_form_info(self, object):
# """
# retrieves arbitrary number of labels, values from form
# Args:
# object (_type_): the object to extract info from
# Returns:
# _type_: _description_
# """
# labels = []
# values = []
# reagents = {}
# for item in object.findChildren(QWidget):
# logger.debug(item.parentWidget())
# # if not isinstance(item.parentWidget(), ReagentTypeForm):
# match item:
# case QLabel():
# labels.append(item.text().replace(" ", "_").strip(":").lower())
# case QLineEdit():
# # ad hoc check to prevent double reporting of qdatedit under lineedit for some reason
# if not isinstance(prev_item, QDateEdit) and not isinstance(prev_item, QComboBox) and not isinstance(prev_item, QSpinBox) and not isinstance(prev_item, QScrollBar):
# logger.debug(f"Previous: {prev_item}")
# logger.debug(f"Item: {item}, {item.text()}")
# values.append(item.text().strip())
# case QComboBox():
# values.append(item.currentText().strip())
# case QDateEdit():
# values.append(item.date().toPyDate())
# case QSpinBox():
# values.append(item.value())
# case ReagentTypeForm():
# re_labels, re_values, _ = self.extract_form_info(item)
# reagent = {item[0]:item[1] for item in zip(re_labels, re_values)}
# logger.debug(reagent)
# # reagent = {reagent['name:']:{'eol':reagent['extension_of_life_(months):']}}
# reagents[reagent["name_(*exactly*_as_it_appears_in_the_excel_submission_form)"].strip()] = {'eol_ext':int(reagent['extension_of_life_(months)'])}
# prev_item = item
# return labels, values, reagents
class ReagentTypeForm(QWidget):
"""
custom widget to add information about a new reagenttype
"""
def __init__(self, parent_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")
# 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)
grid.addWidget(QLabel("Extension of Life (months):"),0,2)
# widget toget extension of life
eol = QSpinBox()
eol.setObjectName('eol')
eol.setMinimum(0)
grid.addWidget(eol, 0,3)
class ControlsDatePicker(QWidget):
"""
custom widget to pick start and end dates for controls graphs
"""
def __init__(self) -> None:
super().__init__()
self.start_date = QDateEdit(calendarPopup=True)
# start date is three month prior to end date by default
# edit: 2 month, but the variable name is the same cause I'm lazy
threemonthsago = QDate.currentDate().addDays(-60)
self.start_date.setDate(threemonthsago)
self.end_date = QDateEdit(calendarPopup=True)
self.end_date.setDate(QDate.currentDate())
self.layout = QHBoxLayout()
self.layout.addWidget(QLabel("Start Date"))
self.layout.addWidget(self.start_date)
self.layout.addWidget(QLabel("End Date"))
self.layout.addWidget(self.end_date)
self.setLayout(self.layout)
self.setSizePolicy(QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Fixed)
def sizeHint(self) -> QSize:
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_", "")
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 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}")
self.addItems(relevant_reagents)
from .misc import *
from .pop_ups import *
from .sub_details import *

334
src/submissions/frontend/custom_widgets/misc.py Normal file
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@@ -0,0 +1,334 @@
'''
Contains miscellaneous widgets for frontend functions
'''
from datetime import date
from PyQt6.QtWidgets import (
QLabel, QVBoxLayout,
QLineEdit, QComboBox, QDialog,
QDialogButtonBox, QDateEdit, QSizePolicy, QWidget,
QGridLayout, QPushButton, QSpinBox,
QHBoxLayout,
)
from PyQt6.QtCore import Qt, QDate, QSize
# from submissions.backend.db import lookup_regent_by_type_name_and_kit_name
from tools import check_not_nan
from ..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_regent_by_type_name_and_kit_name
from backend.excel.parser import SheetParser
from jinja2 import Environment, FileSystemLoader
import sys
from pathlib import Path
import logging
import numpy as np
from .pop_ups import AlertPop
logger = logging.getLogger(f"submissions.{__name__}")
if getattr(sys, 'frozen', False):
loader_path = Path(sys._MEIPASS).joinpath("files", "templates")
else:
loader_path = Path(__file__).parents[2].joinpath('templates').absolute().__str__()
loader = FileSystemLoader(loader_path)
env = Environment(loader=loader)
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) -> None:
super().__init__()
if reagent_lot == None:
reagent_lot = ""
self.setWindowTitle("Add Reagent")
QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
self.buttonBox = QDialogButtonBox(QBtn)
self.buttonBox.accepted.connect(self.accept)
self.buttonBox.rejected.connect(self.reject)
# widget to get lot info
lot_input = QLineEdit()
lot_input.setObjectName("lot")
lot_input.setText(reagent_lot)
# widget to get expiry info
exp_input = QDateEdit(calendarPopup=True)
exp_input.setObjectName('expiry')
# if expiry is not passed in from gui, use today
if expiry == None:
exp_input.setDate(QDate.currentDate())
else:
exp_input.setDate(expiry)
# widget to get reagent type info
type_input = QComboBox()
type_input.setObjectName('type')
type_input.addItems([item.replace("_", " ").title() for item in get_all_reagenttype_names(ctx=ctx)])
logger.debug(f"Trying to find index of {reagent_type}")
# convert input to user friendly string?
try:
reagent_type = reagent_type.replace("_", " ").title()
except AttributeError:
reagent_type = None
# set parsed reagent type to top of list
index = type_input.findText(reagent_type, Qt.MatchFlag.MatchEndsWith)
if index >= 0:
type_input.setCurrentIndex(index)
self.layout = QVBoxLayout()
self.layout.addWidget(QLabel("Lot:"))
self.layout.addWidget(lot_input)
self.layout.addWidget(QLabel("Expiry:\n(use exact date on reagent.\nEOL will be calculated from kit automatically)"))
self.layout.addWidget(exp_input)
self.layout.addWidget(QLabel("Type:"))
self.layout.addWidget(type_input)
self.layout.addWidget(self.buttonBox)
self.setLayout(self.layout)
class ReportDatePicker(QDialog):
"""
custom dialog to ask for report start/stop dates
"""
def __init__(self) -> None:
super().__init__()
self.setWindowTitle("Select Report Date Range")
# make confirm/reject buttons
QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
self.buttonBox = QDialogButtonBox(QBtn)
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.layout = QVBoxLayout()
self.layout.addWidget(QLabel("Start Date"))
self.layout.addWidget(start_date)
self.layout.addWidget(QLabel("End Date"))
self.layout.addWidget(end_date)
self.layout.addWidget(self.buttonBox)
self.setLayout(self.layout)
class KitAdder(QWidget):
"""
dialog to get information to add kit
"""
def __init__(self, parent_ctx:dict) -> None:
super().__init__()
self.ctx = parent_ctx
self.grid = QGridLayout()
self.setLayout(self.grid)
# insert submit button at top
self.submit_btn = QPushButton("Submit")
self.grid.addWidget(self.submit_btn,0,0,1,1)
self.grid.addWidget(QLabel("Kit Name:"),2,0)
# widget to get kit name
kit_name = QLineEdit()
kit_name.setObjectName("kit_name")
self.grid.addWidget(kit_name,2,1)
self.grid.addWidget(QLabel("Used For Sample Type:"),3,0)
# widget to get uses of kit
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.setEditable(True)
self.grid.addWidget(used_for,3,1)
# set cost per run
self.grid.addWidget(QLabel("Constant cost per full plate (plates, work hours, etc.):"),4,0)
# widget to get constant cost
const_cost = QSpinBox()
const_cost.setObjectName("const_cost")
const_cost.setMinimum(0)
const_cost.setMaximum(9999)
self.grid.addWidget(const_cost,4,1)
self.grid.addWidget(QLabel("Mutable cost per full plate (tips, reagents, etc.):"),5,0)
# widget to get mutable costs
mut_cost = QSpinBox()
mut_cost.setObjectName("mut_cost")
mut_cost.setMinimum(0)
mut_cost.setMaximum(9999)
self.grid.addWidget(mut_cost,5,1)
# button to add additional reagent types
self.add_RT_btn = QPushButton("Add Reagent Type")
self.grid.addWidget(self.add_RT_btn)
self.add_RT_btn.clicked.connect(self.add_RT)
self.submit_btn.clicked.connect(self.submit)
def add_RT(self) -> None:
"""
insert new reagent type row
"""
# get bottommost row
maxrow = self.grid.rowCount()
reg_form = ReagentTypeForm(parent_ctx=self.ctx)
reg_form.setObjectName(f"ReagentForm_{maxrow}")
self.grid.addWidget(reg_form, maxrow + 1,0,1,2)
def submit(self) -> None:
"""
send kit to database
"""
# get form info
info, reagents = extract_form_info(self)
logger.debug(f"kit info: {info}")
yml_type = {}
try:
yml_type['password'] = info['password']
except KeyError:
pass
used = info['used_for'].replace(" ", "_").lower()
yml_type[used] = {}
yml_type[used]['kits'] = {}
yml_type[used]['kits'][info['kit_name']] = {}
yml_type[used]['kits'][info['kit_name']]['constant_cost'] = info["const_cost"]
yml_type[used]['kits'][info['kit_name']]['mutable_cost'] = info["mut_cost"]
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)
msg = AlertPop(message=result['message'], status=result['status'])
msg.exec()
# def extract_form_info(self, object):
# """
# retrieves arbitrary number of labels, values from form
# Args:
# object (_type_): the object to extract info from
# Returns:
# _type_: _description_
# """
# labels = []
# values = []
# reagents = {}
# for item in object.findChildren(QWidget):
# logger.debug(item.parentWidget())
# # if not isinstance(item.parentWidget(), ReagentTypeForm):
# match item:
# case QLabel():
# labels.append(item.text().replace(" ", "_").strip(":").lower())
# case QLineEdit():
# # ad hoc check to prevent double reporting of qdatedit under lineedit for some reason
# if not isinstance(prev_item, QDateEdit) and not isinstance(prev_item, QComboBox) and not isinstance(prev_item, QSpinBox) and not isinstance(prev_item, QScrollBar):
# logger.debug(f"Previous: {prev_item}")
# logger.debug(f"Item: {item}, {item.text()}")
# values.append(item.text().strip())
# case QComboBox():
# values.append(item.currentText().strip())
# case QDateEdit():
# values.append(item.date().toPyDate())
# case QSpinBox():
# values.append(item.value())
# case ReagentTypeForm():
# re_labels, re_values, _ = self.extract_form_info(item)
# reagent = {item[0]:item[1] for item in zip(re_labels, re_values)}
# logger.debug(reagent)
# # reagent = {reagent['name:']:{'eol':reagent['extension_of_life_(months):']}}
# reagents[reagent["name_(*exactly*_as_it_appears_in_the_excel_submission_form)"].strip()] = {'eol_ext':int(reagent['extension_of_life_(months)'])}
# prev_item = item
# return labels, values, reagents
class ReagentTypeForm(QWidget):
"""
custom widget to add information about a new reagenttype
"""
def __init__(self, parent_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")
# 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)
grid.addWidget(QLabel("Extension of Life (months):"),0,2)
# widget toget extension of life
eol = QSpinBox()
eol.setObjectName('eol')
eol.setMinimum(0)
grid.addWidget(eol, 0,3)
class ControlsDatePicker(QWidget):
"""
custom widget to pick start and end dates for controls graphs
"""
def __init__(self) -> None:
super().__init__()
self.start_date = QDateEdit(calendarPopup=True)
# start date is three month prior to end date by default
# NOTE: 2 month, but the variable name is the same cause I'm lazy
threemonthsago = QDate.currentDate().addDays(-60)
self.start_date.setDate(threemonthsago)
self.end_date = QDateEdit(calendarPopup=True)
self.end_date.setDate(QDate.currentDate())
self.layout = QHBoxLayout()
self.layout.addWidget(QLabel("Start Date"))
self.layout.addWidget(self.start_date)
self.layout.addWidget(QLabel("End Date"))
self.layout.addWidget(self.end_date)
self.setLayout(self.layout)
self.setSizePolicy(QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Fixed)
def sizeHint(self) -> QSize:
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_", "")
logger.debug(f"Import Reagent is looking at: {prsr.sub[item]} 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.")
relevant_reagents.insert(0, relevant_reagents.pop(relevant_reagents.index(prsr.sub[item]['lot'])))
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.addItems(relevant_reagents)

3
src/submissions/frontend/custom_widgets/pop_ups.py
View File

@@ -1,3 +1,6 @@
'''
Contains dialogs for notification and prompting.
'''
from PyQt6.QtWidgets import (
QLabel, QVBoxLayout, QDialog,
QDialogButtonBox, QMessageBox

3
src/submissions/frontend/custom_widgets/sub_details.py
View File

@@ -1,3 +1,6 @@
'''
Contains widgets specific to the submission summary and submission details.
'''
from PyQt6.QtWidgets import (
QVBoxLayout, QDialog, QTableView,
QTextEdit, QPushButton, QScrollArea,

113
src/submissions/frontend/functions.py
View File

@@ -1,80 +1,53 @@
# from ..models import *
from backend.db.models import *
import logging
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__}")
def check_kit_integrity(sub:BasicSubmission|KitType, reagenttypes:list|None=None) -> dict|None:
def extract_form_info(object) -> dict:
"""
Ensures all reagents expected in kit are listed in Submission
retrieves object names and values from form
Args:
sub (BasicSubmission | KitType): Object containing complete list of reagent types.
reagenttypes (list | None, optional): List to check against complete list. Defaults to None.
object (_type_): the form widget
Returns:
dict|None: Result object containing a message and any missing components.
"""
logger.debug(type(sub))
# What type is sub?
match sub:
case BasicSubmission():
ext_kit_rtypes = [reagenttype.name for reagenttype in sub.extraction_kit.reagent_types]
# Overwrite function parameter reagenttypes
reagenttypes = [reagent.type.name for reagent in sub.reagents]
case KitType():
ext_kit_rtypes = [reagenttype.name for reagenttype in sub.reagent_types]
logger.debug(f"Kit reagents: {ext_kit_rtypes}")
logger.debug(f"Submission reagents: {reagenttypes}")
# check if lists are equal
check = set(ext_kit_rtypes) == set(reagenttypes)
logger.debug(f"Checking if reagents match kit contents: {check}")
# what reagent types are in both lists?
# common = list(set(ext_kit_rtypes).intersection(reagenttypes))
missing = list(set(ext_kit_rtypes).difference(reagenttypes))
logger.debug(f"Missing reagents types: {missing}")
# if lists are equal return no problem
if len(missing)==0:
result = None
else:
# missing = [x for x in ext_kit_rtypes if x not in common]
result = {'message' : f"Couldn't verify reagents match listed kit components.\n\nIt looks like you are missing: {[item.upper() for item in missing]}\n\nAlternatively, you may have set the wrong extraction kit.", 'missing': missing}
return result
# Below is depreciated:
# 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
dict: dictionary of objectName:text items
"""
from frontend.custom_widgets import ReagentTypeForm
dicto = {}
reagents = {}
logger.debug(f"Object type: {type(object)}")
# grab all widgets in form
try:
all_children = object.layout.parentWidget().findChildren(QWidget)
except AttributeError:
all_children = object.layout().parentWidget().findChildren(QWidget)
for item in all_children:
logger.debug(f"Looking at: {item.objectName()}")
match item:
case QLineEdit():
dicto[item.objectName()] = item.text()
case QComboBox():
dicto[item.objectName()] = item.currentText()
case QDateEdit():
dicto[item.objectName()] = item.date().toPyDate()
case QSpinBox():
dicto[item.objectName()] = item.value()
case ReagentTypeForm():
reagent = extract_form_info(item)
# reagent = {item[0]:item[1] for item in zip(re_labels, re_values)}
logger.debug(reagent)
# reagent = {reagent['name:']:{'eol':reagent['extension_of_life_(months):']}}
reagents[reagent["name"].strip()] = {'eol_ext':int(reagent['eol'])}
# value for ad hoc check above
if reagents != {}:
return dicto, reagents
return dicto

40
src/submissions/frontend/static/css/data_browser.css
View File

@@ -1,40 +0,0 @@
Screen {
}
.box {
height: 3;
border: solid green;
}
#tree-view {
display: none;
scrollbar-gutter: stable;
overflow: auto;
width: auto;
height: 100%;
dock: left;
}
DataBrowser.-show-tree #tree-view {
display: block;
max-width: 50%;
}
#code-view {
overflow: auto scroll;
min-width: 100%;
}
#code {
width: auto;
}
FormField {
width: 70%;
height: 3;
padding: 1 2;
background: $primary;
border: $secondary tall;
content-align: center middle;
}

0
src/submissions/frontend/static/css/styles.css
View File

4
src/submissions/frontend/visualizations/__init__.py
View File

@@ -0,0 +1,4 @@
'''
Contains all operations for creating charts, graphs and visual effects.
'''
from .control_charts import *

32
src/submissions/frontend/visualizations/charts.py → src/submissions/frontend/visualizations/control_charts.py
View File

@@ -1,3 +1,6 @@
'''
Functions for constructing controls graphs using plotly.
'''
import plotly.express as px
import pandas as pd
from pathlib import Path
@@ -149,8 +152,19 @@ def output_figures(settings:dict, figs:list, group_name:str):
def construct_chart(ctx:dict, df:pd.DataFrame, modes:list, ytitle:str|None=None) -> Figure:
fig = Figure()
"""
Creates a plotly chart for controls from a pandas dataframe
Args:
ctx (dict): settings passed down from gui
df (pd.DataFrame): input dataframe of controls
modes (list): analysis modes to construct charts for
ytitle (str | None, optional): title on the y-axis. Defaults to None.
Returns:
Figure: output stacked bar chart.
"""
fig = Figure()
for ii, mode in enumerate(modes):
if "count" in mode:
df[mode] = pd.to_numeric(df[mode],errors='coerce')
@@ -161,7 +175,6 @@ def construct_chart(ctx:dict, df:pd.DataFrame, modes:list, ytitle:str|None=None)
color_discrete_sequence=None
else:
color = "target"
# print(get_unique_values_in_df_column(df, 'target'))
match get_unique_values_in_df_column(df, 'target'):
case ['Target']:
color_discrete_sequence=["blue"]
@@ -180,7 +193,6 @@ def construct_chart(ctx:dict, df:pd.DataFrame, modes:list, ytitle:str|None=None)
)
bar.update_traces(visible = ii == 0)
fig.add_traces(bar.data)
# sys.exit(f"number of traces={len(fig.data)}")
return generic_figure_markers(fig=fig, modes=modes, ytitle=ytitle)
# Below are the individual construction functions. They must be named "construct_{mode}_chart" and
@@ -264,17 +276,3 @@ def divide_chunks(input_list:list, chunk_count:int):
"""
k, m = divmod(len(input_list), chunk_count)
return (input_list[i*k+min(i, m):(i+1)*k+min(i+1, m)] for i in range(chunk_count))
########This must be at bottom of module###########
function_map = {}
for item in dict(locals().items()):
try:
if dict(locals().items())[item].__module__ == __name__:
try:
function_map[item] = dict(locals().items())[item]
except KeyError:
pass
except AttributeError:
pass
###################################################