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Large scale code cleanup

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This commit is contained in:
Landon Wark
2023-07-26 11:08:30 -05:00
parent 63308674c6
commit 82dffe3af2
16 changed files with 686 additions and 1289 deletions
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40
src/submissions/frontend/main_window_functions.py
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@@ -5,7 +5,6 @@ from datetime import date
import difflib
from getpass import getuser
import inspect
from pathlib import Path
import pprint
import yaml
import json
@@ -16,7 +15,7 @@ import pandas as pd
from backend.db.models import *
import logging
from PyQt6.QtWidgets import (
QMainWindow, QLabel, QWidget, QPushButton, QFileDialog,
QMainWindow, QLabel, QWidget, QPushButton,
QLineEdit, QComboBox, QDateEdit
)
from .all_window_functions import extract_form_info, select_open_file, select_save_file
@@ -25,12 +24,13 @@ from backend.db.functions import (
lookup_all_orgs, lookup_kittype_by_use, lookup_kittype_by_name,
construct_submission_info, lookup_reagent, store_submission, lookup_submissions_by_date_range,
create_kit_from_yaml, create_org_from_yaml, get_control_subtypes, get_all_controls_by_type,
lookup_all_submissions_by_type, get_all_controls, lookup_submission_by_rsl_num, update_ww_sample
lookup_all_submissions_by_type, get_all_controls, lookup_submission_by_rsl_num, update_ww_sample,
check_kit_integrity
)
from backend.excel.parser import SheetParser, PCRParser
from backend.excel.reports import make_report_html, make_report_xlsx, convert_data_list_to_df
from backend.pydant import PydReagent
from tools import check_not_nan, check_kit_integrity
from tools import check_not_nan
from .custom_widgets.pop_ups import AlertPop, QuestionAsker
from .custom_widgets import ReportDatePicker
from .custom_widgets.misc import ImportReagent
@@ -393,9 +393,8 @@ def generate_report_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
# make dataframe from record dictionaries
detailed_df, summary_df = make_report_xlsx(records=records)
html = make_report_html(df=summary_df, start_date=info['start_date'], end_date=info['end_date'])
# setup filedialog to handle save location of report
home_dir = Path(obj.ctx["directory_path"]).joinpath(f"Submissions_Report_{info['start_date']}-{info['end_date']}.pdf").resolve().__str__()
fname = Path(QFileDialog.getSaveFileName(obj, "Save File", home_dir, filter=".pdf")[0])
# get save location of report
fname = select_save_file(obj=obj, default_name=f"Submissions_Report_{info['start_date']}-{info['end_date']}.pdf", extension="pdf")
# logger.debug(f"report output name: {fname}")
with open(fname, "w+b") as f:
pisa.CreatePDF(html, dest=f)
@@ -613,13 +612,16 @@ def link_controls_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
# bcs.control_id.append(control.id)
control.submission = bcs
control.submission_id = bcs.id
obj.ctx["database_session"].add(control)
# obj.ctx["database_session"].add(control)
obj.ctx.database_session.add(control)
count += 1
obj.ctx["database_session"].add(bcs)
# obj.ctx["database_session"].add(bcs)
obj.ctx.database_session.add(bcs)
logger.debug(f"Here is the new control: {[control.name for control in bcs.controls]}")
result = dict(message=f"We added {count} controls to bacterial cultures.", status="information")
logger.debug(result)
obj.ctx['database_session'].commit()
# obj.ctx['database_session'].commit()
obj.ctx.database_session.commit()
# msg = QMessageBox()
# msg.setText("Controls added")
# msg.setInformativeText(result)
@@ -687,8 +689,10 @@ def link_extractions_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
logger.debug(f"Final ext info for {sub.rsl_plate_num}: {sub.extraction_info}")
else:
sub.extraction_info = json.dumps([new_run])
obj.ctx['database_session'].add(sub)
obj.ctx["database_session"].commit()
# obj.ctx['database_session'].add(sub)
# obj.ctx["database_session"].commit()
obj.ctx.database_session.add(sub)
obj.ctx.database_session.commit()
result = dict(message=f"We added {count} logs to the database.", status='information')
return obj, result
@@ -750,8 +754,10 @@ def link_pcr_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
logger.debug(f"Final ext info for {sub.rsl_plate_num}: {sub.pcr_info}")
else:
sub.pcr_info = json.dumps([new_run])
obj.ctx['database_session'].add(sub)
obj.ctx["database_session"].commit()
# obj.ctx['database_session'].add(sub)
# obj.ctx["database_session"].commit()
obj.ctx.database_session.add(sub)
obj.ctx.database_session.commit()
result = dict(message=f"We added {count} logs to the database.", status='information')
return obj, result
@@ -801,10 +807,12 @@ def import_pcr_results_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
logger.debug(f"Final pcr info for {sub.rsl_plate_num}: {sub.pcr_info}")
else:
sub.pcr_info = json.dumps([parser.pcr])
obj.ctx['database_session'].add(sub)
# obj.ctx['database_session'].add(sub)
obj.ctx.database_session.add(sub)
logger.debug(f"Existing {type(sub.pcr_info)}: {sub.pcr_info}")
logger.debug(f"Inserting {type(json.dumps(parser.pcr))}: {json.dumps(parser.pcr)}")
obj.ctx["database_session"].commit()
# obj.ctx["database_session"].commit()
obj.ctx.database_session.commit()
logger.debug(f"Got {len(parser.samples)} samples to update!")
logger.debug(f"Parser samples: {parser.samples}")
for sample in parser.samples: