def tumour_biopsy_data(self):
module_name = "tumour_biopsy_data"
columns_list = names(module_name)
df_cols = columns_list[:-2]
data_list_df = pd.DataFrame(columns=df_cols)
try:
ihc_biopsy = sql.get_value(col_name='IHC_report_PCCM_yes_no', table=self.table,
file_number=self.file_number, cursor=self.cursor)
except sqlite3.Error:
ihc_biopsy = ask.ask_y_n_na("Is the IHC report available?", yes_ans="IHC_report_PCCM_yes",
no_ans="IHC_report_PCCM_no", na_ans="IHC Not Done")
check = False
while not check:
try:
breast_biopsy = sql.get_value(col_name='Breast_Biopsy', table=self.table,
file_number=self.file_number, cursor=self.cursor)
except sqlite3.Error:
breast_biopsy = ask.ask_option('Breast that biopsy has been done for',
['Right Breast', 'Left Breast', 'Unilateral', "Bilateral"])
breasts = BlockDescription.breast_list(breast_biopsy)
for breast in breasts:
check_breast = False
while not check_breast:
print('Please input all data for ' + breast + ' block only')
tumour_er, tumour_er_percent, tumour_pr, tumour_pr_percent, tumour_her2, tumour_her2_grade, \
tumour_fish, tumour_ki67 = (ihc_biopsy, )* 8
if ihc_biopsy == 'IHC_report_PCCM_yes':
ihc_data = BlockDescription.ihc_report()
tumour_er, tumour_er_percent, tumour_pr, tumour_pr_percent, tumour_her2, tumour_her2_grade, \
tumour_fish, tumour_ki67 = ihc_data
fnac = ask.ask_y_n_na(question=("Lymph Node biopsy FNAC for " + breast),
yes_ans="Lymph_Node_biopsy_FNAC_yes",
no_ans="Lymph_Node_biopsy_FNAC_no", na_ans="Data not in report")
fnac_location, fnac_diagnosis = (fnac,) * 2
if fnac == "Lymph_Node_biopsy_FNAC_yes":
fnac_location = input("Please enter lymph node biopsy location: ")
fnac_diagnosis = ask.ask_option("Lymph Node biopsy diagnosis",
["Lymph_Node_biopsy_malignant",
"Lymph_Node_biopsy_non_malignant",
"Data not in report"])
df_data = [tumour_er, tumour_er_percent, tumour_pr, tumour_pr_percent, tumour_her2,
tumour_her2_grade, tumour_fish, tumour_ki67, fnac, fnac_location, fnac_diagnosis]
print('Data entered for ' + breast + 'is as follows:\n')
check_breast = sql.review_input(self.file_number, df_cols, df_data)
data_list_df.loc[breast] = df_data
data_list = BlockDescription.rb_lb_data(data_list_df, df_cols)
check = sql.review_input(self.file_number, columns_list, data_list)
last_update = datetime.now().strftime("%Y-%b-%d %H:%M")
data_list = data_list+[last_update]+[self.user_name]
return data_list
def biopsy_report_info(self, file_number='test'):
module_name = "biopsy_report_info"
df_cols = names('biopsy_report_info_df')
data_list_df = pd.DataFrame(columns=df_cols)
check = False
while not check:
biopsy_report_pccm = ask.ask_y_n_na("Is the biopsy report available?", yes_ans="Biopsy_report_PCCM_yes",
no_ans="Biopsy_report_PCCM_no", na_ans="Biopsy Not Done")
ihc_report_pccm = ask.ask_y_n_na("Is the IHC report available?", yes_ans="IHC_report_PCCM_yes",
no_ans="IHC_report_PCCM_no", na_ans="IHC Not Done")
breast_biopsy = biopsy_report_pccm
data_list = [biopsy_report_pccm] * 11
data_list_df.loc[biopsy_report_pccm] = data_list
if biopsy_report_pccm == 'Biopsy_report_PCCM_yes':
data_list_df, breast_biopsy = BiopsyData.biopsy_details(self, df_cols)
data_all = BlockDescription.rb_lb_data(data_list_df, df_cols)
data_list = [biopsy_report_pccm, ihc_report_pccm, breast_biopsy]+data_all
columns_list = names(module_name)
check = sql.review_input(file_number, columns_list, data_list)
return data_list