Big update, semi-functional
This commit is contained in:
Landon Wark
@@ -34,7 +34,7 @@ from backend.pydant import PydReagent
|
||||
from tools import check_not_nan
|
||||
from .custom_widgets.pop_ups import AlertPop, KitSelector, QuestionAsker
|
||||
from .custom_widgets import ReportDatePicker
|
||||
from .custom_widgets.misc import ImportReagent
|
||||
from .custom_widgets.misc import ImportReagent, ParsedQLabel
|
||||
from .visualizations.control_charts import create_charts, construct_html
|
||||
|
||||
logger = logging.getLogger(f"submissions.{__name__}")
|
||||
@@ -54,8 +54,9 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
|
||||
logger.debug(obj.ctx)
|
||||
# initialize samples
|
||||
obj.samples = []
|
||||
obj.reagents = {}
|
||||
obj.reagents = []
|
||||
obj.missing_reagents = []
|
||||
obj.missing_info = []
|
||||
|
||||
# set file dialog
|
||||
fname = select_open_file(obj, file_extension="xlsx")
|
||||
@@ -72,7 +73,7 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
|
||||
# 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}")
|
||||
logger.debug(f"Submission dictionary:\n{pprint.pformat(prsr.sub)}")
|
||||
pyd = prsr.to_pydantic()
|
||||
logger.debug(f"Pydantic result: \n\n{pprint.pformat(pyd)}\n\n")
|
||||
except Exception as e:
|
||||
@@ -85,7 +86,7 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
|
||||
# if hasattr(sample, "elution_well"):
|
||||
# logger.debug(f"Sample from import: {sample.elution_well}")
|
||||
# I don't remember why this is here.
|
||||
missing_info = [k for k,v in pyd if v == None]
|
||||
|
||||
obj.current_submission_type = pyd.submission_type['value']
|
||||
# destroy any widgets from previous imports
|
||||
for item in obj.table_widget.formlayout.parentWidget().findChildren(QWidget):
|
||||
@@ -101,51 +102,55 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
|
||||
if isinstance(value, dict) and field != 'ctx':
|
||||
logger.debug(f"The field {field} is a dictionary: {value}")
|
||||
if not value['parsed']:
|
||||
missing_info.append(field)
|
||||
value = value['value']
|
||||
obj.missing_info.append(field)
|
||||
label = ParsedQLabel(value, field)
|
||||
match field:
|
||||
case 'submitting_lab':
|
||||
# create label
|
||||
label = QLabel(field.replace("_", " ").title())
|
||||
logger.debug(f"{field}: {value}")
|
||||
# label = QLabel(field.replace("_", " ").title())
|
||||
# label = ParsedQLabel(value, field)
|
||||
logger.debug(f"{field}: {value['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(value, labs, len(labs), 0)
|
||||
labs = difflib.get_close_matches(value['value'], labs, len(labs), 0)
|
||||
except (TypeError, ValueError):
|
||||
pass
|
||||
# set combobox values to lookedup values
|
||||
add_widget.addItems(labs)
|
||||
case 'extraction_kit':
|
||||
# create label
|
||||
label = QLabel(field.replace("_", " ").title())
|
||||
# label = QLabel(field.replace("_", " ").title())
|
||||
|
||||
# if extraction kit not available, all other values fail
|
||||
if not check_not_nan(value):
|
||||
if not check_not_nan(value['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=pyd.submission_type['value'].lower())]
|
||||
logger.debug(f"Kits received for {pyd.submission_type}: {uses}")
|
||||
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
|
||||
# uses = [item.__str__() for item in lookup_kittype_by_use(ctx=obj.ctx, used_by=pyd.submission_type['value'].lower())]
|
||||
logger.debug(f"Looking up kits used for {pyd.submission_type['value']}")
|
||||
uses = [item.__str__() for item in lookup_kittype_by_use(ctx=obj.ctx, used_by=pyd.submission_type['value'])]
|
||||
logger.debug(f"Kits received for {pyd.submission_type['value']}: {uses}")
|
||||
if check_not_nan(value['value']):
|
||||
logger.debug(f"The extraction kit in parser was: {value['value']}")
|
||||
uses.insert(0, uses.pop(uses.index(value['value'])))
|
||||
obj.ext_kit = value['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
|
||||
label = QLabel(field.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(value)
|
||||
add_widget.setDate(value['value'])
|
||||
# if not found, use today
|
||||
except:
|
||||
add_widget.setDate(date.today())
|
||||
@@ -160,19 +165,28 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
|
||||
for reagent in value:
|
||||
# create label
|
||||
# reg_label = QLabel(reagent['type'].replace("_", " ").title())
|
||||
try:
|
||||
reg_label = QLabel(reagent.type.replace("_", " ").title())
|
||||
except AttributeError:
|
||||
reg_label = ParsedQLabel(reagent, reagent['value'].type, title=False)
|
||||
if reagent['parsed']:
|
||||
# try:
|
||||
# reg_label = QLabel(f"Parsed Lot: {reagent['value'].type}")
|
||||
obj.reagents.append(reagent['value'])
|
||||
# except AttributeError:
|
||||
# continue
|
||||
else:
|
||||
# try:
|
||||
# reg_label = QLabel(f"MISSING Lot: {reagent['value'].type}")
|
||||
obj.missing_reagents.append(reagent['value'].type)
|
||||
continue
|
||||
# except AttributeError:
|
||||
# continue
|
||||
# reg_label.setObjectName(f"lot_{reagent['type']}_label")
|
||||
reg_label.setObjectName(f"lot_{reagent.type}_label")
|
||||
reg_label.setObjectName(f"lot_{reagent['value'].type}_label")
|
||||
# create reagent choice widget
|
||||
add_widget = ImportReagent(ctx=obj.ctx, reagent=reagent)
|
||||
add_widget.setObjectName(f"lot_{reagent.type}")
|
||||
add_widget = ImportReagent(ctx=obj.ctx, reagent=reagent['value'])
|
||||
add_widget.setObjectName(f"lot_{reagent['value'].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
|
||||
continue
|
||||
# case "rsl_plate_num":
|
||||
# label = QLabel(field.replace("_", " ").title())
|
||||
@@ -181,10 +195,10 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
|
||||
# add_widget.setText(str(value['value']).replace("_", " "))
|
||||
case _:
|
||||
# anything else gets added in as a line edit
|
||||
label = QLabel(field.replace("_", " ").title())
|
||||
# label = QLabel(field.replace("_", " ").title())
|
||||
add_widget = QLineEdit()
|
||||
logger.debug(f"Setting widget text to {str(value).replace('_', ' ')}")
|
||||
add_widget.setText(str(value).replace("_", " "))
|
||||
logger.debug(f"Setting widget text to {str(value['value']).replace('_', ' ')}")
|
||||
add_widget.setText(str(value['value']).replace("_", " "))
|
||||
try:
|
||||
add_widget.setObjectName(field)
|
||||
logger.debug(f"Widget name set to: {add_widget.objectName()}")
|
||||
@@ -195,7 +209,7 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
|
||||
# compare obj.reagents with expected reagents in kit
|
||||
if hasattr(obj, 'ext_kit'):
|
||||
obj.kit_integrity_completion()
|
||||
obj.missing_reagents = obj.missing_reagents + missing_info
|
||||
# obj.missing_reagents = obj.missing_reagents + missing_info
|
||||
logger.debug(f"Imported reagents: {obj.reagents}")
|
||||
if prsr.sample_result != None:
|
||||
msg = AlertPop(message=prsr.sample_result, status="WARNING")
|
||||
@@ -247,21 +261,24 @@ def kit_integrity_completion_function(obj:QMainWindow) -> Tuple[QMainWindow, dic
|
||||
obj.ext_kit = kit_widget.currentText()
|
||||
logger.debug(f"Checking integrity of {obj.ext_kit}")
|
||||
# get the kit from database using current kit info
|
||||
kit = lookup_kittype_by_name(ctx=obj.ctx, name=obj.ext_kit)
|
||||
# kit = lookup_kittype_by_name(ctx=obj.ctx, name=obj.ext_kit)
|
||||
# get all reagents stored in the QWindow object
|
||||
reagents_to_lookup = [item.replace("lot_", "") for item in obj.reagents]
|
||||
logger.debug(f"Reagents for lookup for {kit.name}: {reagents_to_lookup}")
|
||||
# reagents_to_lookup = [item.name for item in obj.missing_reagents]
|
||||
# logger.debug(f"Reagents for lookup for {kit.name}: {reagents_to_lookup}")
|
||||
# make sure kit contains all necessary info
|
||||
kit_integrity = check_kit_integrity(kit, reagents_to_lookup)
|
||||
# kit_integrity = check_kit_integrity(kit, reagents_to_lookup)
|
||||
# if kit integrity comes back with an error, make widgets with missing reagents using default info
|
||||
if kit_integrity != None:
|
||||
result = dict(message=kit_integrity['message'], status="Warning")
|
||||
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, name=None)
|
||||
add_widget = ImportReagent(ctx=obj.ctx, reagent=PydReagent(**reagent))#item=item)
|
||||
obj.table_widget.formlayout.addWidget(add_widget)
|
||||
# if kit_integrity != None:
|
||||
# result = dict(message=kit_integrity['message'], status="Warning")
|
||||
# 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")
|
||||
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)
|
||||
add_widget = ImportReagent(ctx=obj.ctx, reagent=PydReagent(**reagent))#item=item)
|
||||
obj.table_widget.formlayout.addWidget(add_widget)
|
||||
submit_btn = QPushButton("Submit")
|
||||
submit_btn.setObjectName("lot_submit_btn")
|
||||
obj.table_widget.formlayout.addWidget(submit_btn)
|
||||
@@ -297,11 +314,13 @@ def submit_new_sample_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
|
||||
# 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?")
|
||||
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"checking reagent: {reagent} in obj.reagents. Result: {obj.reagents[reagent]}")
|
||||
expiry_date = obj.reagents[reagent].exp
|
||||
wanted_reagent = obj.add_reagent(reagent_lot=r_lot, reagent_type=reagent.replace("lot_", ""), expiry=expiry_date)
|
||||
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"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)
|
||||
else:
|
||||
# In this case we will have an empty reagent and the submission will fail kit integrity check
|
||||
logger.debug("Will not add reagent.")
|
||||
@@ -357,10 +376,10 @@ def submit_new_sample_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
|
||||
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.replace('_', ' ').title())
|
||||
excel_map.update(extraction_kit.used_for[obj.current_submission_type.replace('_', ' ').title()])
|
||||
excel_map = extraction_kit.construct_xl_map_for_use(obj.current_submission_type)
|
||||
# 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)
|
||||
autofill_excel(obj=obj, xl_map=excel_map, reagents=input_reagents, missing_reagents=obj.missing_reagents, info=info, missing_info=obj.missing_info)
|
||||
if hasattr(obj, 'csv'):
|
||||
dlg = QuestionAsker("Export CSV?", "Would you like to export the csv file?")
|
||||
if dlg.exec():
|
||||
@@ -827,29 +846,31 @@ def import_pcr_results_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
|
||||
result = dict(message=f"We added PCR info to {sub.rsl_plate_num}.", status='information')
|
||||
return obj, result
|
||||
|
||||
def autofill_excel(obj:QMainWindow, xl_map:dict, reagents:List[dict], missing_reagents:List[str], info:dict):
|
||||
def autofill_excel(obj:QMainWindow, xl_map:dict, reagents:List[dict], missing_reagents:List[str], info:dict, missing_info:List[str]):
|
||||
"""
|
||||
Automatically fills in excel cells with submission info.
|
||||
|
||||
Args:
|
||||
obj (QMainWindow): Original main app window
|
||||
xl_map (dict): Map of where each reagent goes in the excel workbook.
|
||||
reagents (List[dict]): All reagents used in the kit.
|
||||
xl_map (dict): Map of where each item goes in the excel workbook.
|
||||
reagents (List[dict]): All reagents placed in the submission form.
|
||||
missing_reagents (List[str]): Reagents that are required for the kit that were not present.
|
||||
info (dict): Dictionary of misc info from submission
|
||||
missing_info (List[str]): Plate info missing from the excel sheet.
|
||||
"""
|
||||
# logger.debug(reagents)
|
||||
|
||||
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}")
|
||||
# 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}
|
||||
# pare down reagents to only what's missing
|
||||
relevant_reagents = [item for item in reagents if item['type'] in missing_reagents]
|
||||
# hacky manipulation of submission type so it looks better.
|
||||
info['submission_type'] = info['submission_type'].replace("_", " ").title()
|
||||
# info['submission_type'] = info['submission_type'].replace("_", " ").title()
|
||||
# pare down info to just what's missing
|
||||
relevant_info = {k:v for k,v in info.items() if k in missing_reagents}
|
||||
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 = []
|
||||
|
||||
Reference in New Issue
Block a user