Pydantic added for validation.
This commit is contained in:
Landon Wark
@@ -7,7 +7,6 @@ from getpass import getuser
|
||||
import inspect
|
||||
from pathlib import Path
|
||||
import pprint
|
||||
import re
|
||||
import yaml
|
||||
import json
|
||||
from typing import Tuple
|
||||
@@ -30,7 +29,7 @@ from backend.db.functions import (
|
||||
)
|
||||
from backend.excel.parser import SheetParser, PCRParser
|
||||
from backend.excel.reports import make_report_html, make_report_xlsx, convert_data_list_to_df
|
||||
from tools import RSLNamer, check_not_nan, check_kit_integrity
|
||||
from tools import check_not_nan, check_kit_integrity
|
||||
from .custom_widgets.pop_ups import AlertPop, QuestionAsker
|
||||
from .custom_widgets import ReportDatePicker
|
||||
from .custom_widgets.misc import ImportReagent
|
||||
@@ -40,6 +39,16 @@ from .visualizations.control_charts import create_charts, construct_html
|
||||
logger = logging.getLogger(f"submissions.{__name__}")
|
||||
|
||||
def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]:
|
||||
"""
|
||||
_summary_
|
||||
|
||||
Args:
|
||||
obj (QMainWindow): _description_
|
||||
|
||||
Returns:
|
||||
Tuple[QMainWindow, dict|None]: _description_
|
||||
"""
|
||||
logger.debug(f"\n\nStarting Import...\n\n")
|
||||
result = None
|
||||
logger.debug(obj.ctx)
|
||||
# initialize samples
|
||||
@@ -57,102 +66,192 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
|
||||
except PermissionError:
|
||||
logger.error(f"Couldn't get permission to access file: {fname}")
|
||||
return
|
||||
if prsr.sub['rsl_plate_num'] == None:
|
||||
prsr.sub['rsl_plate_num'] = RSLNamer(fname.__str__()).parsed_name
|
||||
logger.debug(f"prsr.sub = {prsr.sub}")
|
||||
for sample in prsr.sub['samples']:
|
||||
try:
|
||||
pyd = prsr.to_pydantic()
|
||||
logger.debug(f"Pydantic result: \n\n{pyd}\n\n")
|
||||
# with open("pickled.pkl", "wb") as f:
|
||||
# pickle.dump(pyd, f)
|
||||
except Exception as e:
|
||||
return obj, dict(message= f"Problem creating pydantic model:\n\n{e}", status="critical")
|
||||
# moved to pydantic model
|
||||
# if prsr.sub['rsl_plate_num'] == None:
|
||||
# prsr.sub['rsl_plate_num'] = RSLNamer(fname.__str__()).parsed_name
|
||||
# logger.debug(f"prsr.sub = {prsr.sub}")
|
||||
for sample in pyd.samples:
|
||||
if hasattr(sample, "elution_well"):
|
||||
logger.debug(f"Sample from import: {sample.elution_well}")
|
||||
obj.current_submission_type = prsr.sub['submission_type']
|
||||
# obj.current_submission_type = prsr.sub['submission_type']
|
||||
obj.current_submission_type = pyd.submission_type
|
||||
# destroy any widgets from previous imports
|
||||
for item in obj.table_widget.formlayout.parentWidget().findChildren(QWidget):
|
||||
item.setParent(None)
|
||||
# regex to parser out different variable types for decision making
|
||||
variable_parser = re.compile(r"""
|
||||
(?P<extraction_kit>^extraction_kit$) |
|
||||
(?P<submitted_date>^submitted_date$) |
|
||||
(?P<submitting_lab>)^submitting_lab$ |
|
||||
(?P<samples>)^samples$ |
|
||||
(?P<reagent>^lot_.*$) |
|
||||
(?P<csv>^csv$)
|
||||
""", re.VERBOSE)
|
||||
for item in prsr.sub:
|
||||
logger.debug(f"Item: {item}")
|
||||
# attempt to match variable name to regex group
|
||||
try:
|
||||
mo = variable_parser.fullmatch(item).lastgroup
|
||||
except AttributeError:
|
||||
mo = "other"
|
||||
logger.debug(f"Mo: {mo}")
|
||||
match mo:
|
||||
# # regex to parser out different variable types for decision making
|
||||
# variable_parser = re.compile(r"""
|
||||
# (?P<extraction_kit>^extraction_kit$) |
|
||||
# (?P<submitted_date>^submitted_date$) |
|
||||
# (?P<submitting_lab>)^submitting_lab$ |
|
||||
# (?P<samples>)^samples$ |
|
||||
# (?P<reagent>^lot_.*$) |
|
||||
# (?P<csv>^csv$)
|
||||
# """, re.VERBOSE)
|
||||
# for item in prsr.sub:
|
||||
# logger.debug(f"Item: {item}")
|
||||
# # attempt to match variable name to regex group
|
||||
# try:
|
||||
# mo = variable_parser.fullmatch(item).lastgroup
|
||||
# except AttributeError:
|
||||
# mo = "other"
|
||||
# logger.debug(f"Mo: {mo}")
|
||||
# match mo:
|
||||
# case 'submitting_lab':
|
||||
# # create label
|
||||
# obj.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
|
||||
# logger.debug(f"{item}: {prsr.sub[item]}")
|
||||
# # create combobox to hold looked up submitting labs
|
||||
# add_widget = QComboBox()
|
||||
# labs = [item.__str__() for item in lookup_all_orgs(ctx=obj.ctx)]
|
||||
# # try to set closest match to top of list
|
||||
# try:
|
||||
# labs = difflib.get_close_matches(prsr.sub[item], labs, len(labs), 0)
|
||||
# except (TypeError, ValueError):
|
||||
# pass
|
||||
# # set combobox values to lookedup values
|
||||
# add_widget.addItems(labs)
|
||||
# case 'extraction_kit':
|
||||
# # create label
|
||||
# obj.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
|
||||
# # if extraction kit not available, all other values fail
|
||||
# if not check_not_nan(prsr.sub[item]):
|
||||
# msg = AlertPop(message="Make sure to check your extraction kit in the excel sheet!", status="warning")
|
||||
# msg.exec()
|
||||
# # create combobox to hold looked up kits
|
||||
# add_widget = QComboBox()
|
||||
# # lookup existing kits by 'submission_type' decided on by sheetparser
|
||||
# uses = [item.__str__() for item in lookup_kittype_by_use(ctx=obj.ctx, used_by=prsr.sub['submission_type'])]
|
||||
# if check_not_nan(prsr.sub[item]):
|
||||
# logger.debug(f"The extraction kit in parser was: {prsr.sub[item]}")
|
||||
# uses.insert(0, uses.pop(uses.index(prsr.sub[item])))
|
||||
# obj.ext_kit = prsr.sub[item]
|
||||
# else:
|
||||
# logger.error(f"Couldn't find {prsr.sub['extraction_kit']}")
|
||||
# obj.ext_kit = uses[0]
|
||||
# add_widget.addItems(uses)
|
||||
# case 'submitted_date':
|
||||
# # create label
|
||||
# obj.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
|
||||
# # uses base calendar
|
||||
# add_widget = QDateEdit(calendarPopup=True)
|
||||
# # sets submitted date based on date found in excel sheet
|
||||
# try:
|
||||
# add_widget.setDate(prsr.sub[item])
|
||||
# # if not found, use today
|
||||
# except:
|
||||
# add_widget.setDate(date.today())
|
||||
# case 'reagent':
|
||||
# # create label
|
||||
# reg_label = QLabel(item.replace("_", " ").title())
|
||||
# reg_label.setObjectName(f"lot_{item}_label")
|
||||
# obj.table_widget.formlayout.addWidget(reg_label)
|
||||
# # create reagent choice widget
|
||||
# add_widget = ImportReagent(ctx=obj.ctx, item=item, prsr=prsr)
|
||||
# obj.reagents[item] = prsr.sub[item]
|
||||
# case 'samples':
|
||||
# # hold samples in 'obj' until form submitted
|
||||
# logger.debug(f"{item}: {prsr.sub[item]}")
|
||||
# obj.samples = prsr.sub[item]
|
||||
# add_widget = None
|
||||
# case 'csv':
|
||||
# obj.csv = prsr.sub[item]
|
||||
# case _:
|
||||
# # anything else gets added in as a line edit
|
||||
# obj.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
|
||||
# add_widget = QLineEdit()
|
||||
# logger.debug(f"Setting widget text to {str(prsr.sub[item]).replace('_', ' ')}")
|
||||
# add_widget.setText(str(prsr.sub[item]).replace("_", " "))
|
||||
fields = list(pyd.model_fields.keys())
|
||||
fields.remove('filepath')
|
||||
logger.debug(f"pydantic fields: {fields}")
|
||||
for field in fields:
|
||||
value = getattr(pyd, field)
|
||||
if not check_not_nan(value):
|
||||
continue
|
||||
match field:
|
||||
case 'submitting_lab':
|
||||
# create label
|
||||
obj.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
|
||||
logger.debug(f"{item}: {prsr.sub[item]}")
|
||||
label = QLabel(field.replace("_", " ").title())
|
||||
logger.debug(f"{field}: {value}")
|
||||
# create combobox to hold looked up submitting labs
|
||||
add_widget = QComboBox()
|
||||
labs = [item.__str__() for item in lookup_all_orgs(ctx=obj.ctx)]
|
||||
# try to set closest match to top of list
|
||||
try:
|
||||
labs = difflib.get_close_matches(prsr.sub[item], labs, len(labs), 0)
|
||||
labs = difflib.get_close_matches(value, labs, len(labs), 0)
|
||||
except (TypeError, ValueError):
|
||||
pass
|
||||
# set combobox values to lookedup values
|
||||
add_widget.addItems(labs)
|
||||
case 'extraction_kit':
|
||||
# create label
|
||||
obj.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
|
||||
label = QLabel(field.replace("_", " ").title())
|
||||
# if extraction kit not available, all other values fail
|
||||
if not check_not_nan(prsr.sub[item]):
|
||||
if not check_not_nan(value):
|
||||
msg = AlertPop(message="Make sure to check your extraction kit in the excel sheet!", status="warning")
|
||||
msg.exec()
|
||||
# create combobox to hold looked up kits
|
||||
add_widget = QComboBox()
|
||||
# lookup existing kits by 'submission_type' decided on by sheetparser
|
||||
uses = [item.__str__() for item in lookup_kittype_by_use(ctx=obj.ctx, used_by=prsr.sub['submission_type'])]
|
||||
if check_not_nan(prsr.sub[item]):
|
||||
logger.debug(f"The extraction kit in parser was: {prsr.sub[item]}")
|
||||
uses.insert(0, uses.pop(uses.index(prsr.sub[item])))
|
||||
obj.ext_kit = prsr.sub[item]
|
||||
uses = [item.__str__() for item in lookup_kittype_by_use(ctx=obj.ctx, used_by=pyd.submission_type)]
|
||||
if check_not_nan(value):
|
||||
logger.debug(f"The extraction kit in parser was: {value}")
|
||||
uses.insert(0, uses.pop(uses.index(value)))
|
||||
obj.ext_kit = value
|
||||
else:
|
||||
logger.error(f"Couldn't find {prsr.sub['extraction_kit']}")
|
||||
obj.ext_kit = uses[0]
|
||||
add_widget.addItems(uses)
|
||||
case 'submitted_date':
|
||||
# create label
|
||||
obj.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
|
||||
label = QLabel(field.replace("_", " ").title())
|
||||
# uses base calendar
|
||||
add_widget = QDateEdit(calendarPopup=True)
|
||||
# sets submitted date based on date found in excel sheet
|
||||
try:
|
||||
add_widget.setDate(prsr.sub[item])
|
||||
add_widget.setDate(value)
|
||||
# if not found, use today
|
||||
except:
|
||||
add_widget.setDate(date.today())
|
||||
case 'reagent':
|
||||
# create label
|
||||
reg_label = QLabel(item.replace("_", " ").title())
|
||||
reg_label.setObjectName(f"lot_{item}_label")
|
||||
obj.table_widget.formlayout.addWidget(reg_label)
|
||||
# create reagent choice widget
|
||||
add_widget = ImportReagent(ctx=obj.ctx, item=item, prsr=prsr)
|
||||
obj.reagents[item] = prsr.sub[item]
|
||||
case 'samples':
|
||||
# hold samples in 'obj' until form submitted
|
||||
logger.debug(f"{item}: {prsr.sub[item]}")
|
||||
obj.samples = prsr.sub[item]
|
||||
add_widget = None
|
||||
logger.debug(f"{field}:\n\t{value}")
|
||||
obj.samples = value
|
||||
continue
|
||||
case 'csv':
|
||||
obj.csv = prsr.sub[item]
|
||||
obj.csv = value
|
||||
continue
|
||||
case 'reagents':
|
||||
for reagent in value:
|
||||
# create label
|
||||
reg_label = QLabel(reagent['type'].replace("_", " ").title())
|
||||
reg_label.setObjectName(f"lot_{reagent['type']}_label")
|
||||
# obj.table_widget.formlayout.addWidget(reg_label)
|
||||
# create reagent choice widget
|
||||
add_widget = ImportReagent(ctx=obj.ctx, reagent=reagent)
|
||||
add_widget.setObjectName(f"lot_{reagent['type']}")
|
||||
logger.debug(f"Widget name set to: {add_widget.objectName()}")
|
||||
obj.table_widget.formlayout.addWidget(reg_label)
|
||||
obj.table_widget.formlayout.addWidget(add_widget)
|
||||
obj.reagents[reagent['type']] = reagent['lot']
|
||||
continue
|
||||
case _:
|
||||
# anything else gets added in as a line edit
|
||||
obj.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
|
||||
label = QLabel(field.replace("_", " ").title())
|
||||
add_widget = QLineEdit()
|
||||
logger.debug(f"Setting widget text to {str(prsr.sub[item]).replace('_', ' ')}")
|
||||
add_widget.setText(str(prsr.sub[item]).replace("_", " "))
|
||||
logger.debug(f"Setting widget text to {str(value).replace('_', ' ')}")
|
||||
add_widget.setText(str(value).replace("_", " "))
|
||||
try:
|
||||
add_widget.setObjectName(item)
|
||||
add_widget.setObjectName(field)
|
||||
logger.debug(f"Widget name set to: {add_widget.objectName()}")
|
||||
obj.table_widget.formlayout.addWidget(label)
|
||||
obj.table_widget.formlayout.addWidget(add_widget)
|
||||
except AttributeError as e:
|
||||
logger.error(e)
|
||||
@@ -199,7 +298,7 @@ def kit_integrity_completion_function(obj:QMainWindow) -> QMainWindow:
|
||||
result = dict(message=kit_integrity['message'], status="Warning")
|
||||
for item in kit_integrity['missing']:
|
||||
obj.table_widget.formlayout.addWidget(QLabel(f"Lot {item.replace('_', ' ').title()}"))
|
||||
add_widget = ImportReagent(ctx=obj.ctx, item=item)
|
||||
add_widget = ImportReagent(ctx=obj.ctx, reagent=dict(type=item, lot=None, exp=None))#item=item)
|
||||
obj.table_widget.formlayout.addWidget(add_widget)
|
||||
submit_btn = QPushButton("Submit")
|
||||
submit_btn.setObjectName("lot_submit_btn")
|
||||
@@ -208,6 +307,7 @@ def kit_integrity_completion_function(obj:QMainWindow) -> QMainWindow:
|
||||
return obj, result
|
||||
|
||||
def submit_new_sample_function(obj:QMainWindow) -> QMainWindow:
|
||||
logger.debug(f"\n\nBeginning Submission\n\n")
|
||||
result = None
|
||||
# extract info from the form widgets
|
||||
info = extract_form_info(obj.table_widget.tab1)
|
||||
@@ -219,7 +319,8 @@ def submit_new_sample_function(obj:QMainWindow) -> QMainWindow:
|
||||
parsed_reagents = []
|
||||
# compare reagents in form to reagent database
|
||||
for reagent in reagents:
|
||||
wanted_reagent = lookup_reagent(ctx=obj.ctx, reagent_lot=reagents[reagent])
|
||||
# TODO: have this lookup by type and lot
|
||||
wanted_reagent = lookup_reagent(ctx=obj.ctx, reagent_lot=reagents[reagent], type_name=reagent)
|
||||
logger.debug(f"Looked up reagent: {wanted_reagent}")
|
||||
# if reagent not found offer to add to database
|
||||
if wanted_reagent == None:
|
||||
@@ -431,7 +532,7 @@ def chart_maker_function(obj:QMainWindow) -> QMainWindow:
|
||||
data = [control.convert_by_mode(mode=obj.mode) for control in controls]
|
||||
# flatten data to one dimensional list
|
||||
data = [item for sublist in data for item in sublist]
|
||||
logger.debug(f"Control objects going into df conversion: {data}")
|
||||
logger.debug(f"Control objects going into df conversion: {type(data)}")
|
||||
if data == []:
|
||||
return obj, dict(status="Critical", message="No data found for controls in given date range.")
|
||||
# send to dataframe creator
|
||||
|
||||
Reference in New Issue
Block a user