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Before creating info and reagent parser classes.

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This commit is contained in:
Landon Wark
2023-08-21 13:50:38 -05:00
parent af810ae528
commit b6de159631
20 changed files with 1176 additions and 571 deletions
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55
src/submissions/frontend/custom_widgets/misc.py
View File

@@ -10,11 +10,10 @@ from PyQt6.QtWidgets import (
QHBoxLayout
)
from PyQt6.QtCore import Qt, QDate, QSize
from tools import check_not_nan
from tools import check_not_nan, jinja_template_loading, Settings
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 tools import jinja_template_loading
lookup_regent_by_type_name, lookup_last_used_reagenttype_lot, lookup_all_reagent_names_by_role
import logging
import numpy as np
from .pop_ups import AlertPop
@@ -28,9 +27,9 @@ class AddReagentForm(QDialog):
"""
dialog to add gather info about new reagent
"""
def __init__(self, ctx:dict, reagent_lot:str|None, reagent_type:str|None, expiry:date|None=None) -> None:
def __init__(self, ctx:dict, reagent_lot:str|None, reagent_type:str|None, expiry:date|None=None, reagent_name:str|None=None) -> None:
super().__init__()
self.ctx = ctx
if reagent_lot == None:
reagent_lot = ""
@@ -42,21 +41,26 @@ class AddReagentForm(QDialog):
self.buttonBox.accepted.connect(self.accept)
self.buttonBox.rejected.connect(self.reject)
# widget to get lot info
lot_input = QLineEdit()
lot_input.setObjectName("lot")
lot_input.setText(reagent_lot)
self.name_input = QComboBox()
self.name_input.setObjectName("name")
self.name_input.setEditable(True)
self.name_input.setCurrentText(reagent_name)
# self.name_input.setText(reagent_name)
self.lot_input = QLineEdit()
self.lot_input.setObjectName("lot")
self.lot_input.setText(reagent_lot)
# widget to get expiry info
exp_input = QDateEdit(calendarPopup=True)
exp_input.setObjectName('expiry')
self.exp_input = QDateEdit(calendarPopup=True)
self.exp_input.setObjectName('expiry')
# if expiry is not passed in from gui, use today
if expiry == None:
exp_input.setDate(QDate.currentDate())
self.exp_input.setDate(QDate.currentDate())
else:
exp_input.setDate(expiry)
self.exp_input.setDate(expiry)
# widget to get reagent type info
type_input = QComboBox()
type_input.setObjectName('type')
type_input.addItems([item.replace("_", " ").title() for item in get_all_reagenttype_names(ctx=ctx)])
self.type_input = QComboBox()
self.type_input.setObjectName('type')
self.type_input.addItems([item.replace("_", " ").title() for item in get_all_reagenttype_names(ctx=ctx)])
logger.debug(f"Trying to find index of {reagent_type}")
# convert input to user friendly string?
try:
@@ -64,18 +68,26 @@ class AddReagentForm(QDialog):
except AttributeError:
reagent_type = None
# set parsed reagent type to top of list
index = type_input.findText(reagent_type, Qt.MatchFlag.MatchEndsWith)
index = self.type_input.findText(reagent_type, Qt.MatchFlag.MatchEndsWith)
if index >= 0:
type_input.setCurrentIndex(index)
self.type_input.setCurrentIndex(index)
self.layout = QVBoxLayout()
self.layout.addWidget(QLabel("Name:"))
self.layout.addWidget(self.name_input)
self.layout.addWidget(QLabel("Lot:"))
self.layout.addWidget(lot_input)
self.layout.addWidget(self.lot_input)
self.layout.addWidget(QLabel("Expiry:\n(use exact date on reagent.\nEOL will be calculated from kit automatically)"))
self.layout.addWidget(exp_input)
self.layout.addWidget(self.exp_input)
self.layout.addWidget(QLabel("Type:"))
self.layout.addWidget(type_input)
self.layout.addWidget(self.type_input)
self.layout.addWidget(self.buttonBox)
self.setLayout(self.layout)
self.type_input.currentTextChanged.connect(self.update_names)
def update_names(self):
logger.debug(self.type_input.currentText())
self.name_input.clear()
self.name_input.addItems(item for item in lookup_all_reagent_names_by_role(ctx=self.ctx, role_name=self.type_input.currentText().replace(" ", "_").lower()))
class ReportDatePicker(QDialog):
@@ -111,7 +123,7 @@ class KitAdder(QWidget):
"""
dialog to get information to add kit
"""
def __init__(self, parent_ctx:dict) -> None:
def __init__(self, parent_ctx:Settings) -> None:
super().__init__()
self.ctx = parent_ctx
self.grid = QGridLayout()
@@ -196,6 +208,7 @@ class KitAdder(QWidget):
result = create_kit_from_yaml(ctx=self.ctx, exp=yml_type)
msg = AlertPop(message=result['message'], status=result['status'])
msg.exec()
self.__init__(self.ctx)
class ReagentTypeForm(QWidget):

31
src/submissions/frontend/custom_widgets/pop_ups.py
View File

@@ -7,7 +7,7 @@ from PyQt6.QtWidgets import (
)
from tools import jinja_template_loading
import logging
from backend.db.functions import lookup_kittype_by_use
from backend.db.functions import lookup_kittype_by_use, lookup_all_sample_types
logger = logging.getLogger(f"submissions.{__name__}")
@@ -78,4 +78,31 @@ class KitSelector(QDialog):
# r = dlg.exec_()
# if r:
# return dlg.getValues()
# return None
# return None
class SubmissionTypeSelector(QDialog):
"""
dialog to ask yes/no questions
"""
def __init__(self, ctx:dict, title:str, message:str) -> QDialog:
super().__init__()
self.setWindowTitle(title)
self.widget = QComboBox()
sub_type = lookup_all_sample_types(ctx=ctx)
self.widget.addItems(sub_type)
self.widget.setEditable(False)
# set yes/no buttons
QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
self.buttonBox = QDialogButtonBox(QBtn)
self.buttonBox.accepted.connect(self.accept)
self.buttonBox.rejected.connect(self.reject)
self.layout = QVBoxLayout()
# Text for the yes/no question
message = QLabel(message)
self.layout.addWidget(message)
self.layout.addWidget(self.widget)
self.layout.addWidget(self.buttonBox)
self.setLayout(self.layout)
def getValues(self):
return self.widget.currentText()

11
src/submissions/frontend/custom_widgets/sub_details.py
View File

@@ -4,6 +4,7 @@ Contains widgets specific to the submission summary and submission details.
import base64
from datetime import datetime
from io import BytesIO
import pprint
from PyQt6 import QtPrintSupport
from PyQt6.QtWidgets import (
QVBoxLayout, QDialog, QTableView,
@@ -215,7 +216,8 @@ class SubmissionsSheet(QTableView):
if iii > 3:
logger.error(f"Error: Had to truncate number of plates to 4.")
continue
plate_dicto = hitpick_plate(submission=sub, plate_number=iii+1)
# plate_dicto = hitpick_plate(submission=sub, plate_number=iii+1)
plate_dicto = sub.hitpick_plate(plate_number=iii+1)
if plate_dicto == None:
continue
image = make_plate_map(plate_dicto)
@@ -236,7 +238,7 @@ class SubmissionsSheet(QTableView):
return
date = datetime.strftime(datetime.today(), "%Y-%m-%d")
# ask for filename and save as csv.
home_dir = Path(self.ctx["directory_path"]).joinpath(f"Hitpicks_{date}.csv").resolve().__str__()
home_dir = Path(self.ctx.directory_path).joinpath(f"Hitpicks_{date}.csv").resolve().__str__()
fname = Path(QFileDialog.getSaveFileName(self, "Save File", home_dir, filter=".csv")[0])
if fname.__str__() == ".":
logger.debug("Saving csv was cancelled.")
@@ -265,7 +267,7 @@ class SubmissionDetails(QDialog):
interior.setParent(self)
# get submision from db
data = lookup_submission_by_id(ctx=ctx, id=id)
logger.debug(f"Submission details data:\n{data.to_dict()}")
logger.debug(f"Submission details data:\n{pprint.pformat(data.to_dict())}")
self.base_dict = data.to_dict()
# don't want id
del self.base_dict['id']
@@ -291,7 +293,8 @@ class SubmissionDetails(QDialog):
# interior.setWidget(txt_editor)
self.base_dict['barcode'] = base64.b64encode(make_plate_barcode(self.base_dict['Plate Number'], width=120, height=30)).decode('utf-8')
sub = lookup_submission_by_rsl_num(ctx=self.ctx, rsl_num=self.base_dict['Plate Number'])
plate_dicto = hitpick_plate(sub)
# plate_dicto = hitpick_plate(sub)
plate_dicto = sub.hitpick_plate()
platemap = make_plate_map(plate_dicto)
logger.debug(f"platemap: {platemap}")
image_io = BytesIO()

36
src/submissions/frontend/main_window_functions.py
View File

@@ -8,7 +8,8 @@ import inspect
import pprint
import yaml
import json
from typing import Tuple
from typing import Tuple, List
from openpyxl import load_workbook
from openpyxl.utils import get_column_letter
from xhtml2pdf import pisa
import pandas as pd
@@ -25,19 +26,16 @@ from backend.db.functions import (
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,
check_kit_integrity
check_kit_integrity, get_reagents_in_extkit
)
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
from .custom_widgets.pop_ups import AlertPop, QuestionAsker
from .custom_widgets.pop_ups import AlertPop, KitSelector, QuestionAsker
from .custom_widgets import ReportDatePicker
from .custom_widgets.misc import ImportReagent
from .visualizations.control_charts import create_charts, construct_html
from typing import List
from openpyxl import load_workbook
logger = logging.getLogger(f"submissions.{__name__}")
@@ -71,6 +69,7 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
except PermissionError:
logger.error(f"Couldn't get permission to access file: {fname}")
return obj, result
# prsr.sub = import_validation_check(ctx=obj.ctx, parser_sub=prsr.sub)
# obj.column_count = prsr.column_count
try:
logger.debug(f"Submission dictionary: {prsr.sub}")
@@ -260,7 +259,7 @@ def kit_integrity_completion_function(obj:QMainWindow) -> Tuple[QMainWindow, dic
obj.missing_reagents = kit_integrity['missing']
for item in kit_integrity['missing']:
obj.table_widget.formlayout.addWidget(QLabel(f"Lot {item.replace('_', ' ').title()}"))
reagent = dict(type=item, lot=None, exp=None)
reagent = dict(type=item, lot=None, exp=None, name=None)
add_widget = ImportReagent(ctx=obj.ctx, reagent=PydReagent(**reagent))#item=item)
obj.table_widget.formlayout.addWidget(add_widget)
submit_btn = QPushButton("Submit")
@@ -306,9 +305,11 @@ def submit_new_sample_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
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)
wanted_reagent.type.last_used = reagents[reagent]
# obj.ctx.database_session.rollback()
return obj, dict(message="Failed integrity check", status="critical")
# if wanted_reagent != None:
parsed_reagents.append(wanted_reagent)
wanted_reagent.type.last_used = reagents[reagent]
# move samples into preliminary submission dict
info['samples'] = obj.samples
info['uploaded_by'] = getuser()
@@ -325,6 +326,7 @@ def submit_new_sample_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
# Do not add duplicate reagents.
base_submission.reagents = []
else:
obj.ctx.database_session.rollback()
return obj, dict(message="Overwrite cancelled", status="Information")
# code 2: No RSL plate number given
case 2:
@@ -340,7 +342,7 @@ def submit_new_sample_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
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_submission(ctx=obj.ctx, base_submission=base_submission)
result = store_submission(ctx=obj.ctx, base_submission=base_submission, samples=obj.samples)
# check result of storing for issues
# update summary sheet
obj.table_widget.sub_wid.setData()
@@ -353,7 +355,10 @@ def submit_new_sample_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
extraction_kit = lookup_kittype_by_name(obj.ctx, name=obj.ext_kit)
logger.debug(f"We have the extraction kit: {extraction_kit.name}")
logger.debug(f"Extraction kit map:\n\n{extraction_kit.used_for[obj.current_submission_type.replace('_', ' ')]}")
excel_map = extraction_kit.used_for[obj.current_submission_type.replace('_', ' ')]
# TODO replace below with function in KitType object. Update Kittype associations.
# excel_map = extraction_kit.used_for[obj.current_submission_type.replace('_', ' ')]
excel_map = extraction_kit.construct_xl_map_for_use(obj.current_submission_type.replace('_', ' ').title())
excel_map.update(extraction_kit.used_for[obj.current_submission_type.replace('_', ' ').title()])
input_reagents = [item.to_reagent_dict() for item in parsed_reagents]
autofill_excel(obj=obj, xl_map=excel_map, reagents=input_reagents, missing_reagents=obj.missing_reagents, info=info)
if hasattr(obj, 'csv'):
@@ -430,7 +435,7 @@ def add_kit_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
"""
result = None
# setup file dialog to find yaml flie
fname = select_open_file(obj, extension="yml")
fname = select_open_file(obj, file_extension="yml")
assert fname.exists()
# read yaml file
try:
@@ -587,7 +592,7 @@ def link_controls_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
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]
samples = [sample.submitter_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"...
@@ -897,6 +902,7 @@ def autofill_excel(obj:QMainWindow, xl_map:dict, reagents:List[dict], missing_re
worksheet.cell(row=item['location']['row'], column=item['location']['column'], value=item['value'])
# Hacky way to
if info['submission_type'] == "Bacterial Culture":
workbook["Sample List"].cell(row=14, column=2, value=getuser())
workbook["Sample List"].cell(row=14, column=2, value=getuser()[0:2].upper())
fname = select_save_file(obj=obj, default_name=info['rsl_plate_num'], extension="xlsx")
workbook.save(filename=fname.__str__())