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Renaming ReagentType to ReagentRole

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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
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36
src/submissions/frontend/widgets/submission_widget.py
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@@ -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)