landon/Submissions-App
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Before creating info and reagent parser classes.

Browse Source
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
Download Patch File Download Diff File Expand all files Collapse all files

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__())