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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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3
src/submissions/frontend/__init__.py
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@@ -31,7 +31,8 @@ class App(QMainWindow):
self.ctx = ctx
# indicate version and connected database in title bar
try:
self.title = f"Submissions App (v{ctx['package'].__version__}) - {ctx['database']}"
# self.title = f"Submissions App (v{ctx['package'].__version__}) - {ctx['database']}"
self.title = f"Submissions App (v{ctx.package.__version__}) - {ctx.database_path}"
except (AttributeError, KeyError):
self.title = f"Submissions App"
# set initial app position and size

9
src/submissions/frontend/all_window_functions.py
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@@ -1,3 +1,6 @@
'''
functions used by all windows in the application's frontend
'''
from pathlib import Path
import logging
from PyQt6.QtWidgets import (
@@ -19,7 +22,8 @@ def select_open_file(obj:QMainWindow, file_extension:str) -> Path:
Returns:
Path: Path of file to be opened
"""
home_dir = str(Path(obj.ctx["directory_path"]))
# home_dir = str(Path(obj.ctx["directory_path"]))
home_dir = str(Path(obj.ctx.directory_path))
fname = Path(QFileDialog.getOpenFileName(obj, 'Open file', home_dir, filter = f"{file_extension}(*.{file_extension})")[0])
return fname
@@ -36,7 +40,8 @@ def select_save_file(obj:QMainWindow, default_name:str, extension:str) -> Path:
Path: Path of file to be opened
"""
try:
home_dir = Path(obj.ctx["directory_path"]).joinpath(default_name).resolve().__str__()
# home_dir = Path(obj.ctx["directory_path"]).joinpath(default_name).resolve().__str__()
home_dir = Path(obj.ctx.directory_path).joinpath(default_name).resolve().__str__()
except FileNotFoundError:
home_dir = Path.home().resolve().__str__()
fname = Path(QFileDialog.getSaveFileName(obj, "Save File", home_dir, filter = f"{extension}(*.{extension})")[0])

54
src/submissions/frontend/custom_widgets/misc.py
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@@ -14,7 +14,7 @@ from tools import check_not_nan
from ..all_window_functions import extract_form_info
from backend.db import get_all_reagenttype_names, lookup_all_sample_types, create_kit_from_yaml, \
lookup_regent_by_type_name, lookup_last_used_reagenttype_lot
from configure import jinja_template_loading
from tools import jinja_template_loading
import logging
import numpy as np
from .pop_ups import AlertPop
@@ -300,55 +300,3 @@ class ImportReagent(QComboBox):
self.setObjectName(f"lot_{reagent.type}")
self.addItems(relevant_reagents)
# class ImportReagent(QComboBox):
# def __init__(self, ctx:dict, reagent:dict):
# super().__init__()
# self.setEditable(True)
# # 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 {reagent['type']}")
# if isinstance(reagent['lot'], np.float64):
# logger.debug(f"{reagent['lot']} is a numpy float!")
# try:
# reagent['lot'] = int(reagent['lot'])
# except ValueError:
# pass
# # query for reagents using type name from sheet and kit from sheet
# logger.debug(f"Attempting lookup of reagents by type: {query_var}")
# # below was lookup_reagent_by_type_name_and_kit_name, but I couldn't get it to work.
# relevant_reagents = [item.__str__() for item in lookup_regent_by_type_name(ctx=ctx, type_name=query_var)]
# output_reg = []
# for rel_reagent in relevant_reagents:
# # extract strings from any sets.
# if isinstance(rel_reagent, set):
# for thing in rel_reagent:
# output_reg.append(thing)
# elif isinstance(rel_reagent, str):
# output_reg.append(rel_reagent)
# relevant_reagents = output_reg
# # if reagent in sheet is not found insert it into the front of relevant reagents so it shows
# logger.debug(f"Relevant reagents for {reagent['lot']}: {relevant_reagents}")
# if str(reagent['lot']) not in relevant_reagents:
# if check_not_nan(reagent['lot']):
# relevant_reagents.insert(0, str(reagent['lot']))
# else:
# # TODO: look up the last used reagent of this type in the database
# looked_up_reg = lookup_last_used_reagenttype_lot(ctx=ctx, type_name=reagent['type'])
# logger.debug(f"Because there was no reagent listed for {reagent}, we will insert the last lot used: {looked_up_reg}")
# if looked_up_reg != None:
# relevant_reagents.remove(str(looked_up_reg.lot))
# relevant_reagents.insert(0, str(looked_up_reg.lot))
# else:
# if len(relevant_reagents) > 1:
# logger.debug(f"Found {reagent['lot']} in relevant reagents: {relevant_reagents}. Moving to front of list.")
# idx = relevant_reagents.index(str(reagent['lot']))
# logger.debug(f"The index we got for {reagent['lot']} in {relevant_reagents} was {idx}")
# moved_reag = relevant_reagents.pop(idx)
# relevant_reagents.insert(0, moved_reag)
# else:
# logger.debug(f"Found {reagent['lot']} in relevant reagents: {relevant_reagents}. But no need to move due to short list.")
# logger.debug(f"New relevant reagents: {relevant_reagents}")
# self.setObjectName(f"lot_{reagent['type']}")
# self.addItems(relevant_reagents)

2
src/submissions/frontend/custom_widgets/pop_ups.py
View File

@@ -5,7 +5,7 @@ from PyQt6.QtWidgets import (
QLabel, QVBoxLayout, QDialog,
QDialogButtonBox, QMessageBox, QComboBox
)
from configure import jinja_template_loading
from tools import jinja_template_loading
import logging
from backend.db.functions import lookup_kittype_by_use

2
src/submissions/frontend/custom_widgets/sub_details.py
View File

@@ -16,7 +16,7 @@ from PyQt6.QtCore import Qt, QAbstractTableModel, QSortFilterProxyModel
from PyQt6.QtGui import QAction, QCursor, QPixmap, QPainter
from backend.db import submissions_to_df, lookup_submission_by_id, delete_submission_by_id, lookup_submission_by_rsl_num, hitpick_plate
from backend.excel import make_hitpicks
from configure import jinja_template_loading
from tools import jinja_template_loading
from xhtml2pdf import pisa
from pathlib import Path
import logging

40
src/submissions/frontend/main_window_functions.py
View File

@@ -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: