Code cleanup, dependency update, various bug fixes
This commit is contained in:
lwark
@@ -110,7 +110,7 @@ class SubmissionsSheet(QTableView):
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self.menu = QMenu(self)
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self.con_actions = submission.custom_context_events()
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for k in self.con_actions.keys():
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logger.debug(f"Adding {k}")
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# logger.debug(f"Adding {k}")
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action = QAction(k, self)
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action.triggered.connect(lambda _, action_name=k: self.triggered_action(action_name=action_name))
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self.menu.addAction(action)
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@@ -124,8 +124,8 @@ class SubmissionsSheet(QTableView):
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Args:
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action_name (str): name of the action from the menu
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"""
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logger.debug(f"Action: {action_name}")
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logger.debug(f"Responding with {self.con_actions[action_name]}")
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# logger.debug(f"Action: {action_name}")
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# logger.debug(f"Responding with {self.con_actions[action_name]}")
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func = self.con_actions[action_name]
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func(obj=self)
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@@ -162,50 +162,20 @@ class SubmissionsSheet(QTableView):
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experiment_name=run[4].strip(),
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end_time=run[5].strip()
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)
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# elution columns are item 6 in the comma split list to the end
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# NOTE: elution columns are item 6 in the comma split list to the end
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for ii in range(6, len(run)):
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new_run[f"column{str(ii-5)}_vol"] = run[ii]
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# Lookup imported submissions
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# sub = BasicSubmission.query(rsl_number=new_run['rsl_plate_num'])
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# NOTE: Lookup imported submissions
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sub = BasicSubmission.query(rsl_plate_num=new_run['rsl_plate_num'])
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# If no such submission exists, move onto the next run
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# NOTE: If no such submission exists, move onto the next run
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if sub == None:
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continue
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try:
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logger.debug(f"Found submission: {sub.rsl_plate_num}")
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# logger.debug(f"Found submission: {sub.rsl_plate_num}")
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count += 1
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except AttributeError:
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continue
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sub.set_attribute('extraction_info', new_run)
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# if sub.extraction_info != None:
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# # existing = json.loads(sub.extraction_info)
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# existing = sub.extraction_info
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# else:
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# existing = None
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# # Check if the new info already exists in the imported submission
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# try:
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# # if json.dumps(new_run) in sub.extraction_info:
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# if new_run in sub.extraction_info:
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# logger.debug(f"Looks like we already have that info.")
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# continue
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# except TypeError:
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# pass
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# # Update or create the extraction info
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# if existing != None:
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# try:
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# logger.debug(f"Updating {type(existing)}: {existing} with {type(new_run)}: {new_run}")
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# existing.append(new_run)
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# logger.debug(f"Setting: {existing}")
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# # sub.extraction_info = json.dumps(existing)
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# sub.extraction_info = existing
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# except TypeError:
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# logger.error(f"Error updating!")
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# # sub.extraction_info = json.dumps([new_run])
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# sub.extraction_info = [new_run]
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# logger.debug(f"Final ext info for {sub.rsl_plate_num}: {sub.extraction_info}")
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# else:
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# # sub.extraction_info = json.dumps([new_run])
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# sub.extraction_info = [new_run]
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sub.save()
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self.report.add_result(Result(msg=f"We added {count} logs to the database.", status='Information'))
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@@ -230,7 +200,7 @@ class SubmissionsSheet(QTableView):
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"""
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fname = select_open_file(self, file_extension="csv")
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with open(fname.__str__(), 'r') as f:
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# split csv rows on comma
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# NOTE: split csv rows on comma
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runs = [col.strip().split(",") for col in f.readlines()]
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count = 0
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for run in runs:
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@@ -242,49 +212,17 @@ class SubmissionsSheet(QTableView):
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experiment_name=run[4].strip(),
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end_time=run[5].strip()
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)
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# lookup imported submission
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# sub = lookup_submission_by_rsl_num(ctx=obj.ctx, rsl_num=new_run['rsl_plate_num'])
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# sub = lookup_submissions(ctx=obj.ctx, rsl_number=new_run['rsl_plate_num'])
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# NOTE: lookup imported submission
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sub = BasicSubmission.query(rsl_number=new_run['rsl_plate_num'])
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# if imported submission doesn't exist move on to next run
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# NOTE: if imported submission doesn't exist move on to next run
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if sub == None:
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continue
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try:
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logger.debug(f"Found submission: {sub.rsl_plate_num}")
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except AttributeError:
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continue
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sub.set_attribute('pcr_info', new_run)
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# # check if pcr_info already exists
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# if hasattr(sub, 'pcr_info') and sub.pcr_info != None:
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# # existing = json.loads(sub.pcr_info)
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# existing = sub.pcr_info
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# else:
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# existing = None
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# # check if this entry already exists in imported submission
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# try:
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# # if json.dumps(new_run) in sub.pcr_info:
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# if new_run in sub.pcr_info:
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# logger.debug(f"Looks like we already have that info.")
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# continue
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# else:
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# count += 1
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# except TypeError:
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# logger.error(f"No json to dump")
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# if existing is not None:
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# try:
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# logger.debug(f"Updating {type(existing)}: {existing} with {type(new_run)}: {new_run}")
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# existing.append(new_run)
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# logger.debug(f"Setting: {existing}")
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# # sub.pcr_info = json.dumps(existing)
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# sub.pcr_info = existing
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# except TypeError:
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# logger.error(f"Error updating!")
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# # sub.pcr_info = json.dumps([new_run])
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# sub.pcr_info = [new_run]
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# logger.debug(f"Final ext info for {sub.rsl_plate_num}: {sub.pcr_info}")
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# else:
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# # sub.pcr_info = json.dumps([new_run])
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# sub.pcr_info = [new_run]
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# logger.debug(f"Found submission: {sub.rsl_plate_num}")
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# except AttributeError:
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# continue
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sub.set_attribute('pcr_info', new_run)
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# NOTE: check if pcr_info already exists
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sub.save()
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self.report.add_result(Result(msg=f"We added {count} logs to the database.", status='Information'))
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@@ -308,23 +246,21 @@ class SubmissionsSheet(QTableView):
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Tuple[QMainWindow, dict]: Collection of new main app window and result dict
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"""
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report = Report()
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# ask for date ranges
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# NOTE: ask for date ranges
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dlg = ReportDatePicker()
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if dlg.exec():
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info = dlg.parse_form()
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logger.debug(f"Report info: {info}")
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# find submissions based on date range
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# logger.debug(f"Report info: {info}")
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# NOTE: find submissions based on date range
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subs = BasicSubmission.query(start_date=info['start_date'], end_date=info['end_date'])
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# convert each object to dict
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# NOTE: convert each object to dict
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records = [item.to_dict(report=True) for item in subs]
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logger.debug(f"Records: {pformat(records)}")
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# make dataframe from record dictionaries
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# NOTE: make dataframe from record dictionaries
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detailed_df, summary_df = make_report_xlsx(records=records)
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html = make_report_html(df=summary_df, start_date=info['start_date'], end_date=info['end_date'])
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# get save location of report
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# NOTE: get save location of report
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fname = select_save_file(obj=self, default_name=f"Submissions_Report_{info['start_date']}-{info['end_date']}.pdf", extension="pdf")
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# with open(fname, "w+b") as f:
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# pisa.CreatePDF(html, dest=f)
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html_to_pdf(html=html, output_file=fname)
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writer = pd.ExcelWriter(fname.with_suffix(".xlsx"), engine='openpyxl')
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summary_df.to_excel(writer, sheet_name="Report")
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@@ -337,14 +273,13 @@ class SubmissionsSheet(QTableView):
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len(str(series.name)) # len of column name/header
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)) + 20 # adding a little extra space
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try:
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# worksheet.column_dimensions[get_column_letter(idx=idx)].width = max_len
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# Convert idx to letter
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# NOTE: Convert idx to letter
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col_letter = chr(ord('@') + idx)
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worksheet.column_dimensions[col_letter].width = max_len
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except ValueError:
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pass
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blank_row = get_first_blank_df_row(summary_df) + 1
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logger.debug(f"Blank row index = {blank_row}")
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# logger.debug(f"Blank row index = {blank_row}")
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for col in range(3,6):
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col_letter = row_map[col]
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worksheet.cell(row=blank_row, column=col, value=f"=SUM({col_letter}2:{col_letter}{str(blank_row-1)})")
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