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new parsers/DB objects, pre code cleanup

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Landon Wark
2023-09-06 08:41:08 -05:00
parent bc7a3b8f5f
commit e0b80f6c7a
12 changed files with 263 additions and 137 deletions
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47
src/submissions/frontend/main_window_functions.py
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@@ -26,13 +26,13 @@ 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, get_reagents_in_extkit
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
from .custom_widgets.pop_ups import AlertPop, KitSelector, QuestionAsker
from .custom_widgets.pop_ups import AlertPop, QuestionAsker
from .custom_widgets import ReportDatePicker
from .custom_widgets.misc import ImportReagent, ParsedQLabel
from .visualizations.control_charts import create_charts, construct_html
@@ -92,7 +92,7 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
for item in obj.table_widget.formlayout.parentWidget().findChildren(QWidget):
item.setParent(None)
# Get list of fields from pydantic model.
fields = list(pyd.model_fields.keys())
fields = list(pyd.model_fields.keys()) + list(pyd.model_extra.keys())
fields.remove('filepath')
logger.debug(f"pydantic fields: {fields}")
for field in fields:
@@ -175,7 +175,7 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
else:
# try:
# reg_label = QLabel(f"MISSING Lot: {reagent['value'].type}")
obj.missing_reagents.append(reagent['value'].type)
obj.missing_reagents.append(reagent['value'])
continue
# except AttributeError:
# continue
@@ -273,10 +273,10 @@ def kit_integrity_completion_function(obj:QMainWindow) -> Tuple[QMainWindow, dic
# obj.missing_reagents = kit_integrity['missing']
# for item in kit_integrity['missing']:
if len(obj.missing_reagents) > 0:
result = dict(message=f"The submission you are importing is missing some reagents expected by the kit.\n\nIt looks like you are missing: {[item.upper() for item in obj.missing_reagents]}\n\nAlternatively, you may have set the wrong extraction kit.\n\nThe program will populate lists using existing reagents.\n\nPlease make sure you check the lots carefully!", status="Warning")
result = dict(message=f"The submission you are importing is missing some reagents expected by the kit.\n\nIt looks like you are missing: {[item.type.upper() for item in obj.missing_reagents]}\n\nAlternatively, you may have set the wrong extraction kit.\n\nThe program will populate lists using existing reagents.\n\nPlease make sure you check the lots carefully!", status="Warning")
for item in obj.missing_reagents:
obj.table_widget.formlayout.addWidget(ParsedQLabel({'parsed':False}, item, title=False))
reagent = dict(type=item, lot=None, exp=None, name=None)
obj.table_widget.formlayout.addWidget(ParsedQLabel({'parsed':False}, item.type, title=False))
reagent = dict(type=item.type, lot=None, exp=date.today(), name=None)
add_widget = ImportReagent(ctx=obj.ctx, reagent=PydReagent(**reagent))#item=item)
obj.table_widget.formlayout.addWidget(add_widget)
submit_btn = QPushButton("Submit")
@@ -316,8 +316,12 @@ def submit_new_sample_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
r_lot = reagents[reagent]
dlg = QuestionAsker(title=f"Add {r_lot}?", message=f"Couldn't find reagent type {reagent.strip('Lot')}: {r_lot} in the database.\n\nWould you like to add it?")
if dlg.exec():
logger.debug(f"Looking through {obj.reagents} for reagent {reagent}")
picked_reagent = [item for item in obj.reagents if item.type == reagent][0]
logger.debug(f"Looking through {pprint.pformat(obj.reagents)} for reagent {reagent}")
try:
picked_reagent = [item for item in obj.reagents if item.type == reagent][0]
except IndexError:
logger.error(f"Couldn't find {reagent} in obj.reagents. Checking missing reagents {pprint.pformat(obj.missing_reagents)}")
picked_reagent = [item for item in obj.missing_reagents if item.type == reagent][0]
logger.debug(f"checking reagent: {reagent} in obj.reagents. Result: {picked_reagent}")
expiry_date = picked_reagent.exp
wanted_reagent = obj.add_reagent(reagent_lot=r_lot, reagent_type=reagent.replace("lot_", ""), expiry=expiry_date, name=picked_reagent.name)
@@ -369,14 +373,15 @@ def submit_new_sample_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
for item in obj.table_widget.formlayout.parentWidget().findChildren(QWidget):
item.setParent(None)
logger.debug(f"All attributes of obj: {pprint.pformat(obj.__dict__)}")
if len(obj.missing_reagents) > 0:
if len(obj.missing_reagents + obj.missing_info) > 0:
logger.debug(f"We have blank reagents in the excel sheet.\n\tLet's try to fill them in.")
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('_', ' ')]}")
# 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)
logger.debug(f"Extraction kit map:\n\n{pprint.pformat(excel_map)}")
# 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, missing_info=obj.missing_info)
@@ -863,41 +868,47 @@ def autofill_excel(obj:QMainWindow, xl_map:dict, reagents:List[dict], missing_re
logger.debug(f"Here is the info dict coming in:\n{pprint.pformat(info)}")
logger.debug(f"Here are the missing reagents:\n{missing_reagents}")
logger.debug(f"Here are the missing info:\n{missing_info}")
logger.debug(f"Here is the xl map: {pprint.pformat(xl_map)}")
# pare down the xl map to only the missing data.
relevant_map = {k:v for k,v in xl_map.items() if k in missing_reagents}
relevant_reagent_map = {k:v for k,v in xl_map.items() if k in [reagent.type for reagent in missing_reagents]}
# pare down reagents to only what's missing
relevant_reagents = [item for item in reagents if item['type'] in missing_reagents]
relevant_reagents = [item for item in reagents if item['type'] in [reagent.type for reagent in missing_reagents]]
logger.debug(f"Here are the relevant reagents: {pprint.pformat(relevant_reagents)}")
# hacky manipulation of submission type so it looks better.
# info['submission_type'] = info['submission_type'].replace("_", " ").title()
# pare down info to just what's missing
relevant_info_map = {k:v for k,v in xl_map['info'].items() if k in missing_info and k != 'samples'}
relevant_info = {k:v for k,v in info.items() if k in missing_info}
logger.debug(f"Here is the relevant info: {pprint.pformat(relevant_info)}")
# construct new objects to put into excel sheets:
new_reagents = []
logger.debug(f"Parsing from relevant reagent map: {pprint.pformat(relevant_reagent_map)}")
for reagent in relevant_reagents:
new_reagent = {}
new_reagent['type'] = reagent['type']
new_reagent['lot'] = relevant_map[new_reagent['type']]['lot']
new_reagent['lot'] = relevant_reagent_map[new_reagent['type']]['lot']
new_reagent['lot']['value'] = reagent['lot']
new_reagent['expiry'] = relevant_map[new_reagent['type']]['expiry']
new_reagent['expiry'] = relevant_reagent_map[new_reagent['type']]['expiry']
new_reagent['expiry']['value'] = reagent['expiry']
new_reagent['sheet'] = relevant_map[new_reagent['type']]['sheet']
new_reagent['sheet'] = relevant_reagent_map[new_reagent['type']]['sheet']
# name is only present for Bacterial Culture
try:
new_reagent['name'] = relevant_map[new_reagent['type']]['name']
new_reagent['name'] = relevant_reagent_map[new_reagent['type']]['name']
new_reagent['name']['value'] = reagent['type']
except:
pass
new_reagents.append(new_reagent)
# construct new info objects to put into excel sheets
new_info = []
logger.debug(f"Parsing from relevant info map: {pprint.pformat(relevant_info_map)}")
for item in relevant_info:
new_item = {}
new_item['type'] = item
new_item['location'] = relevant_map[item]
new_item['location'] = relevant_info_map[item]
new_item['value'] = relevant_info[item]
new_info.append(new_item)
logger.debug(f"New reagents: {new_reagents}")
logger.debug(f"New info: {new_info}")
# open the workbook using openpyxl
workbook = load_workbook(obj.xl)
# get list of sheet names