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Minor bug fixes.

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This commit is contained in:
Landon Wark
2023-12-07 12:50:03 -06:00
parent cbf36a5b0b
commit 0dd51827a0
22 changed files with 308 additions and 370 deletions
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39
src/submissions/frontend/widgets/submission_widget.py
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@@ -5,23 +5,20 @@ from PyQt6.QtWidgets import (
from PyQt6.QtCore import pyqtSignal
from pathlib import Path
from . import select_open_file, select_save_file
import logging
import logging, difflib, inspect, json, sys
from pathlib import Path
from tools import Report, Result, check_not_nan
from backend.excel.parser import SheetParser, PCRParser
from backend.validators import PydSubmission, PydReagent
from backend.db import (
check_kit_integrity, KitType, Organization, SubmissionType, Reagent,
KitType, Organization, SubmissionType, Reagent,
ReagentType, KitTypeReagentTypeAssociation, BasicSubmission
)
from pprint import pformat
from .pop_ups import QuestionAsker, AlertPop
# from .misc import ReagentFormWidget
from typing import List, Tuple
import difflib
from datetime import date
import inspect
import json
logger = logging.getLogger(f"submissions.{__name__}")
@@ -143,14 +140,14 @@ class SubmissionFormContainer(QWidget):
return
except AttributeError:
self.prsr = SheetParser(ctx=self.app.ctx, filepath=fname)
try:
logger.debug(f"Submission dictionary:\n{pformat(self.prsr.sub)}")
self.pyd = self.prsr.to_pydantic()
logger.debug(f"Pydantic result: \n\n{pformat(self.pyd)}\n\n")
except Exception as e:
report.add_result(Result(msg=f"Problem creating pydantic model:\n\n{e}", status="Critical"))
self.report.add_result(report)
return
# try:
logger.debug(f"Submission dictionary:\n{pformat(self.prsr.sub)}")
self.pyd = self.prsr.to_pydantic()
logger.debug(f"Pydantic result: \n\n{pformat(self.pyd)}\n\n")
# except Exception as e:
# report.add_result(Result(msg=f"Problem creating pydantic model:\n\n{e}", status="Critical"))
# self.report.add_result(report)
# return
self.form = self.pyd.toForm(parent=self)
self.layout().addWidget(self.form)
kit_widget = self.form.find_widgets(object_name="extraction_kit")[0].input
@@ -265,7 +262,8 @@ class SubmissionFormContainer(QWidget):
self.pyd: PydSubmission = self.form.parse_form()
logger.debug(f"Submission: {pformat(self.pyd)}")
logger.debug("Checking kit integrity...")
result = check_kit_integrity(sub=self.pyd)
# result = check_kit_integrity(sub=self.pyd)
result = self.pyd.check_kit_integrity()
report.add_result(result)
if len(result.results) > 0:
self.report.add_result(report)
@@ -417,7 +415,8 @@ class SubmissionFormWidget(QWidget):
# self.ignore = [None, "", "qt_spinbox_lineedit", "qt_scrollarea_viewport", "qt_scrollarea_hcontainer",
# "qt_scrollarea_vcontainer", "submit_btn"
# ]
self.ignore = ['filepath', 'samples', 'reagents', 'csv', 'ctx']
self.ignore = ['filepath', 'samples', 'reagents', 'csv', 'ctx', 'comment']
self.recover = ['filepath', 'samples', 'csv', 'comment']
layout = QVBoxLayout()
for k, v in kwargs.items():
if k not in self.ignore:
@@ -448,8 +447,6 @@ class SubmissionFormWidget(QWidget):
logger.debug(f"Hello from form parser!")
info = {}
reagents = []
if hasattr(self, 'csv'):
info['csv'] = self.csv
for widget in self.findChildren(QWidget):
# logger.debug(f"Parsed widget of type {type(widget)}")
match widget:
@@ -463,9 +460,13 @@ class SubmissionFormWidget(QWidget):
info[field] = value
logger.debug(f"Info: {pformat(info)}")
logger.debug(f"Reagents: {pformat(reagents)}")
# sys.exit()
# logger.debug(f"Attrs not in info: {[k for k, v in self.__dict__.items() if k not in info.keys()]}")
for item in self.recover:
if hasattr(self, item):
info[item] = getattr(self, item)
# app = self.parent().parent().parent().parent().parent().parent().parent().parent
submission = PydSubmission(filepath=self.filepath, reagents=reagents, samples=self.samples, **info)
# submission = PydSubmission(filepath=self.filepath, reagents=reagents, samples=self.samples, **info)
submission = PydSubmission(reagents=reagents, **info)
return submission
class InfoItem(QWidget):