Addition of autofilling excel forms. Improved pydantic validation.
This commit is contained in:
Landon Wark
@@ -10,14 +10,12 @@ from PyQt6.QtWidgets import (
|
||||
)
|
||||
from PyQt6.QtGui import QAction
|
||||
from PyQt6.QtWebEngineWidgets import QWebEngineView
|
||||
# import pandas as pd
|
||||
from pathlib import Path
|
||||
from backend.db import (
|
||||
construct_reagent, get_all_Control_Types_names, get_all_available_modes, store_reagent
|
||||
)
|
||||
from .main_window_functions import *
|
||||
from tools import check_if_app
|
||||
# from backend.excel.reports import
|
||||
from frontend.custom_widgets import SubmissionsSheet, AlertPop, AddReagentForm, KitAdder, ControlsDatePicker
|
||||
import logging
|
||||
from datetime import date
|
||||
@@ -31,7 +29,7 @@ class App(QMainWindow):
|
||||
def __init__(self, ctx: dict = {}):
|
||||
super().__init__()
|
||||
self.ctx = ctx
|
||||
# indicate version and database connected in title bar
|
||||
# indicate version and connected database in title bar
|
||||
try:
|
||||
self.title = f"Submissions App (v{ctx['package'].__version__}) - {ctx['database']}"
|
||||
except (AttributeError, KeyError):
|
||||
@@ -123,11 +121,17 @@ class App(QMainWindow):
|
||||
self.docsAction.triggered.connect(self.openDocs)
|
||||
|
||||
def showAbout(self):
|
||||
"""
|
||||
Show the 'about' message
|
||||
"""
|
||||
output = f"Version: {self.ctx['package'].__version__}\n\nAuthor: {self.ctx['package'].__author__['name']} - {self.ctx['package'].__author__['email']}\n\nCopyright: {self.ctx['package'].__copyright__}"
|
||||
about = AlertPop(message=output, status="information")
|
||||
about.exec()
|
||||
|
||||
def openDocs(self):
|
||||
"""
|
||||
Open the documentation html pages
|
||||
"""
|
||||
if check_if_app():
|
||||
url = Path(sys._MEIPASS).joinpath("files", "docs", "index.html")
|
||||
else:
|
||||
@@ -135,8 +139,13 @@ class App(QMainWindow):
|
||||
logger.debug(f"Attempting to open {url}")
|
||||
webbrowser.get('windows-default').open(f"file://{url.__str__()}")
|
||||
|
||||
# All main window functions return a result which is reported here, unless it is None
|
||||
def result_reporter(self, result:dict|None=None):
|
||||
"""
|
||||
Report any anomolous results - if any - to the user
|
||||
|
||||
Args:
|
||||
result (dict | None, optional): The result from a function. Defaults to None.
|
||||
"""
|
||||
if result != None:
|
||||
msg = AlertPop(message=result['message'], status=result['status'])
|
||||
msg.exec()
|
||||
@@ -149,14 +158,12 @@ class App(QMainWindow):
|
||||
logger.debug(f"Import result: {result}")
|
||||
self.result_reporter(result)
|
||||
|
||||
|
||||
def kit_reload(self):
|
||||
"""
|
||||
Removes all reagents from form before running kit integrity completion.
|
||||
"""
|
||||
self, result = kit_reload_function(self)
|
||||
self.result_reporter(result)
|
||||
|
||||
|
||||
def kit_integrity_completion(self):
|
||||
"""
|
||||
@@ -166,7 +173,6 @@ class App(QMainWindow):
|
||||
"""
|
||||
self, result = kit_integrity_completion_function(self)
|
||||
self.result_reporter(result)
|
||||
|
||||
|
||||
def submit_new_sample(self):
|
||||
"""
|
||||
@@ -174,82 +180,6 @@ class App(QMainWindow):
|
||||
"""
|
||||
self, result = submit_new_sample_function(self)
|
||||
self.result_reporter(result)
|
||||
# get info from form
|
||||
# info = extract_form_info(self.table_widget.tab1)
|
||||
# reagents = {k: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_")}
|
||||
# logger.debug(f"Info: {info}")
|
||||
# logger.debug(f"Reagents: {reagents}")
|
||||
# parsed_reagents = []
|
||||
# # compare reagents in form to reagent database
|
||||
# for reagent in reagents:
|
||||
# wanted_reagent = lookup_reagent(ctx=self.ctx, reagent_lot=reagents[reagent])
|
||||
# logger.debug(f"Looked up reagent: {wanted_reagent}")
|
||||
# # if reagent not found offer to add to database
|
||||
# if wanted_reagent == None:
|
||||
# r_lot = reagents[reagent]
|
||||
# dlg = QuestionAsker(title=f"Add {r_lot}?", message=f"Couldn't find reagent type {reagent.replace('_', ' ').title().strip('Lot')}: {r_lot} in the database.\n\nWould you like to add it?")
|
||||
# if dlg.exec():
|
||||
# logger.debug(f"checking reagent: {reagent} in self.reagents. Result: {self.reagents[reagent]}")
|
||||
# expiry_date = self.reagents[reagent]['exp']
|
||||
# wanted_reagent = self.add_reagent(reagent_lot=r_lot, reagent_type=reagent.replace("lot_", ""), expiry=expiry_date)
|
||||
# else:
|
||||
# # In this case we will have an empty reagent and the submission will fail kit integrity check
|
||||
# logger.debug("Will not add reagent.")
|
||||
# if wanted_reagent != None:
|
||||
# parsed_reagents.append(wanted_reagent)
|
||||
# # move samples into preliminary submission dict
|
||||
# info['samples'] = self.samples
|
||||
# info['uploaded_by'] = getuser()
|
||||
# # construct submission object
|
||||
# logger.debug(f"Here is the info_dict: {pprint.pformat(info)}")
|
||||
# base_submission, result = construct_submission_info(ctx=self.ctx, info_dict=info)
|
||||
# # check output message for issues
|
||||
# match result['code']:
|
||||
# # code 1: ask for overwrite
|
||||
# case 1:
|
||||
# dlg = QuestionAsker(title=f"Review {base_submission.rsl_plate_num}?", message=result['message'])
|
||||
# if dlg.exec():
|
||||
# base_submission.reagents = []
|
||||
# else:
|
||||
# return
|
||||
# # code 2: No RSL plate number given
|
||||
# case 2:
|
||||
# dlg = AlertPop(message=result['message'], status='critical')
|
||||
# dlg.exec()
|
||||
# return
|
||||
# case _:
|
||||
# pass
|
||||
# # add reagents to submission object
|
||||
# for reagent in parsed_reagents:
|
||||
# base_submission.reagents.append(reagent)
|
||||
# logger.debug("Checking kit integrity...")
|
||||
# kit_integrity = check_kit_integrity(base_submission)
|
||||
# if kit_integrity != None:
|
||||
# msg = AlertPop(message=kit_integrity['message'], status="critical")
|
||||
# msg.exec()
|
||||
# return
|
||||
# logger.debug(f"Sending submission: {base_submission.rsl_plate_num} to database.")
|
||||
# result = store_submission(ctx=self.ctx, base_submission=base_submission)
|
||||
# # check result of storing for issues
|
||||
# if result != None:
|
||||
# msg = AlertPop(result['message'])
|
||||
# msg.exec()
|
||||
# # update summary sheet
|
||||
# self.table_widget.sub_wid.setData()
|
||||
# # reset form
|
||||
# for item in self.table_widget.formlayout.parentWidget().findChildren(QWidget):
|
||||
# item.setParent(None)
|
||||
# if hasattr(self, 'csv'):
|
||||
# dlg = QuestionAsker("Export CSV?", "Would you like to export the csv file?")
|
||||
# if dlg.exec():
|
||||
# home_dir = Path(self.ctx["directory_path"]).joinpath(f"{base_submission.rsl_plate_num}.csv").resolve().__str__()
|
||||
# fname = Path(QFileDialog.getSaveFileName(self, "Save File", home_dir, filter=".csv")[0])
|
||||
# try:
|
||||
# self.csv.to_csv(fname.__str__(), index=False)
|
||||
# except PermissionError:
|
||||
# logger.debug(f"Could not get permissions to {fname}. Possibly the request was cancelled.")
|
||||
|
||||
|
||||
def add_reagent(self, reagent_lot:str|None=None, reagent_type:str|None=None, expiry:date|None=None):
|
||||
"""
|
||||
@@ -277,7 +207,6 @@ class App(QMainWindow):
|
||||
# send reagent to db
|
||||
store_reagent(ctx=self.ctx, reagent=reagent)
|
||||
return reagent
|
||||
|
||||
|
||||
def generateReport(self):
|
||||
"""
|
||||
@@ -285,42 +214,6 @@ class App(QMainWindow):
|
||||
"""
|
||||
self, result = generate_report_function(self)
|
||||
self.result_reporter(result)
|
||||
# Custom two date picker for start & end dates
|
||||
# dlg = ReportDatePicker()
|
||||
# if dlg.exec():
|
||||
# info = extract_form_info(dlg)
|
||||
# logger.debug(f"Report info: {info}")
|
||||
# # find submissions based on date range
|
||||
# subs = lookup_submissions_by_date_range(ctx=self.ctx, start_date=info['start_date'], end_date=info['end_date'])
|
||||
# # convert each object to dict
|
||||
# records = [item.report_dict() for item in subs]
|
||||
# # make dataframe from record dictionaries
|
||||
# df = make_report_xlsx(records=records)
|
||||
# html = make_report_html(df=df, start_date=info['start_date'], end_date=info['end_date'])
|
||||
# # setup filedialog to handle save location of report
|
||||
# home_dir = Path(self.ctx["directory_path"]).joinpath(f"Submissions_Report_{info['start_date']}-{info['end_date']}.pdf").resolve().__str__()
|
||||
# fname = Path(QFileDialog.getSaveFileName(self, "Save File", home_dir, filter=".pdf")[0])
|
||||
# # logger.debug(f"report output name: {fname}")
|
||||
# with open(fname, "w+b") as f:
|
||||
# pisa.CreatePDF(html, dest=f)
|
||||
# writer = pd.ExcelWriter(fname.with_suffix(".xlsx"), engine='openpyxl')
|
||||
# df.to_excel(writer, sheet_name="Report")
|
||||
# worksheet = writer.sheets['Report']
|
||||
# for idx, col in enumerate(df): # loop through all columns
|
||||
# series = df[col]
|
||||
# max_len = max((
|
||||
# series.astype(str).map(len).max(), # len of largest item
|
||||
# len(str(series.name)) # len of column name/header
|
||||
# )) + 20 # adding a little extra space
|
||||
# try:
|
||||
# worksheet.column_dimensions[get_column_letter(idx)].width = max_len
|
||||
# except ValueError:
|
||||
# pass
|
||||
# for cell in worksheet['D']:
|
||||
# if cell.row > 1:
|
||||
# cell.style = 'Currency'
|
||||
# writer.close()
|
||||
|
||||
|
||||
def add_kit(self):
|
||||
"""
|
||||
@@ -328,29 +221,6 @@ class App(QMainWindow):
|
||||
"""
|
||||
self, result = add_kit_function(self)
|
||||
self.result_reporter(result)
|
||||
# setup file dialog to find yaml flie
|
||||
# home_dir = str(Path(self.ctx["directory_path"]))
|
||||
# fname = Path(QFileDialog.getOpenFileName(self, 'Open file', home_dir, filter = "yml(*.yml)")[0])
|
||||
# assert fname.exists()
|
||||
# # read yaml file
|
||||
# try:
|
||||
# with open(fname.__str__(), "r") as stream:
|
||||
# try:
|
||||
# exp = yaml.load(stream, Loader=yaml.Loader)
|
||||
# except yaml.YAMLError as exc:
|
||||
# logger.error(f'Error reading yaml file {fname}: {exc}')
|
||||
# return {}
|
||||
# except PermissionError:
|
||||
# return
|
||||
# # send to kit creator function
|
||||
# result = create_kit_from_yaml(ctx=self.ctx, exp=exp)
|
||||
# match result['code']:
|
||||
# case 0:
|
||||
# msg = AlertPop(message=result['message'], status='info')
|
||||
# case 1:
|
||||
# msg = AlertPop(message=result['message'], status='critical')
|
||||
# msg.exec()
|
||||
|
||||
|
||||
def add_org(self):
|
||||
"""
|
||||
@@ -358,29 +228,6 @@ class App(QMainWindow):
|
||||
"""
|
||||
self, result = add_org_function(self)
|
||||
self.result_reporter(result)
|
||||
# # setup file dialog to find yaml flie
|
||||
# home_dir = str(Path(self.ctx["directory_path"]))
|
||||
# fname = Path(QFileDialog.getOpenFileName(self, 'Open file', home_dir, filter = "yml(*.yml)")[0])
|
||||
# assert fname.exists()
|
||||
# # read yaml file
|
||||
# try:
|
||||
# with open(fname.__str__(), "r") as stream:
|
||||
# try:
|
||||
# org = yaml.load(stream, Loader=yaml.Loader)
|
||||
# except yaml.YAMLError as exc:
|
||||
# logger.error(f'Error reading yaml file {fname}: {exc}')
|
||||
# return {}
|
||||
# except PermissionError:
|
||||
# return
|
||||
# # send to kit creator function
|
||||
# result = create_org_from_yaml(ctx=self.ctx, org=org)
|
||||
# match result['code']:
|
||||
# case 0:
|
||||
# msg = AlertPop(message=result['message'], status='information')
|
||||
# case 1:
|
||||
# msg = AlertPop(message=result['message'], status='critical')
|
||||
# msg.exec()
|
||||
|
||||
|
||||
def _controls_getter(self):
|
||||
"""
|
||||
@@ -388,39 +235,6 @@ class App(QMainWindow):
|
||||
"""
|
||||
self, result = controls_getter_function(self)
|
||||
self.result_reporter(result)
|
||||
# # subtype defaults to disabled
|
||||
# try:
|
||||
# self.table_widget.sub_typer.disconnect()
|
||||
# except TypeError:
|
||||
# pass
|
||||
# # correct start date being more recent than end date and rerun
|
||||
# if self.table_widget.datepicker.start_date.date() > self.table_widget.datepicker.end_date.date():
|
||||
# logger.warning("Start date after end date is not allowed!")
|
||||
# threemonthsago = self.table_widget.datepicker.end_date.date().addDays(-60)
|
||||
# # block signal that will rerun controls getter and set start date
|
||||
# with QSignalBlocker(self.table_widget.datepicker.start_date) as blocker:
|
||||
# self.table_widget.datepicker.start_date.setDate(threemonthsago)
|
||||
# self._controls_getter()
|
||||
# return
|
||||
# # convert to python useable date object
|
||||
# self.start_date = self.table_widget.datepicker.start_date.date().toPyDate()
|
||||
# self.end_date = self.table_widget.datepicker.end_date.date().toPyDate()
|
||||
# self.con_type = self.table_widget.control_typer.currentText()
|
||||
# self.mode = self.table_widget.mode_typer.currentText()
|
||||
# self.table_widget.sub_typer.clear()
|
||||
# # lookup subtypes
|
||||
# sub_types = get_control_subtypes(ctx=self.ctx, type=self.con_type, mode=self.mode)
|
||||
# if sub_types != []:
|
||||
# # block signal that will rerun controls getter and update sub_typer
|
||||
# with QSignalBlocker(self.table_widget.sub_typer) as blocker:
|
||||
# self.table_widget.sub_typer.addItems(sub_types)
|
||||
# self.table_widget.sub_typer.setEnabled(True)
|
||||
# self.table_widget.sub_typer.currentTextChanged.connect(self._chart_maker)
|
||||
# else:
|
||||
# self.table_widget.sub_typer.clear()
|
||||
# self.table_widget.sub_typer.setEnabled(False)
|
||||
# self._chart_maker()
|
||||
|
||||
|
||||
def _chart_maker(self):
|
||||
"""
|
||||
@@ -428,42 +242,6 @@ class App(QMainWindow):
|
||||
"""
|
||||
self, result = chart_maker_function(self)
|
||||
self.result_reporter(result)
|
||||
# logger.debug(f"Control getter context: \n\tControl type: {self.con_type}\n\tMode: {self.mode}\n\tStart Date: {self.start_date}\n\tEnd Date: {self.end_date}")
|
||||
# if self.table_widget.sub_typer.currentText() == "":
|
||||
# self.subtype = None
|
||||
# else:
|
||||
# self.subtype = self.table_widget.sub_typer.currentText()
|
||||
# logger.debug(f"Subtype: {self.subtype}")
|
||||
# # query all controls using the type/start and end dates from the gui
|
||||
# controls = get_all_controls_by_type(ctx=self.ctx, con_type=self.con_type, start_date=self.start_date, end_date=self.end_date)
|
||||
# # if no data found from query set fig to none for reporting in webview
|
||||
# if controls == None:
|
||||
# fig = None
|
||||
# else:
|
||||
# # change each control to list of dicts
|
||||
# data = [control.convert_by_mode(mode=self.mode) for control in controls]
|
||||
# # flatten data to one dimensional list
|
||||
# data = [item for sublist in data for item in sublist]
|
||||
# # send to dataframe creator
|
||||
# df = convert_data_list_to_df(ctx=self.ctx, input=data, subtype=self.subtype)
|
||||
# if self.subtype == None:
|
||||
# title = self.mode
|
||||
# else:
|
||||
# title = f"{self.mode} - {self.subtype}"
|
||||
# # send dataframe to chart maker
|
||||
# fig = create_charts(ctx=self.ctx, df=df, ytitle=title)
|
||||
# logger.debug(f"Updating figure...")
|
||||
# # construct html for webview
|
||||
# html = '<html><body>'
|
||||
# if fig != None:
|
||||
# html += plotly.offline.plot(fig, output_type='div', include_plotlyjs='cdn')#, image = 'png', auto_open=True, image_filename='plot_image')
|
||||
# else:
|
||||
# html += "<h1>No data was retrieved for the given parameters.</h1>"
|
||||
# html += '</body></html>'
|
||||
# self.table_widget.webengineview.setHtml(html)
|
||||
# self.table_widget.webengineview.update()
|
||||
# logger.debug("Figure updated... I hope.")
|
||||
|
||||
|
||||
def linkControls(self):
|
||||
"""
|
||||
@@ -471,52 +249,6 @@ class App(QMainWindow):
|
||||
"""
|
||||
self, result = link_controls_function(self)
|
||||
self.result_reporter(result)
|
||||
# all_bcs = lookup_all_submissions_by_type(self.ctx, "Bacterial Culture")
|
||||
# logger.debug(all_bcs)
|
||||
# all_controls = get_all_controls(self.ctx)
|
||||
# ac_list = [control.name for control in all_controls]
|
||||
# count = 0
|
||||
# for bcs in all_bcs:
|
||||
# logger.debug(f"Running for {bcs.rsl_plate_num}")
|
||||
# logger.debug(f"Here is the current control: {[control.name for control in bcs.controls]}")
|
||||
# samples = [sample.sample_id for sample in bcs.samples]
|
||||
# logger.debug(bcs.controls)
|
||||
# for sample in samples:
|
||||
# # replace below is a stopgap method because some dingus decided to add spaces in some of the ATCC49... so it looks like "ATCC 49"...
|
||||
# if " " in sample:
|
||||
# logger.warning(f"There is not supposed to be a space in the sample name!!!")
|
||||
# sample = sample.replace(" ", "")
|
||||
# # if sample not in ac_list:
|
||||
# if not any([ac.startswith(sample) for ac in ac_list]):
|
||||
# continue
|
||||
# else:
|
||||
# for control in all_controls:
|
||||
# diff = difflib.SequenceMatcher(a=sample, b=control.name).ratio()
|
||||
# if control.name.startswith(sample):
|
||||
# logger.debug(f"Checking {sample} against {control.name}... {diff}")
|
||||
# logger.debug(f"Found match:\n\tSample: {sample}\n\tControl: {control.name}\n\tDifference: {diff}")
|
||||
# if control in bcs.controls:
|
||||
# logger.debug(f"{control.name} already in {bcs.rsl_plate_num}, skipping")
|
||||
# continue
|
||||
# else:
|
||||
# logger.debug(f"Adding {control.name} to {bcs.rsl_plate_num} as control")
|
||||
# bcs.controls.append(control)
|
||||
# # bcs.control_id.append(control.id)
|
||||
# control.submission = bcs
|
||||
# control.submission_id = bcs.id
|
||||
# self.ctx["database_session"].add(control)
|
||||
# count += 1
|
||||
# self.ctx["database_session"].add(bcs)
|
||||
# logger.debug(f"Here is the new control: {[control.name for control in bcs.controls]}")
|
||||
# result = f"We added {count} controls to bacterial cultures."
|
||||
# logger.debug(result)
|
||||
# self.ctx['database_session'].commit()
|
||||
# msg = QMessageBox()
|
||||
# msg.setText("Controls added")
|
||||
# msg.setInformativeText(result)
|
||||
# msg.setWindowTitle("Controls added")
|
||||
# msg.exec()
|
||||
|
||||
|
||||
def linkExtractions(self):
|
||||
"""
|
||||
@@ -524,55 +256,6 @@ class App(QMainWindow):
|
||||
"""
|
||||
self, result = link_extractions_function(self)
|
||||
self.result_reporter(result)
|
||||
# home_dir = str(Path(self.ctx["directory_path"]))
|
||||
# fname = Path(QFileDialog.getOpenFileName(self, 'Open file', home_dir, filter = "csv(*.csv)")[0])
|
||||
# with open(fname.__str__(), 'r') as f:
|
||||
# runs = [col.strip().split(",") for col in f.readlines()]
|
||||
# count = 0
|
||||
# for run in runs:
|
||||
# obj = dict(
|
||||
# start_time=run[0].strip(),
|
||||
# rsl_plate_num=run[1].strip(),
|
||||
# sample_count=run[2].strip(),
|
||||
# status=run[3].strip(),
|
||||
# experiment_name=run[4].strip(),
|
||||
# end_time=run[5].strip()
|
||||
# )
|
||||
# for ii in range(6, len(run)):
|
||||
# obj[f"column{str(ii-5)}_vol"] = run[ii]
|
||||
# sub = lookup_submission_by_rsl_num(ctx=self.ctx, rsl_num=obj['rsl_plate_num'])
|
||||
# try:
|
||||
# logger.debug(f"Found submission: {sub.rsl_plate_num}")
|
||||
# count += 1
|
||||
# except AttributeError:
|
||||
# continue
|
||||
# if sub.extraction_info != None:
|
||||
# existing = json.loads(sub.extraction_info)
|
||||
# else:
|
||||
# existing = None
|
||||
# try:
|
||||
# if json.dumps(obj) in sub.extraction_info:
|
||||
# logger.debug(f"Looks like we already have that info.")
|
||||
# continue
|
||||
# except TypeError:
|
||||
# pass
|
||||
# if existing != None:
|
||||
# try:
|
||||
# logger.debug(f"Updating {type(existing)}: {existing} with {type(obj)}: {obj}")
|
||||
# existing.append(obj)
|
||||
# logger.debug(f"Setting: {existing}")
|
||||
# sub.extraction_info = json.dumps(existing)
|
||||
# except TypeError:
|
||||
# logger.error(f"Error updating!")
|
||||
# sub.extraction_info = json.dumps([obj])
|
||||
# logger.debug(f"Final ext info for {sub.rsl_plate_num}: {sub.extraction_info}")
|
||||
# else:
|
||||
# sub.extraction_info = json.dumps([obj])
|
||||
# self.ctx['database_session'].add(sub)
|
||||
# self.ctx["database_session"].commit()
|
||||
# dlg = AlertPop(message=f"We added {count} logs to the database.", status='information')
|
||||
# dlg.exec()
|
||||
|
||||
|
||||
def linkPCR(self):
|
||||
"""
|
||||
@@ -580,56 +263,6 @@ class App(QMainWindow):
|
||||
"""
|
||||
self, result = link_pcr_function(self)
|
||||
self.result_reporter(result)
|
||||
# home_dir = str(Path(self.ctx["directory_path"]))
|
||||
# fname = Path(QFileDialog.getOpenFileName(self, 'Open file', home_dir, filter = "csv(*.csv)")[0])
|
||||
# with open(fname.__str__(), 'r') as f:
|
||||
# runs = [col.strip().split(",") for col in f.readlines()]
|
||||
# count = 0
|
||||
# for run in runs:
|
||||
# obj = dict(
|
||||
# start_time=run[0].strip(),
|
||||
# rsl_plate_num=run[1].strip(),
|
||||
# biomek_status=run[2].strip(),
|
||||
# quant_status=run[3].strip(),
|
||||
# experiment_name=run[4].strip(),
|
||||
# end_time=run[5].strip()
|
||||
# )
|
||||
# # for ii in range(6, len(run)):
|
||||
# # obj[f"column{str(ii-5)}_vol"] = run[ii]
|
||||
# sub = lookup_submission_by_rsl_num(ctx=self.ctx, rsl_num=obj['rsl_plate_num'])
|
||||
# try:
|
||||
# logger.debug(f"Found submission: {sub.rsl_plate_num}")
|
||||
# except AttributeError:
|
||||
# continue
|
||||
# if hasattr(sub, 'pcr_info') and sub.pcr_info != None:
|
||||
# existing = json.loads(sub.pcr_info)
|
||||
# else:
|
||||
# existing = None
|
||||
# try:
|
||||
# if json.dumps(obj) in sub.pcr_info:
|
||||
# logger.debug(f"Looks like we already have that info.")
|
||||
# continue
|
||||
# else:
|
||||
# count += 1
|
||||
# except TypeError:
|
||||
# logger.error(f"No json to dump")
|
||||
# if existing != None:
|
||||
# try:
|
||||
# logger.debug(f"Updating {type(existing)}: {existing} with {type(obj)}: {obj}")
|
||||
# existing.append(obj)
|
||||
# logger.debug(f"Setting: {existing}")
|
||||
# sub.pcr_info = json.dumps(existing)
|
||||
# except TypeError:
|
||||
# logger.error(f"Error updating!")
|
||||
# sub.pcr_info = json.dumps([obj])
|
||||
# logger.debug(f"Final ext info for {sub.rsl_plate_num}: {sub.pcr_info}")
|
||||
# else:
|
||||
# sub.pcr_info = json.dumps([obj])
|
||||
# self.ctx['database_session'].add(sub)
|
||||
# self.ctx["database_session"].commit()
|
||||
# dlg = AlertPop(message=f"We added {count} logs to the database.", status='information')
|
||||
# dlg.exec()
|
||||
|
||||
|
||||
def importPCRResults(self):
|
||||
"""
|
||||
@@ -637,54 +270,6 @@ class App(QMainWindow):
|
||||
"""
|
||||
self, result = import_pcr_results_function(self)
|
||||
self.result_reporter(result)
|
||||
# home_dir = str(Path(self.ctx["directory_path"]))
|
||||
# fname = Path(QFileDialog.getOpenFileName(self, 'Open file', home_dir, filter = "xlsx(*.xlsx)")[0])
|
||||
# parser = PCRParser(ctx=self.ctx, filepath=fname)
|
||||
# logger.debug(f"Attempting lookup for {parser.plate_num}")
|
||||
# sub = lookup_submission_by_rsl_num(ctx=self.ctx, rsl_num=parser.plate_num)
|
||||
# try:
|
||||
# logger.debug(f"Found submission: {sub.rsl_plate_num}")
|
||||
# except AttributeError:
|
||||
# logger.error(f"Submission of number {parser.plate_num} not found. Attempting rescue of plate repeat.")
|
||||
# parser.plate_num = "-".join(parser.plate_num.split("-")[:-1])
|
||||
# sub = lookup_submission_by_rsl_num(ctx=self.ctx, rsl_num=parser.plate_num)
|
||||
# try:
|
||||
# logger.debug(f"Found submission: {sub.rsl_plate_num}")
|
||||
# except AttributeError:
|
||||
# logger.error(f"Rescue of {parser.plate_num} failed.")
|
||||
# return
|
||||
# # jout = json.dumps(parser.pcr)
|
||||
# count = 0
|
||||
# if hasattr(sub, 'pcr_info') and sub.pcr_info != None:
|
||||
# existing = json.loads(sub.pcr_info)
|
||||
# else:
|
||||
# # jout = None
|
||||
# existing = None
|
||||
# if existing != None:
|
||||
# try:
|
||||
# logger.debug(f"Updating {type(existing)}: {existing} with {type(parser.pcr)}: {parser.pcr}")
|
||||
# if json.dumps(parser.pcr) not in sub.pcr_info:
|
||||
# existing.append(parser.pcr)
|
||||
# logger.debug(f"Setting: {existing}")
|
||||
# sub.pcr_info = json.dumps(existing)
|
||||
# except TypeError:
|
||||
# logger.error(f"Error updating!")
|
||||
# sub.pcr_info = json.dumps([parser.pcr])
|
||||
# logger.debug(f"Final pcr info for {sub.rsl_plate_num}: {sub.pcr_info}")
|
||||
# else:
|
||||
# sub.pcr_info = json.dumps([parser.pcr])
|
||||
# self.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)}")
|
||||
# self.ctx["database_session"].commit()
|
||||
# logger.debug(f"Got {len(parser.samples)} to update!")
|
||||
# for sample in parser.samples:
|
||||
# logger.debug(f"Running update on: {sample['sample']}")
|
||||
# sample['plate_rsl'] = sub.rsl_plate_num
|
||||
# update_ww_sample(ctx=self.ctx, sample_obj=sample)
|
||||
# dlg = AlertPop(message=f"We added PCR info to {sub.rsl_plate_num}.", status='information')
|
||||
# dlg.exec()
|
||||
|
||||
|
||||
class AddSubForm(QWidget):
|
||||
|
||||
@@ -756,4 +341,3 @@ class AddSubForm(QWidget):
|
||||
self.layout.addWidget(self.tabs)
|
||||
self.setLayout(self.layout)
|
||||
|
||||
|
||||
|
||||
Reference in New Issue
Block a user