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

Renaming ReagentType to ReagentRole

Browse Source
This commit is contained in:
lwark
2024-06-03 13:32:04 -05:00
parent 1a716984a7
commit cdcce80898
10 changed files with 182 additions and 140 deletions
Download Patch File Download Diff File Expand all files Collapse all files

22
src/submissions/frontend/widgets/kit_creator.py
View File

@@ -5,8 +5,8 @@ from PyQt6.QtWidgets import (
QSpinBox, QDateEdit
)
from sqlalchemy import FLOAT, INTEGER
from backend.db import SubmissionTypeKitTypeAssociation, SubmissionType, ReagentType
from backend.validators import PydReagentType, PydKit
from backend.db import SubmissionTypeKitTypeAssociation, SubmissionType, ReagentRole
from backend.validators import PydReagentRole, PydKit
import logging
from pprint import pformat
from tools import Report
@@ -81,7 +81,7 @@ class KitAdder(QWidget):
"""
# get bottommost row
maxrow = self.grid.rowCount()
reg_form = ReagentTypeForm(parent=self)
reg_form = ReagentRoleForm(parent=self)
reg_form.setObjectName(f"ReagentForm_{maxrow}")
self.grid.addWidget(reg_form, maxrow,0,1,4)
@@ -95,11 +95,11 @@ class KitAdder(QWidget):
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
info['reagent_roles'] = reagents
# logger.debug(pformat(info))
# send to kit constructor
kit = PydKit(name=info['kit_name'])
for reagent in info['reagent_types']:
for reagent in info['reagent_roles']:
uses = {
info['used_for']:
{'sheet':reagent['sheet'],
@@ -107,7 +107,7 @@ class KitAdder(QWidget):
'lot':reagent['lot'],
'expiry':reagent['expiry']
}}
kit.reagent_types.append(PydReagentType(name=reagent['rtname'], eol_ext=reagent['eol'], uses=uses))
kit.reagent_roles.append(PydReagentRole(name=reagent['rtname'], eol_ext=reagent['eol'], uses=uses))
# logger.debug(f"Output pyd object: {kit.__dict__}")
sqlobj, result = kit.toSQL(self.ctx)
report.add_result(result=result)
@@ -125,11 +125,11 @@ class KitAdder(QWidget):
# 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)]
widgets = [widget for widget in self.findChildren(QWidget) if widget.objectName() not in self.ignore and not isinstance(widget.parent(), ReagentRoleForm)]
for widget in widgets:
# logger.debug(f"Parsed widget: {widget.objectName()} of type {type(widget)} with parent {widget.parent()}")
match widget:
case ReagentTypeForm():
case ReagentRoleForm():
reagents.append(widget.parse_form())
case QLineEdit():
info[widget.objectName()] = widget.text()
@@ -139,7 +139,7 @@ class KitAdder(QWidget):
info[widget.objectName()] = widget.date().toPyDate()
return info, reagents
class ReagentTypeForm(QWidget):
class ReagentRoleForm(QWidget):
"""
custom widget to add information about a new reagenttype
"""
@@ -152,13 +152,13 @@ class ReagentTypeForm(QWidget):
self.reagent_getter = QComboBox()
self.reagent_getter.setObjectName("rtname")
# lookup all reagent type names from db
lookup = ReagentType.query()
lookup = ReagentRole.query()
# logger.debug(f"Looked up ReagentType names: {lookup}")
self.reagent_getter.addItems([item.name 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 to get extension of life
# NOTE: widget to get extension of life
self.eol = QSpinBox()
self.eol.setObjectName('eol')
self.eol.setMinimum(0)

16
src/submissions/frontend/widgets/misc.py
View File

@@ -23,10 +23,10 @@ class AddReagentForm(QDialog):
"""
dialog to add gather info about new reagent
"""
def __init__(self, reagent_lot:str|None=None, reagent_type:str|None=None, expiry:date|None=None, reagent_name:str|None=None) -> None:
def __init__(self, reagent_lot:str|None=None, reagent_role: str | None=None, expiry: date | None=None, reagent_name: str | None=None) -> None:
super().__init__()
if reagent_lot == None:
reagent_lot = reagent_type
reagent_lot = reagent_role
self.setWindowTitle("Add Reagent")
@@ -57,15 +57,15 @@ class AddReagentForm(QDialog):
# widget to get reagent type info
self.type_input = QComboBox()
self.type_input.setObjectName('type')
self.type_input.addItems([item.name for item in ReagentType.query()])
self.type_input.addItems([item.name for item in ReagentRole.query()])
# logger.debug(f"Trying to find index of {reagent_type}")
# convert input to user friendly string?
try:
reagent_type = reagent_type.replace("_", " ").title()
reagent_role = reagent_role.replace("_", " ").title()
except AttributeError:
reagent_type = None
reagent_role = None
# set parsed reagent type to top of list
index = self.type_input.findText(reagent_type, Qt.MatchFlag.MatchEndsWith)
index = self.type_input.findText(reagent_role, Qt.MatchFlag.MatchEndsWith)
if index >= 0:
self.type_input.setCurrentIndex(index)
self.layout = QVBoxLayout()
@@ -91,7 +91,7 @@ class AddReagentForm(QDialog):
return dict(name=self.name_input.currentText().strip(),
lot=self.lot_input.text().strip(),
expiry=self.exp_input.date().toPyDate(),
type=self.type_input.currentText().strip())
role=self.type_input.currentText().strip())
def update_names(self):
"""
@@ -99,7 +99,7 @@ class AddReagentForm(QDialog):
"""
# logger.debug(self.type_input.currentText())
self.name_input.clear()
lookup = Reagent.query(reagent_type=self.type_input.currentText())
lookup = Reagent.query(reagent_role=self.type_input.currentText())
self.name_input.addItems(list(set([item.name for item in lookup])))
class ReportDatePicker(QDialog):

36
src/submissions/frontend/widgets/submission_widget.py
View File

@@ -14,7 +14,7 @@ from backend.excel.parser import SheetParser
from backend.validators import PydSubmission, PydReagent
from backend.db import (
KitType, Organization, SubmissionType, Reagent,
ReagentType, KitTypeReagentTypeAssociation
ReagentRole, KitTypeReagentRoleAssociation
)
from pprint import pformat
from .pop_ups import QuestionAsker, AlertPop
@@ -112,14 +112,14 @@ class SubmissionFormContainer(QWidget):
# logger.debug(f"Outgoing report: {self.report.results}")
# logger.debug(f"All attributes of submission container:\n{pformat(self.__dict__)}")
def add_reagent(self, reagent_lot: str | None = None, reagent_type: str | None = None, expiry: date | None = None,
def add_reagent(self, reagent_lot: str | None = None, reagent_role: str | None = None, expiry: date | None = None,
name: str | None = None):
"""
Action to create new reagent in DB.
Args:
reagent_lot (str | None, optional): Parsed reagent from import form. Defaults to None.
reagent_type (str | None, optional): Parsed reagent type from import form. Defaults to None.
reagent_role (str | None, optional): Parsed reagent type from import form. Defaults to None.
expiry (date | None, optional): Parsed reagent expiry data. Defaults to None.
name (str | None, optional): Parsed reagent name. Defaults to None.
@@ -130,7 +130,7 @@ class SubmissionFormContainer(QWidget):
if isinstance(reagent_lot, bool):
reagent_lot = ""
# NOTE: create form
dlg = AddReagentForm(reagent_lot=reagent_lot, reagent_type=reagent_type, expiry=expiry, reagent_name=name)
dlg = AddReagentForm(reagent_lot=reagent_lot, reagent_role=reagent_role, expiry=expiry, reagent_name=name)
if dlg.exec():
# extract form info
info = dlg.parse_form()
@@ -581,13 +581,13 @@ class SubmissionFormWidget(QWidget):
"""
lot = self.lot.currentText()
# logger.debug(f"Using this lot for the reagent {self.reagent}: {lot}")
wanted_reagent = Reagent.query(lot_number=lot, reagent_type=self.reagent.type)
wanted_reagent = Reagent.query(lot_number=lot, reagent_role=self.reagent.role)
# NOTE: if reagent doesn't exist in database, offer to add it (uses App.add_reagent)
if wanted_reagent == None:
dlg = QuestionAsker(title=f"Add {lot}?",
message=f"Couldn't find reagent type {self.reagent.type}: {lot} in the database.\n\nWould you like to add it?")
if dlg.exec():
wanted_reagent = self.parent().parent().add_reagent(reagent_lot=lot, reagent_type=self.reagent.type,
wanted_reagent = self.parent().parent().add_reagent(reagent_lot=lot, reagent_role=self.reagent.role,
expiry=self.reagent.expiry,
name=self.reagent.name)
return wanted_reagent, None
@@ -598,10 +598,10 @@ class SubmissionFormWidget(QWidget):
else:
# NOTE: Since this now gets passed in directly from the parser -> pyd -> form and the parser gets the name
# from the db, it should no longer be necessary to query the db with reagent/kit, but with rt name directly.
rt = ReagentType.query(name=self.reagent.type)
rt = ReagentRole.query(name=self.reagent.role)
if rt == None:
rt = ReagentType.query(kit_type=self.extraction_kit, reagent=wanted_reagent)
return PydReagent(name=wanted_reagent.name, lot=wanted_reagent.lot, type=rt.name,
rt = ReagentRole.query(kit_type=self.extraction_kit, reagent=wanted_reagent)
return PydReagent(name=wanted_reagent.name, lot=wanted_reagent.lot, role=rt.name,
expiry=wanted_reagent.expiry, missing=False), None
def updated(self):
@@ -619,20 +619,20 @@ class SubmissionFormWidget(QWidget):
check = not reagent.missing
except:
check = False
self.setObjectName(f"{reagent.type}_label")
self.setObjectName(f"{reagent.role}_label")
if check:
self.setText(f"Parsed {reagent.type}")
self.setText(f"Parsed {reagent.role}")
else:
self.setText(f"MISSING {reagent.type}")
self.setText(f"MISSING {reagent.role}")
def updated(self, reagent_type: str):
def updated(self, reagent_role: str):
"""
Marks widget as updated
Args:
reagent_type (str): _description_
reagent_role (str): _description_
"""
self.setText(f"UPDATED {reagent_type}")
self.setText(f"UPDATED {reagent_role}")
class ReagentLot(QComboBox):
@@ -641,7 +641,7 @@ class SubmissionFormWidget(QWidget):
self.setEditable(True)
# logger.debug(f"Attempting lookup of reagents by type: {reagent.type}")
# NOTE: below was lookup_reagent_by_type_name_and_kit_name, but I couldn't get it to work.
lookup = Reagent.query(reagent_type=reagent.type)
lookup = Reagent.query(reagent_role=reagent.role)
relevant_reagents = [str(item.lot) for item in lookup]
output_reg = []
for rel_reagent in relevant_reagents:
@@ -658,7 +658,7 @@ class SubmissionFormWidget(QWidget):
if check_not_nan(reagent.lot):
relevant_reagents.insert(0, str(reagent.lot))
else:
looked_up_rt = KitTypeReagentTypeAssociation.query(reagent_type=reagent.type,
looked_up_rt = KitTypeReagentRoleAssociation.query(reagent_role=reagent.role,
kit_type=extraction_kit)
try:
looked_up_reg = Reagent.query(lot_number=looked_up_rt.last_used)
@@ -684,5 +684,5 @@ class SubmissionFormWidget(QWidget):
# logger.debug(f"Found {reagent.lot} in relevant reagents: {relevant_reagents}. But no need to move due to short list.")
pass
# logger.debug(f"New relevant reagents: {relevant_reagents}")
self.setObjectName(f"lot_{reagent.type}")
self.setObjectName(f"lot_{reagent.role}")
self.addItems(relevant_reagents)