landon/Submissions-App
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Increased robustness of form parsers.

Browse Source
This commit is contained in:
Landon Wark
2023-10-06 14:22:59 -05:00
parent e484eabb22
commit 1b6d415788
27 changed files with 747 additions and 284 deletions
Download Patch File Download Diff File Expand all files Collapse all files

230
src/submissions/frontend/custom_widgets/misc.py
View File

@@ -2,22 +2,25 @@
Contains miscellaneous widgets for frontend functions
'''
from datetime import date
from pprint import pformat
from PyQt6.QtWidgets import (
QLabel, QVBoxLayout,
QLineEdit, QComboBox, QDialog,
QDialogButtonBox, QDateEdit, QSizePolicy, QWidget,
QGridLayout, QPushButton, QSpinBox, QDoubleSpinBox,
QHBoxLayout
QHBoxLayout, QScrollArea
)
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 construct_kit_from_yaml, \
from backend.db.functions import construct_kit_from_yaml, \
lookup_reagent_types, lookup_reagents, lookup_submission_type, lookup_reagenttype_kittype_association
from backend.db.models import SubmissionTypeKitTypeAssociation
from sqlalchemy import FLOAT, INTEGER, String
import logging
import numpy as np
from .pop_ups import AlertPop
from backend.pydant import PydReagent
from typing import Tuple
logger = logging.getLogger(f"submissions.{__name__}")
@@ -84,6 +87,12 @@ class AddReagentForm(QDialog):
self.setLayout(self.layout)
self.type_input.currentTextChanged.connect(self.update_names)
def parse_form(self):
return dict(name=self.name_input.currentText(),
lot=self.lot_input.text(),
expiry=self.exp_input.date().toPyDate(),
type=self.type_input.currentText())
def update_names(self):
"""
Updates reagent names form field with examples from reagent type
@@ -121,6 +130,9 @@ class ReportDatePicker(QDialog):
self.layout.addWidget(self.buttonBox)
self.setLayout(self.layout)
def parse_form(self):
return dict(start_date=self.start_date.date().toPyDate(), end_date = self.end_date.date().toPyDate())
class KitAdder(QWidget):
"""
dialog to get information to add kit
@@ -128,8 +140,14 @@ class KitAdder(QWidget):
def __init__(self, parent_ctx:Settings) -> None:
super().__init__()
self.ctx = parent_ctx
main_box = QVBoxLayout(self)
scroll = QScrollArea(self)
main_box.addWidget(scroll)
scroll.setWidgetResizable(True)
scrollContent = QWidget(scroll)
self.grid = QGridLayout()
self.setLayout(self.grid)
# self.setLayout(self.grid)
scrollContent.setLayout(self.grid)
# insert submit button at top
self.submit_btn = QPushButton("Submit")
self.grid.addWidget(self.submit_btn,0,0,1,1)
@@ -138,42 +156,65 @@ class KitAdder(QWidget):
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)
self.grid.addWidget(QLabel("Used For Submission 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.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
self.grid.addWidget(QLabel("Constant cost per full plate (plates, work hours, etc.):"),4,0)
# widget to get constant cost
const_cost = QDoubleSpinBox() #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("Cost per column (multidrop reagents, etc.):"),5,0)
# widget to get mutable costs per column
mut_cost_col = QDoubleSpinBox() #QSpinBox()
mut_cost_col.setObjectName("mut_cost_col")
mut_cost_col.setMinimum(0)
mut_cost_col.setMaximum(9999)
self.grid.addWidget(mut_cost_col,5,1)
self.grid.addWidget(QLabel("Cost per sample (tips, reagents, etc.):"),6,0)
# widget to get mutable costs per column
mut_cost_samp = QDoubleSpinBox() #QSpinBox()
mut_cost_samp.setObjectName("mut_cost_samp")
mut_cost_samp.setMinimum(0)
mut_cost_samp.setMaximum(9999)
self.grid.addWidget(mut_cost_samp,6,1)
# Get all fields in SubmissionTypeKitTypeAssociation
self.columns = [item for item in SubmissionTypeKitTypeAssociation.__table__.columns if len(item.foreign_keys) == 0]
for iii, column in enumerate(self.columns):
idx = iii + 4
# convert field name to human readable.
field_name = column.name.replace("_", " ").title()
self.grid.addWidget(QLabel(field_name),idx,0)
match column.type:
case FLOAT():
add_widget = QDoubleSpinBox()
add_widget.setMinimum(0)
add_widget.setMaximum(9999)
case INTEGER():
add_widget = QSpinBox()
add_widget.setMinimum(0)
add_widget.setMaximum(9999)
case _:
add_widget = QLineEdit()
add_widget.setObjectName(column.name)
self.grid.addWidget(add_widget, idx,1)
# self.grid.addWidget(QLabel("Constant cost per full plate (plates, work hours, etc.):"),4,0)
# # widget to get constant cost
# const_cost = QDoubleSpinBox() #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("Cost per column (multidrop reagents, etc.):"),5,0)
# # widget to get mutable costs per column
# mut_cost_col = QDoubleSpinBox() #QSpinBox()
# mut_cost_col.setObjectName("mut_cost_col")
# mut_cost_col.setMinimum(0)
# mut_cost_col.setMaximum(9999)
# self.grid.addWidget(mut_cost_col,5,1)
# self.grid.addWidget(QLabel("Cost per sample (tips, reagents, etc.):"),6,0)
# # widget to get mutable costs per column
# mut_cost_samp = QDoubleSpinBox() #QSpinBox()
# mut_cost_samp.setObjectName("mut_cost_samp")
# mut_cost_samp.setMinimum(0)
# mut_cost_samp.setMaximum(9999)
# self.grid.addWidget(mut_cost_samp,6,1)
# 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)
scroll.setWidget(scrollContent)
self.ignore = [None, "", "qt_spinbox_lineedit", "qt_scrollarea_viewport", "qt_scrollarea_hcontainer",
"qt_scrollarea_vcontainer", "submit_btn"
]
def add_RT(self) -> None:
"""
@@ -181,9 +222,11 @@ class KitAdder(QWidget):
"""
# get bottommost row
maxrow = self.grid.rowCount()
reg_form = ReagentTypeForm(parent_ctx=self.ctx)
reg_form = ReagentTypeForm(ctx=self.ctx)
reg_form.setObjectName(f"ReagentForm_{maxrow}")
self.grid.addWidget(reg_form, maxrow + 1,0,1,2)
# self.grid.addWidget(reg_form, maxrow + 1,0,1,2)
self.grid.addWidget(reg_form, maxrow,0,1,4)
def submit(self) -> None:
@@ -191,40 +234,62 @@ class KitAdder(QWidget):
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']
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_column'] = info["mut_cost_col"]
yml_type[used]['kits'][info['kit_name']]['mutable_cost_sample'] = info["mut_cost_samp"]
yml_type[used]['kits'][info['kit_name']]['reagenttypes'] = reagents
logger.debug(yml_type)
info, reagents = self.parse_form()
# info, reagents = extract_form_info(self)
info = {k:v for k,v in info.items() if k in [column.name for column in self.columns] + ['kit_name', 'used_for']}
logger.debug(f"kit info: {pformat(info)}")
logger.debug(f"kit reagents: {pformat(reagents)}")
info['reagent_types'] = reagents
# for reagent in reagents:
# new_dict = {}
# for k,v in reagent.items():
# if "_" in k:
# key, sub_key = k.split("_")
# if key not in new_dict.keys():
# new_dict[key] = {}
# logger.debug(f"Adding key {key}, {sub_key} and value {v} to {new_dict}")
# new_dict[key][sub_key] = v
# else:
# new_dict[k] = v
# info['reagent_types'].append(new_dict)
logger.debug(pformat(info))
# send to kit constructor
result = construct_kit_from_yaml(ctx=self.ctx, exp=yml_type)
result = construct_kit_from_yaml(ctx=self.ctx, kit_dict=info)
msg = AlertPop(message=result['message'], status=result['status'])
msg.exec()
self.__init__(self.ctx)
def parse_form(self) -> Tuple[dict, list]:
logger.debug(f"Hello from {self.__class__} parser!")
info = {}
reagents = []
widgets = [widget for widget in self.findChildren(QWidget) if widget.objectName() not in self.ignore and not isinstance(widget.parent(), ReagentTypeForm)]
for widget in widgets:
# logger.debug(f"Parsed widget: {widget.objectName()} of type {type(widget)} with parent {widget.parent()}")
match widget:
case ReagentTypeForm():
reagents.append(widget.parse_form())
case QLineEdit():
info[widget.objectName()] = widget.text()
case QComboBox():
info[widget.objectName()] = widget.currentText()
case QDateEdit():
info[widget.objectName()] = widget.date().toPyDate()
return info, reagents
class ReagentTypeForm(QWidget):
"""
custom widget to add information about a new reagenttype
"""
def __init__(self, ctx:dict) -> None:
def __init__(self, ctx:Settings) -> None:
super().__init__()
grid = QGridLayout()
self.setLayout(grid)
grid.addWidget(QLabel("Name (*Exactly* as it appears in the excel submission form):"),0,0)
grid.addWidget(QLabel("Reagent Type Name"),0,0)
# Widget to get reagent info
self.reagent_getter = QComboBox()
self.reagent_getter.setObjectName("name")
self.reagent_getter.setObjectName("rtname")
# lookup all reagent type names from db
lookup = lookup_reagent_types(ctx=ctx)
logger.debug(f"Looked up ReagentType names: {lookup}")
@@ -233,10 +298,66 @@ class ReagentTypeForm(QWidget):
grid.addWidget(self.reagent_getter,0,1)
grid.addWidget(QLabel("Extension of Life (months):"),0,2)
# widget to get extension of life
eol = QSpinBox()
eol.setObjectName('eol')
eol.setMinimum(0)
grid.addWidget(eol, 0,3)
self.eol = QSpinBox()
self.eol.setObjectName('eol')
self.eol.setMinimum(0)
grid.addWidget(self.eol, 0,3)
grid.addWidget(QLabel("Excel Location Sheet Name:"),1,0)
self.location_sheet_name = QLineEdit()
self.location_sheet_name.setObjectName("sheet")
self.location_sheet_name.setText("e.g. 'Reagent Info'")
grid.addWidget(self.location_sheet_name, 1,1)
for iii, item in enumerate(["Name", "Lot", "Expiry"]):
idx = iii + 2
grid.addWidget(QLabel(f"{item} Row:"), idx, 0)
row = QSpinBox()
row.setFixedWidth(50)
row.setObjectName(f'{item.lower()}_row')
row.setMinimum(0)
grid.addWidget(row, idx, 1)
grid.addWidget(QLabel(f"{item} Column:"), idx, 2)
col = QSpinBox()
col.setFixedWidth(50)
col.setObjectName(f'{item.lower()}_column')
col.setMinimum(0)
grid.addWidget(col, idx, 3)
self.setFixedHeight(175)
max_row = grid.rowCount()
self.r_button = QPushButton("Remove")
self.r_button.clicked.connect(self.remove)
grid.addWidget(self.r_button,max_row,0,1,1)
self.ignore = [None, "", "qt_spinbox_lineedit", "qt_scrollarea_viewport", "qt_scrollarea_hcontainer",
"qt_scrollarea_vcontainer", "submit_btn", "eol", "sheet", "rtname"
]
def remove(self):
self.setParent(None)
self.destroy()
def parse_form(self) -> dict:
logger.debug(f"Hello from {self.__class__} parser!")
info = {}
info['eol'] = self.eol.value()
info['sheet'] = self.location_sheet_name.text()
info['rtname'] = self.reagent_getter.currentText()
widgets = [widget for widget in self.findChildren(QWidget) if widget.objectName() not in self.ignore]
for widget in widgets:
logger.debug(f"Parsed widget: {widget.objectName()} of type {type(widget)} with parent {widget.parent()}")
match widget:
case QLineEdit():
info[widget.objectName()] = widget.text()
case QComboBox():
info[widget.objectName()] = widget.currentText()
case QDateEdit():
info[widget.objectName()] = widget.date().toPyDate()
case QSpinBox() | QDoubleSpinBox():
if "_" in widget.objectName():
key, sub_key = widget.objectName().split("_")
if key not in info.keys():
info[key] = {}
logger.debug(f"Adding key {key}, {sub_key} and value {widget.value()} to {info}")
info[key][sub_key] = widget.value()
return info
class ControlsDatePicker(QWidget):
"""
@@ -336,3 +457,4 @@ class ParsedQLabel(QLabel):
self.setText(f"Parsed {output}")
else:
self.setText(f"MISSING {output}")