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Autofill excel sheet

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This commit is contained in:
Landon Wark
2023-07-21 13:55:15 -05:00
parent ba35696055
commit f6e270f52d
10 changed files with 189 additions and 67 deletions
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59
src/submissions/frontend/main_window_functions.py
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@@ -87,7 +87,7 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
# 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
obj.current_submission_type = pyd.submission_type['value']
# destroy any widgets from previous imports
for item in obj.table_widget.formlayout.parentWidget().findChildren(QWidget):
item.setParent(None)
@@ -98,9 +98,12 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
for field in fields:
value = getattr(pyd, field)
logger.debug(f"Checking: {field}: {value}")
# No longer necessary with addition of pydantic validations
# if not check_not_nan(value):
# continue
# Get from pydantic model whether field was completed in the form
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']
match field:
case 'submitting_lab':
# create label
@@ -120,19 +123,18 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
# create label
label = QLabel(field.replace("_", " ").title())
# if extraction kit not available, all other values fail
if not check_not_nan(value['value']):
if not check_not_nan(value):
msg = AlertPop(message="Make sure to check your extraction kit in the excel sheet!", status="warning")
msg.exec()
if not value['parsed']:
missing_info.append(field)
# 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)]
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['value']}")
uses.insert(0, uses.pop(uses.index(value['value'])))
obj.ext_kit = value['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]
@@ -173,13 +175,11 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
obj.table_widget.formlayout.addWidget(add_widget)
obj.reagents[reagent.type] = reagent
continue
case "rsl_plate_num":
if not value['parsed']:
missing_info.append(field)
label = QLabel(field.replace("_", " ").title())
add_widget = QLineEdit()
logger.debug(f"Setting widget text to {str(value['value']).replace('_', ' ')}")
add_widget.setText(str(value['value']).replace("_", " "))
# case "rsl_plate_num":
# label = QLabel(field.replace("_", " ").title())
# add_widget = QLineEdit()
# logger.debug(f"Setting widget text to {str(value['value']).replace('_', ' ')}")
# add_widget.setText(str(value['value']).replace("_", " "))
case _:
# anything else gets added in as a line edit
label = QLabel(field.replace("_", " ").title())
@@ -352,8 +352,8 @@ def submit_new_sample_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
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]}")
excel_map = extraction_kit.used_for[obj.current_submission_type]
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('_', ' ')]
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'):
@@ -823,6 +823,7 @@ def autofill_excel(obj:QMainWindow, xl_map:dict, reagents:List[dict], missing_re
xl_map (dict): Map of where each reagent goes in the excel workbook.
reagents (List[dict]): All reagents used in the kit.
missing_reagents (List[str]): Reagents that are required for the kit that were not present.
info (dict): Dictionary of misc info from submission
"""
# logger.debug(reagents)
@@ -831,6 +832,7 @@ def autofill_excel(obj:QMainWindow, xl_map:dict, reagents:List[dict], missing_re
relevant_map = {k:v for k,v in xl_map.items() if k in missing_reagents}
# logger.debug(relevant_map)
relevant_reagents = [item for item in reagents if item['type'] in missing_reagents]
info['submission_type'] = info['submission_type'].replace("_", " ").title()
relevant_info = {k:v for k,v in info.items() if k in missing_reagents}
logger.debug(f"Here is the relevant info: {pprint.pformat(relevant_info)}")
# logger.debug(f"Relevant reagents:\n{relevant_reagents}")
@@ -844,6 +846,11 @@ def autofill_excel(obj:QMainWindow, xl_map:dict, reagents:List[dict], missing_re
new_reagent['expiry'] = relevant_map[new_reagent['type']]['expiry']
new_reagent['expiry']['value'] = reagent['expiry']
new_reagent['sheet'] = relevant_map[new_reagent['type']]['sheet']
try:
new_reagent['name'] = relevant_map[new_reagent['type']]['name']
new_reagent['name']['value'] = reagent['type']
except:
pass
new_reagents.append(new_reagent)
new_info = []
for item in relevant_info:
@@ -858,14 +865,20 @@ def autofill_excel(obj:QMainWindow, xl_map:dict, reagents:List[dict], missing_re
logger.debug(workbook.sheetnames)
for sheet in sheets:
worksheet=workbook[sheet]
sheet_reagents = [item for item in new_reagents if item['sheet'] == sheet]
sheet_reagents = [item for item in new_reagents if sheet in item['sheet']]
for reagent in sheet_reagents:
logger.debug(f"Attempting: {reagent['type']}:")
worksheet.cell(row=reagent['lot']['row'], column=reagent['lot']['column'], value=reagent['lot']['value'])
worksheet.cell(row=reagent['expiry']['row'], column=reagent['expiry']['column'], value=reagent['expiry']['value'])
sheet_info = [item for item in new_info if item['location']['sheet'] == sheet]
try:
worksheet.cell(row=reagent['name']['row'], column=reagent['name']['column'], value=reagent['name']['value'].replace("_", " ").upper())
except:
pass
sheet_info = [item for item in new_info if sheet in item['location']['sheets']]
for item in sheet_info:
logger.debug(f"Attempting: {item['type']}")
worksheet.cell(row=item['location']['row'], column=item['location']['column'], value=item['value'])
fname = select_save_file(obj=obj, default_name=Path(obj.xl).stem, extension="xlsx")
if info['submission_type'] == "Bacterial Culture":
workbook["Sample List"].cell(row=14, column=2, value=getuser())
fname = select_save_file(obj=obj, default_name=info['rsl_plate_num'], extension="xlsx")
workbook.save(filename=fname.__str__())