def edit_data(self):
table = "neo_adjuvant_therapy"
enter = sql.review_data(self.conn, self.cursor, table,
self.file_number, names(table))
if enter:
sql.delete_rows(self.cursor, 'nact_drug_table', "file_number",
self.file_number)
sql.delete_rows(self.cursor, 'nact_tox_table', "file_number",
self.file_number)
data = self.nact_test()
data_sql, drug_table, tox_response = data
sql.update_multiple(self.conn, self.cursor, table, names(table),
self.file_number, data_sql)
drug_table.to_sql("nact_drug_table",
self.conn,
index=False,
if_exists="append")
tox_response.to_sql("nact_tox_table",
self.conn,
index=False,
if_exists="append")
print("clip information")
module = "clip_information"
col_list = names(module)
enter = sql.review_data(self.conn, self.cursor, table,
self.file_number, col_list)
if enter:
data = self.clip_information()
sql.update_multiple(self.conn, self.cursor, table, col_list,
self.file_number, data)
def edit_data(conn, cursor, file_number, user_name):
table = "Neo_Adjuvant_Therapy"
enter = review_data(conn, cursor, table, file_number, names(table))
if enter:
delete_rows(cursor, 'NACT_Drug_Table', "File_number", file_number)
delete_rows(cursor, 'NACT_Tox_table', "File_number", file_number)
data = nact_test(file_number, user_name)
data_sql, drug_table, tox_response = data
update_multiple(conn, cursor, table, names(table), file_number,
data_sql)
drug_table.to_sql("NACT_Drug_Table",
conn,
index=False,
if_exists="append")
tox_response.to_sql("NACT_Tox_table",
conn,
index=False,
if_exists="append")
print("Clip Information")
module = "clip_information"
col_list = names(module)
enter = review_data(conn, cursor, table, file_number, col_list)
if enter:
data = clip_information(file_number)
update_multiple(conn, cursor, table, col_list, file_number, data)
def edit_data(conn, cursor, file_number, user_name):
table = "Follow_up_Data"
col_list = names.name_follow_up()
enter = view_multiple(conn, table, col_list, file_number)
if enter == "Add data":
data = follow_up(file_number, user_name)
data.to_sql("Follow_up_Data", conn, index=False, if_exists="append")
if enter == "Re-enter data":
table = "Follow_up_Data"
col_list = ["File_number"] + names.name_follow_up()
sql = ('SELECT ' + ", ".join(col_list[:-2]) + " FROM '" + table +
"' WHERE File_number = '" + file_number + "'")
df = pd.read_sql(sql, conn)
follow_up_period = list(df.loc[:, "Follow_up_Period"])
delete_data = True
while delete_data:
check_delete = False
while not check_delete:
col_data = ask_y_n_statement.ask_option(
"Which entry do you want to modify?", follow_up_period)
check_delete = ask_y_n_statement.ask_y_n(
"Are you sure you want to delete data for follow-up period "
+ col_data)
delete_rows(cursor, table, "Follow_up_Period", col_data)
add_data(conn, file_number, user_name)
delete_data = ask_y_n_statement.ask_y_n(
"Do you want to re-enter another follow up period")
def edit_radio(self, table):
col_list = names(table)
enter = sql.view_multiple(self.conn, table, col_list, self.file_number)
if enter == "Add data":
self.add_radio(table)
elif enter == "Edit data":
sql_statement = ('SELECT ' + ", ".join(col_list) + " FROM '" +
table + "' WHERE file_number = '" +
self.file_number + "'")
df = pd.read_sql(sql_statement, self.conn)
sql.print_df(df)
pk, value_row_to_edit = sql.retrieve_with_pk_to_edit(
df,
value_col='reason_report',
table=table,
cursor=self.cursor,
pk=False)
print('value_row_to_edit: ', value_row_to_edit)
if not value_row_to_edit:
sql.delete_rows(self.cursor,
table,
col_name="file_number",
col_data=self.file_number)
self.add_radio(table)
else:
self.edit_data_pk(pk, value_row_to_edit, table)
else:
print('\n No edits will be made to this table\n')
def edit_data(self):
enter = sql.view_multiple(self.conn, self.table_name,
self.col_list_all, self.file_number)
if enter == "Add data":
self.add_data()
elif enter == "Edit data":
col_list_all = self.col_list_all
sql_statement = ('SELECT ' + ", ".join(col_list_all) + " FROM '" +
self.table_name + "' WHERE file_number = '" +
self.file_number + "'")
df = pd.read_sql(sql_statement, self.conn)
sql.print_df(df)
pk, value_row_to_edit = sql.retrieve_with_pk_to_edit(
df,
value_col='pet_scan_date',
table=self.table_name,
cursor=self.cursor,
pk=False)
print('value_row_to_edit: ', value_row_to_edit)
if not value_row_to_edit:
sql.delete_rows(self.cursor,
self.table_name,
col_name="file_number",
col_data=self.file_number)
self.add_data()
else:
print('edit_data_pk')
self.edit_data_pk(pk, value_row_to_edit)
else:
print('\n No edits will be made to this t able\n')
def edit_data(conn, cursor, file_number, user_name):
table = "Adjuvant_ChemoTherapy"
enter = review_data(conn, cursor, table, file_number, names(table))
if enter:
delete_rows(cursor, 'Chemo_Drug_Table', "File_number", file_number)
delete_rows(cursor, 'Chemo_Tox_table', "File_number", file_number)
data = chemotherapy(file_number, user_name)
data_sql, drug_table, tox_response = data
update_multiple(conn, cursor, table, names(table), file_number,
data_sql)
drug_table.to_sql("Chemo_Drug_Table",
conn,
index=False,
if_exists="append")
tox_response.to_sql("Chemo_Tox_table",
conn,
index=False,
if_exists="append")
def edit_data(self):
print("Surgery Block information")
col_list = names(self.module_list[0])
enter = sql.review_data(self.conn, self.cursor, self.table,
self.file_number, col_list)
if enter:
data = SurgeryBlockData.surgery_block_information_1(self)
sql.update_multiple(self.conn, self.cursor, self.table, col_list,
self.file_number, data)
print("Surgery Block information (Tumour Details)")
col_list = names(self.module_list[1])
enter = sql.review_data(self.conn, self.cursor, self.table,
self.file_number, col_list)
if enter:
sql.delete_rows(self.cursor, 'block_data', "file_number",
self.file_number)
data, block_data_df = SurgeryBlockData.surgery_block_information_2(
self)
sql.update_multiple(self.conn, self.cursor, self.table, col_list,
self.file_number, data)
block_data_df.to_sql("block_data",
self.conn,
index=False,
if_exists="append")
print("Surgery Block information (Node Details)")
col_list = names(self.module_list[2])
enter = sql.review_data(self.conn, self.cursor, self.table,
self.file_number, col_list)
if enter:
data = SurgeryBlockData.surgery_block_information_3(self)
sql.update_multiple(self.conn, self.cursor, self.table, col_list,
self.file_number, data)
print("Pathological Stage")
col_list = names(self.module_list[3])
enter = sql.review_data(self.conn, self.cursor, self.table,
self.file_number, col_list)
if enter:
data = SurgeryBlockData.path_stage(self)
sql.update_multiple(self.conn, self.cursor, self.table, col_list,
self.file_number, data)
def edit_data(self):
enter = sql.view_multiple(self.conn, self.table, self.col_list,
self.file_number)
if enter == "Add data":
data = self.follow_up()
data.to_sql(self.table, self.conn, index=False, if_exists="append")
elif enter == "Edit data":
col_list_all = ["file_number"] + self.col_list
sql_statement = ('SELECT ' + ", ".join(col_list_all) + " FROM '" +
self.table + "' WHERE file_number = '" +
self.file_number + "'")
df = pd.read_sql(sql_statement, self.conn)
#df = df.dropna()
# any row with None in it will be deleted.
sql.print_df(df)
# check_edit = False
# while check_edit:
check_edit, df = sql.edit_table(df,
pk_col='follow_up_period',
df_col=names(),
update_by=self.user_name)
if check_edit:
sql.delete_rows(self.cursor, self.table, "file_number",
self.file_number)
df = self.follow_up()
df.to_sql(self.table,
self.conn,
index=False,
if_exists="append")
else:
sql.delete_rows(self.cursor, self.table, "file_number",
self.file_number)
df.to_sql("follow_up_data",
self.conn,
index=False,
if_exists="append")
else:
print('\n No edits will be made to this t able\n')
def edit_data(self, file_number):
print('view_multiple')
enter = sql.view_multiple(self.conn, self.table_name, self.columns,
file_number)
if enter == "Add data":
self.add_one(file_number)
elif enter == "Edit data":
col_pk = ['pk'] + self.columns
sql_statement = ('SELECT ' + ", ".join(col_pk) + " FROM '" +
self.table_name + "' WHERE file_number = '" +
file_number + "'")
df = pd.read_sql(sql_statement, self.conn)
sql.print_df(df)
# check_delete = False
# while not check_delete:
check_delete, df = sql.edit_table(df,
pk_col='block_id',
df_col=self.columns[:-2],
update_by=self.user_name)
if check_delete:
sql.delete_rows(self.cursor, self.table_name, "file_number",
file_number)
data = self.add_update_patient()
data.to_sql(self.table_name,
self.conn,
index=False,
if_exists="append")
else:
sql.delete_rows(self.cursor, self.table_name, "file_number",
file_number)
df.to_sql(self.table_name,
self.conn,
index=False,
if_exists="append")
else:
print('\n No edits will be made to this table\n')
def nact_regime(file_number, user_name):
col_drug = names("NACT_Drug_per_week")
drug_per_week = pd.DataFrame(columns=col_drug)
col_cycle_all = names("NACT_Drug_Cycle")
data_per_cycle = pd.DataFrame(columns=col_cycle_all)
col_drug_response = names("NACT_Toxicity")
tox_response_all = pd.DataFrame(columns=col_drug_response)
check = False
while not check:
nact = ask_y_n_statement.ask_y_n("Has neo adjuvant therapy been done for the patient?")
if nact:
nact = "Neo Adjuvant therapy given"
place_nact = ask_y_n_statement.ask_y_n_na("Has Chemotherapy been done at PCCM?", "At PCCM", "Outside",
"Not Certain, requires follow-up")
details_nact = ask_y_n_statement.ask_y_n("Are Chemotherapy details available?", "Details Available",
"Details to be taken from patient")
if details_nact == "Details Available":
date_nact = input("Date of starting neo-adjuvant therapy: ")
plan_nact = input("Type of NACT plan: ")
cycle_number, week_number = (1,)*2
week_end, cycle_index, week_index, drug_index = (0,)*4
add_cycle = True
while add_cycle:
check_cycle = False
while not check_cycle:
cyc_name = "Cycle " + str(cycle_number)
print(cyc_name)
week_add = True
while week_add:
check_drug_tox = False
while not check_drug_tox:
week = "Week " + str(week_number)
print(week)
week_check = ask_y_n_statement.ask_y_n("Is week correct?")
if not week_check:
week_number = input("Week number? ")
week_number = int(week_number)
week = "Week " + str(week_number)
patient_wt = input("Patient weight (in kg): ")
drug_per_week, drug_cyc = drug_add(file_number, cyc_name, cycle_number, week, patient_wt, drug_per_week, drug_index)
tox_response = chemo.tox_table(file_number, cyc_name, week, drug_cyc)
tox_grade, tox, tox_treatment, tox_response = tox_response
change_tox = ask_y_n_statement.ask_option("Changes to NACT treatment due to toxicity",
["No change", "NACT regime changed", "NACT stopped"])
if change_tox =="NACT regime changed":
change = input("Please describe changes to NACT regime: ")
change_tox = change_tox+": "+change
data_tox_response = [file_number, cycle_number, week, "/".join(drug_cyc), tox, tox_grade, tox_treatment,
tox_response, change_tox]
tox_response_all.loc[week_index] = data_tox_response
check_drug_tox = review_df(tox_response_all.loc[week_index])
week_number = week_number + 1
week_index = week_index + 1
week_add = ask_y_n_statement.ask_y_n("Add another week to " + cyc_name + " ?")
patient_wt_end_cycle = patient_wt
drug_cycle = drug_per_week.query('Cycle_number==' + str(cycle_number))
tox_cycle = tox_response_all.query('Cycle_number==' + str(cycle_number))
data_cycle, drug_dose = chemo.get_cycle_data(drug_cycle, tox_cycle)
drug_week, tox_week, tox_grade_week, tox_treatment_week, tox_response_week, change_tox_week \
= data_cycle
response_check = ask_y_n_statement.ask_option("Method used to check response to NACT in this cycle",
["Response not checked", "Other"])
if response_check != "Response not checked":
response_nact = ask_y_n_statement.ask_option("Tumour response to NACT treatment",
response_nact = ask_y_n_statement.ask_option("Tumour response to NACT treatment",
["Partial", "Complete", "Progressing", "Static",
"Other"])
response_size = input("Tumour Size as assessed by " + response_check+" (cm): ")
date = input("Date of tumour size assessment: ")
else:
response_nact, response_size, date = ("NA", )*3
week_end = week_number - week_end -1
weeks = str(week_end)+" Weeks"
data_cycle_all = [file_number, cyc_name, weeks, patient_wt_end_cycle, drug_week, tox_week, tox_grade_week,
tox_treatment_week, tox_response_week, change_tox_week, drug_dose, response_check,
response_nact, response_size, date]
data_per_cycle.loc[cycle_index] = data_cycle_all
check_cycle = review_df(data_per_cycle.loc[cycle_index])
cycle_number = cycle_number + 1
cycle_index = cycle_index + 1
add_cycle = ask_y_n_statement.ask_y_n("Add another cycle? ")
trast_nact = ask_y_n_statement.ask_y_n("Trastuzumab used?")
if trast_nact:
trast_regime = ask_y_n_statement.ask_option("Trastuzumab use was", ["Sequential", "Concurrent"])
trast_nact = "Trastuzumab used"
trast_courses = input("Number of courses of trastuzumab/herceptin taken: ")
else:
trast_nact = "Trastuzumab not used"
trast_regime, trast_courses = ("NA",)*2
date_complete = input("Date of completion of NACT")
complete_nact = ask_y_n_statement.ask_y_n("Was NACT completed as per schedule?")
if complete_nact:
reason_incomplete = "NACT completed as per schedule"
else:
reason_incomplete = ask_y_n_statement.ask_option("Reason for discontinuation", ["Toxicity",
"Reluctance of patient", "Progression on chemotherapy", "Advised by treating doctor",
"Death due to toxicity", "Death due to progressive disease", "Preferred treatment at another centre",
"Death due to unrelated cause", "Patient was unable to afford treatment"])
reason_incomplete = "NACT incomplete: "+reason_incomplete
number_cycles = data_per_cycle.shape[0]
number_weeks = week_number -1
drug_dose = []
drug_dose_unit_df = drug_per_week.loc[:,("Drugs", "Dose_unit")].drop_duplicates()
for index in range(1, 2):
dose_ = drug_per_week.loc[:, ("Drugs", "Dose")]
dose_sum_cycle = dose_.groupby("Drugs").sum()
for index in range(0, len(list(dose_sum_cycle.index))):
dose_unit_ = list(drug_dose_unit_df.loc[:, "Dose_unit"])[index]
data = list(dose_sum_cycle.index)[index] + ": " + str(
list(dose_sum_cycle.loc[:, "Dose"])[index]) + " " + dose_unit_
drug_dose.append(data)
drug_admin = "; ".join(drug_dose)
hormone_therapy = ask_y_n_statement.ask_y_n("Was hormone therapy given?")
if hormone_therapy:
hormone_therapy = "Hormone therapy given"
therapy_type = ask_y_n_statement.ask_option("Hormone therapy type", ["Sequential", "Concurrent"])
therapy_duration = input("What was the duration of therapy? ")
therapy_side = ask_y_n_statement.ask_y_n("Were any side effects observed ?")
if therapy_side:
therapy_side = input("Please give details of side effects observed: ")
else:
therapy_side = "NA"
else:
hormone_therapy = "No hormone therapy given"
therapy_type, therapy_duration, therapy_side = ("NA", )*3
else:
date_nact, plan_nact, drug_admin, number_weeks, number_cycles, response_check, response_nact, response_size, \
date, reason_incomplete, date_complete, trast_nact, trast_regime, trast_courses, \
hormone_therapy, therapy_type, therapy_duration, therapy_side = ("Details to be taken from patient",) * 18
else:
nact = "No NeoAdjuvant Therapy given"
date_nact, plan_nact, drug_admin, number_weeks, number_cycles, response_check, response_nact, response_size, \
date, reason_incomplete, date_complete, trast_nact, trast_regime, trast_courses, \
hormone_therapy, therapy_type, therapy_duration, therapy_side, place_nact, details_nact = \
("No NeoAdjuvant Therapy given",)*20
last_update = datetime.now().strftime("%Y-%b-%d %H:%M")
data_list = [nact, date_nact, plan_nact, drug_admin,str(number_weeks), str(number_cycles),
response_check, response_nact, response_size, date, reason_incomplete, date_complete,
trast_nact, trast_regime, trast_courses, hormone_therapy, therapy_type, therapy_duration,
therapy_side, user_name, last_update, place_nact, details_nact]
col_list = names("Neo_Adjuvant_Therapy")
check = review_input(file_number, col_list, data_list)
return data_list, tox_response_all, drug_per_week, data_per_cycle
def clip_information(file_number):
check = False
while not check:
clip = ask_y_n_statement.ask_y_n("Was Clip inserted for surgery?")
if clip:
clip_number = input("Number of clips inserted: ")
clip_date = input("Date of clip insertion: ")
clip_cycle = input("Clip inserted after cycle? ")
else:
clip_date, clip_number, clip_cycle = ("NA", )*3
data_list = clip_number, clip_date, clip_cycle
col_list = names("clip_information")
check = review_input(file_number, col_list, data_list)
return data_list
def add_data(conn, cursor, file_number, user_name):
table = "Neo_Adjuvant_Therapy"
#file_row(cursor, file_number)
data = nact_regime(file_number, user_name)
data_sql, tox_response_all, drug_per_week, data_per_cycle = data
update_multiple(conn, cursor, table, names(table), file_number, data_sql)
tox_response_all.to_sql("NACT_Toxicity", conn, index=False, if_exists="append")
drug_per_week.to_sql("NACT_Drug_per_week", conn, index=False, if_exists="append")
data_per_cycle.to_sql("NACT_Drug_Cycle", conn, index=False, if_exists="append")
enter = ask_y_n_statement.ask_y_n("Input Clip Information")
if enter:
data = clip_information(file_number)
col_list = names("clip_information")
update_multiple(conn, cursor, table, col_list, file_number, data)
def edit_data(conn, cursor, file_number, user_name):
table = "Neo_Adjuvant_Therapy"
enter = review_data(conn, cursor, table, file_number, names(table))
if enter:
data = nact_regime(file_number, user_name)
data_sql, tox_response_all, drug_per_week, data_per_cycle = data
update_multiple(conn, cursor, table, names(table), file_number, data_sql)
delete_rows(cursor, 'NACT_Toxicity', "File_number", file_number)
tox_response_all.to_sql("NACT_Toxicity", conn, index=False, if_exists="append")
delete_rows(cursor, 'NACT_Drug_per_week', "File_number", file_number)
drug_per_week.to_sql("NACT_Drug_per_week", conn, index=False, if_exists="append")
delete_rows(cursor, 'NACT_Drug_Cycle', "File_number", file_number)
data_per_cycle.to_sql("NACT_Drug_Cycle", conn, index=False, if_exists="append")
print("Clip Information")
module = "clip_information"
col_list = names(module)
enter = review_data(conn, cursor, table, file_number, col_list)
if enter:
data = clip_information(file_number)
update_multiple(conn, cursor, table, col_list, file_number, data)