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Pre-removal of constructors module.

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This commit is contained in:
Landon Wark
2023-10-23 09:36:57 -05:00
parent 39b94405e5
commit 4b1f88f1d0
16 changed files with 751 additions and 457 deletions
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30
src/submissions/frontend/__init__.py
View File

@@ -15,8 +15,9 @@ from PyQt6.QtGui import QAction
from PyQt6.QtWebEngineWidgets import QWebEngineView
from pathlib import Path
from backend.db import (
construct_reagent, store_object, lookup_control_types, lookup_modes
store_object, lookup_control_types, lookup_modes, #construct_reagent
)
from backend.validators import PydSubmission, PydReagent
from tools import check_if_app, Settings
from frontend.custom_widgets import SubmissionsSheet, AlertPop, AddReagentForm, KitAdder, ControlsDatePicker, ImportReagent
import logging
@@ -220,10 +221,11 @@ class App(QMainWindow):
info = dlg.parse_form()
logger.debug(f"Reagent info: {info}")
# create reagent object
reagent = construct_reagent(ctx=self.ctx, info_dict=info)
# reagent = construct_reagent(ctx=self.ctx, info_dict=info)
reagent = PydReagent(ctx=self.ctx, **info)
# send reagent to db
# store_reagent(ctx=self.ctx, reagent=reagent)
result = store_object(ctx=self.ctx, object=reagent)
result = store_object(ctx=self.ctx, object=reagent.toSQL()[0])
self.result_reporter(result=result)
return reagent
@@ -322,7 +324,7 @@ class AddSubForm(QWidget):
logger.debug(f"Initializating subform...")
super(QWidget, self).__init__(parent)
self.layout = QVBoxLayout(self)
self.parent = parent
# Initialize tab screen
self.tabs = QTabWidget()
self.tab1 = QWidget()
@@ -396,6 +398,7 @@ class SubmissionFormWidget(QWidget):
def __init__(self, parent: QWidget) -> None:
logger.debug(f"Setting form widget...")
super().__init__(parent)
self.parent = parent
self.ignore = [None, "", "qt_spinbox_lineedit", "qt_scrollarea_viewport", "qt_scrollarea_hcontainer",
"qt_scrollarea_vcontainer", "submit_btn"
]
@@ -411,23 +414,26 @@ class SubmissionFormWidget(QWidget):
fname = Path([u.toLocalFile() for u in event.mimeData().urls()][0])
self.import_drag.emit(fname)
def parse_form(self) -> Tuple[dict, list]:
logger.debug(f"Hello from parser!")
def parse_form(self) -> PydSubmission:
logger.debug(f"Hello from form parser!")
info = {}
reagents = []
samples = self.parent.parent.samples
logger.debug(f"Using samples: {pformat(samples)}")
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)}")
match widget:
case ImportReagent():
reagents.append(dict(name=widget.objectName().replace("lot_", ""), lot=widget.currentText()))
reagent = dict(name=widget.objectName().replace("lot_", ""), lot=widget.currentText(), type=None, exp=None)
reagents.append(PydReagent(ctx=self.parent.parent.ctx, **reagent))
case QLineEdit():
info[widget.objectName()] = widget.text()
info[widget.objectName()] = dict(value=widget.text())
case QComboBox():
info[widget.objectName()] = widget.currentText()
info[widget.objectName()] = dict(value=widget.currentText())
case QDateEdit():
info[widget.objectName()] = widget.date().toPyDate()
info[widget.objectName()] = dict(value=widget.date().toPyDate())
logger.debug(f"Info: {pformat(info)}")
logger.debug(f"Reagents: {pformat(reagents)}")
return info, reagents
submission = PydSubmission(ctx=self.parent.parent.ctx, filepath=self.parent.parent.current_file, reagents=reagents, samples=samples, **info)
return submission

12
src/submissions/frontend/custom_widgets/misc.py
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@@ -13,15 +13,15 @@ from PyQt6.QtWidgets import (
)
from PyQt6.QtCore import Qt, QDate, QSize
from tools import check_not_nan, jinja_template_loading, Settings
from backend.db.functions import construct_kit_from_yaml, \
from backend.db.functions import \
lookup_reagent_types, lookup_reagents, lookup_submission_type, lookup_reagenttype_kittype_association, \
lookup_submissions
lookup_submissions#, construct_kit_from_yaml
from backend.db.models import SubmissionTypeKitTypeAssociation
from sqlalchemy import FLOAT, INTEGER
import logging
import numpy as np
from .pop_ups import AlertPop
from backend.validators import PydSheetReagent
from backend.validators import PydReagent
from typing import Tuple
logger = logging.getLogger(f"submissions.{__name__}")
@@ -92,7 +92,7 @@ class AddReagentForm(QDialog):
def parse_form(self):
return dict(name=self.name_input.currentText(),
lot=self.lot_input.text(),
expiry=self.exp_input.date().toPyDate(),
exp=self.exp_input.date().toPyDate(),
type=self.type_input.currentText())
def update_names(self):
@@ -386,11 +386,11 @@ class ControlsDatePicker(QWidget):
class ImportReagent(QComboBox):
def __init__(self, ctx:Settings, reagent:dict|PydSheetReagent, extraction_kit:str):
def __init__(self, ctx:Settings, reagent:dict|PydReagent, extraction_kit:str):
super().__init__()
self.setEditable(True)
if isinstance(reagent, dict):
reagent = PydSheetReagent(**reagent)
reagent = PydReagent(ctx=ctx, **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 {query_var}")

70
src/submissions/frontend/main_window_functions.py
View File

@@ -24,12 +24,14 @@ from .all_window_functions import select_open_file, select_save_file
from PyQt6.QtCore import QSignalBlocker
from backend.db.models import BasicSubmission
from backend.db.functions import (
construct_submission_info, lookup_reagents, construct_kit_from_yaml, construct_org_from_yaml, get_control_subtypes,
lookup_reagents, get_control_subtypes,
update_subsampassoc_with_pcr, check_kit_integrity, update_last_used, lookup_organizations, lookup_kit_types,
lookup_submissions, lookup_controls, lookup_samples, lookup_submission_sample_association, store_object, lookup_submission_type,
#construct_submission_info, construct_kit_from_yaml, construct_org_from_yaml
)
from backend.excel.parser import SheetParser, PCRParser, SampleParser
from backend.excel.reports import make_report_html, make_report_xlsx, convert_data_list_to_df
from backend.validators import PydSubmission, PydSample, PydReagent
from tools import check_not_nan, convert_well_to_row_column
from .custom_widgets.pop_ups import AlertPop, QuestionAsker
from .custom_widgets import ReportDatePicker
@@ -79,6 +81,7 @@ def import_submission_function(obj:QMainWindow, fname:Path|None=None) -> Tuple[Q
for item in obj.table_widget.formlayout.parentWidget().findChildren(QWidget):
item.setParent(None)
obj.current_submission_type = pyd.submission_type['value']
obj.current_file = pyd.filepath
# Get list of fields from pydantic model.
fields = list(pyd.model_fields.keys()) + list(pyd.model_extra.keys())
fields.remove('filepath')
@@ -97,7 +100,6 @@ def import_submission_function(obj:QMainWindow, fname:Path|None=None) -> Tuple[Q
logger.debug(f"{field}: {value['value']}")
# create combobox to hold looked up submitting labs
add_widget = QComboBox()
# labs = [item.__str__() for item in lookup_all_orgs(ctx=obj.ctx)]
labs = [item.__str__() for item in lookup_organizations(ctx=obj.ctx)]
# try to set closest match to top of list
try:
@@ -149,12 +151,7 @@ def import_submission_function(obj:QMainWindow, fname:Path|None=None) -> Tuple[Q
except ValueError:
cats.insert(0, cats.pop(cats.index(pyd.submission_type['value'])))
add_widget.addItems(cats)
case "ctx":
continue
case 'reagents':
# NOTE: This is now set to run when the extraction kit is updated.
continue
case 'csv':
case "ctx" | 'reagents' | 'csv' | 'filepath':
continue
case _:
# anything else gets added in as a line edit
@@ -178,7 +175,6 @@ def import_submission_function(obj:QMainWindow, fname:Path|None=None) -> Tuple[Q
if "csv" in pyd.model_extra:
obj.csv = pyd.model_extra['csv']
logger.debug(f"All attributes of obj:\n{pprint.pformat(obj.__dict__)}")
return obj, result
def kit_reload_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
@@ -265,41 +261,44 @@ def submit_new_sample_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
# # seperate out reagents
# reagents = {k.replace("lot_", ""):v for k,v in info.items() if k.startswith("lot_")}
# info = {k:v for k,v in info.items() if not k.startswith("lot_")}
info, reagents = obj.table_widget.formwidget.parse_form()
logger.debug(f"Info: {info}")
logger.debug(f"Reagents: {reagents}")
# info, reagents = obj.table_widget.formwidget.parse_form()
submission: PydSubmission = obj.table_widget.formwidget.parse_form()
logger.debug(f"Submission: {pprint.pformat(submission)}")
parsed_reagents = []
# compare reagents in form to reagent database
for reagent in reagents:
for reagent in submission.reagents:
# Lookup any existing reagent of this type with this lot number
wanted_reagent = lookup_reagents(ctx=obj.ctx, lot_number=reagent['lot'], reagent_type=reagent['name'])
wanted_reagent = lookup_reagents(ctx=obj.ctx, lot_number=reagent.lot, reagent_type=reagent.name)
logger.debug(f"Looked up reagent: {wanted_reagent}")
# if reagent not found offer to add to database
if wanted_reagent == None:
# r_lot = reagent[reagent]
r_lot = reagent['lot']
dlg = QuestionAsker(title=f"Add {r_lot}?", message=f"Couldn't find reagent type {reagent['name'].strip('Lot')}: {r_lot} in the database.\n\nWould you like to add it?")
dlg = QuestionAsker(title=f"Add {reagent.lot}?", message=f"Couldn't find reagent type {reagent.name.strip('Lot')}: {reagent.lot} in the database.\n\nWould you like to add it?")
if dlg.exec():
logger.debug(f"Looking through {pprint.pformat(obj.reagents)} for reagent {reagent['name']}")
logger.debug(f"Looking through {pprint.pformat(obj.reagents)} for reagent {reagent.name}")
try:
picked_reagent = [item for item in obj.reagents if item.type == reagent['name']][0]
picked_reagent = [item for item in obj.reagents if item.type == reagent.name][0]
except IndexError:
logger.error(f"Couldn't find {reagent['name']} in obj.reagents. Checking missing reagents {pprint.pformat(obj.missing_reagents)}")
picked_reagent = [item for item in obj.missing_reagents if item.type == reagent['name']][0]
logger.debug(f"checking reagent: {reagent['name']} in obj.reagents. Result: {picked_reagent}")
logger.error(f"Couldn't find {reagent.name} in obj.reagents. Checking missing reagents {pprint.pformat(obj.missing_reagents)}")
picked_reagent = [item for item in obj.missing_reagents if item.type == reagent.name][0]
logger.debug(f"checking reagent: {reagent.name} in obj.reagents. Result: {picked_reagent}")
expiry_date = picked_reagent.exp
wanted_reagent = obj.add_reagent(reagent_lot=r_lot, reagent_type=reagent['name'].replace("lot_", ""), expiry=expiry_date, name=picked_reagent.name)
wanted_reagent = obj.add_reagent(reagent_lot=reagent.lot, reagent_type=reagent.name.replace("lot_", ""), expiry=expiry_date, name=picked_reagent.name)
else:
# In this case we will have an empty reagent and the submission will fail kit integrity check
logger.debug("Will not add reagent.")
return obj, dict(message="Failed integrity check", status="critical")
parsed_reagents.append(wanted_reagent)
# Append the PydReagent object o be added to the submission
parsed_reagents.append(reagent)
# move samples into preliminary submission dict
info['samples'] = obj.samples
info['uploaded_by'] = getuser()
submission.reagents = parsed_reagents
# submission.uploaded_by = getuser()
# construct submission object
logger.debug(f"Here is the info_dict: {pprint.pformat(info)}")
base_submission, result = construct_submission_info(ctx=obj.ctx, info_dict=info)
# logger.debug(f"Here is the info_dict: {pprint.pformat(info)}")
# base_submission, result = construct_submission_info(ctx=obj.ctx, info_dict=info)
base_submission, result = submission.toSQL()
# delattr(base_submission, "ctx")
# raise ValueError(base_submission.__dict__)
# check output message for issues
match result['code']:
# code 1: ask for overwrite
@@ -307,7 +306,8 @@ def submit_new_sample_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
dlg = QuestionAsker(title=f"Review {base_submission.rsl_plate_num}?", message=result['message'])
if dlg.exec():
# Do not add duplicate reagents.
base_submission.reagents = []
# base_submission.reagents = []
pass
else:
obj.ctx.database_session.rollback()
return obj, dict(message="Overwrite cancelled", status="Information")
@@ -317,16 +317,17 @@ def submit_new_sample_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
case _:
pass
# add reagents to submission object
for reagent in parsed_reagents:
base_submission.reagents.append(reagent)
for reagent in base_submission.reagents:
update_last_used(ctx=obj.ctx, reagent=reagent, kit=base_submission.extraction_kit)
logger.debug(f"Parsed reagents: {pprint.pformat(parsed_reagents)}")
logger.debug(f"Here is the final submission: {pprint.pformat(base_submission.__dict__)}")
logger.debug(f"Parsed reagents: {pprint.pformat(base_submission.reagents)}")
logger.debug("Checking kit integrity...")
kit_integrity = check_kit_integrity(base_submission)
if kit_integrity != None:
return obj, dict(message=kit_integrity['message'], status="critical")
logger.debug(f"Sending submission: {base_submission.rsl_plate_num} to database.")
result = store_object(ctx=obj.ctx, object=base_submission)
# result = store_object(ctx=obj.ctx, object=base_submission)
base_submission.save(ctx=obj.ctx)
# update summary sheet
obj.table_widget.sub_wid.setData()
# reset form
@@ -339,9 +340,10 @@ def submit_new_sample_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
logger.debug(f"We have the extraction kit: {extraction_kit.name}")
excel_map = extraction_kit.construct_xl_map_for_use(obj.current_submission_type)
logger.debug(f"Extraction kit map:\n\n{pprint.pformat(excel_map)}")
input_reagents = [item.to_reagent_dict(extraction_kit=base_submission.extraction_kit) for item in parsed_reagents]
input_reagents = [item.to_reagent_dict(extraction_kit=base_submission.extraction_kit) for item in base_submission.reagents]
logger.debug(f"Parsed reagents going into autofile: {pprint.pformat(input_reagents)}")
autofill_excel(obj=obj, xl_map=excel_map, reagents=input_reagents, missing_reagents=obj.missing_reagents, info=info, missing_info=obj.missing_info)
# autofill_excel(obj=obj, xl_map=excel_map, reagents=input_reagents, missing_reagents=obj.missing_reagents, info=info, missing_info=obj.missing_info)
autofill_excel(obj=obj, xl_map=excel_map, reagents=input_reagents, missing_reagents=obj.missing_reagents, info=base_submission.__dict__, missing_info=obj.missing_info)
if hasattr(obj, 'csv'):
dlg = QuestionAsker("Export CSV?", "Would you like to export the csv file?")
if dlg.exec():