def surgery_block_information_3(self):
module_name = self.module_list[2]
check = False
while not check:
surgery_er, surgery_er_percent, surgery_pr, surgery_pr_percent, surgery_her2, surgery_her2_grade, \
surgery_fish, surgery_ki67, = BlockDescription.ihc_report()
sentinel, sent_number_rem, sent_number_pos = SurgeryBlockData.node_details(
"Sentinel")
ax, ax_number_rem, ax_number_pos = SurgeryBlockData.node_details(
"Axillary")
ap, ap_number_rem, ap_number_pos = SurgeryBlockData.node_details(
"Apical")
per_spread = ask.ask_y_n_na("Perinodal Spread",
yes_ans='Yes',
no_ans='No',
na_ans='Data not in Report')
supra_inv = ask.ask_y_n_na("Supraclavicular Node Involvment",
yes_ans='Yes',
no_ans='No',
na_ans='Data not in Report')
data_list = [
surgery_er, surgery_er_percent, surgery_pr, surgery_pr_percent,
surgery_her2, surgery_her2_grade, surgery_fish, surgery_ki67,
sentinel, sent_number_rem, sent_number_pos, ax, ax_number_rem,
ax_number_pos, ap, ap_number_rem, ap_number_pos, per_spread,
supra_inv
]
columns_list = names(module_name)
check = sql.review_input(self.file_number, columns_list, data_list)
return (tuple(data_list))
def surgery_block_information_3(self):
module_name = self.module_list[3]
review_surgery_date, review_surgery_source, review_surgery_diagnosis, review_surgery_diagnosis_comment, \
review_surgery_block_id, review_surgery_er, review_surgery_er_percent, review_surgery_pr, review_surgery_pr_percent, \
review_surgery_her2, review_surgery_her2_grade, review_surgery_fish, review_surgery_ki67 = ['NA', ] * 13
data_list = ['NA', ] * 13
check = False
while not check:
review = ask.ask_y_n('Has a review (of diagnosis or IHC details) been done of this surgery block?')
if review:
review_surgery_date = ask.check_date('Date of review (if multiple dates?): ')
review_surgery_source = input(
'Name of Review Laboratory (Enter multiple if required Lab_test): ')
review_surgery_diagnosis = input('Enter diagnosis of review: ')
review_surgery_diagnosis_comment = input('Additional comments for review diagnosis: ')
review_surgery_block_id = self.surgery_block_id
block_id = ask.ask_y_n('Has the block been relabelled in the review?')
if block_id:
old_block_id = input('Please enter old block id: ')
new_block_id = input('Please enter new block id: ')
review_surgery_block_id = old_block_id + ' relabelled to ' + new_block_id
review_ihc = ask.ask_y_n('Has the IHC result for any marker been reviewed by another lab?')
if review_ihc:
review_surgery_er, review_surgery_er_percent, review_surgery_pr, review_surgery_pr_percent, \
review_surgery_her2, review_surgery_her2_grade, review_surgery_fish, review_surgery_ki67 = \
BlockDescription.ihc_report('review_surgery')
data_list = [review_surgery_date, review_surgery_source, review_surgery_diagnosis,
review_surgery_diagnosis_comment, review_surgery_block_id, review_surgery_er,
review_surgery_er_percent, review_surgery_pr, review_surgery_pr_percent, review_surgery_her2,
review_surgery_her2_grade, review_surgery_fish, review_surgery_ki67]
col_list = names(module_name)
check = sql.review_input(self.file_number, col_list[:-2], data_list)
data = data_list + [self.user_name, sql.last_update()]
return data
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 ihc_data(self, block_id):
module_name = "ihc_data"
columns_list = names.names_biopsy_x(module_name)
check = False
while not check:
print('Please input all data for ' + block_id + ' block only')
tumour_er, tumour_er_percent, tumour_pr, tumour_pr_percent, tumour_her2, tumour_her2_grade, \
tumour_fish, tumour_ki67 = BlockDescription.ihc_report('Tumour_biopsy')
fnac = ask.ask_y_n_na(question="Lymph Node biopsy FNAC",
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"])
data_list = [tumour_er, tumour_er_percent, tumour_pr, tumour_pr_percent, tumour_her2,
tumour_her2_grade, tumour_fish, tumour_ki67, fnac, fnac_location, fnac_diagnosis]
check = sql.review_input(self.file_number, columns_list, data_list)
return data_list
def surgery_block_information_2(self):
module_name = self.module_list[2]
data_list = ['NA', ] * 18
check = False
while not check:
ihc_report = BlockDescription.ihc_report(ihc_type='Tumour_surgery_block')
surgery_er, surgery_er_percent, surgery_pr, surgery_pr_percent, surgery_her2, surgery_her2_grade, \
surgery_fish, surgery_ki67 = ihc_report
surgery_subtype = breast_cancer_subtype('surgery', surgery_er, surgery_pr, surgery_her2,
surgery_her2_grade, surgery_fish)
node_details = self.node_details()
sentinel_node_number_removed, sentinel_node_number_positive, axillary_node_number_removed, \
axillary_node_number_positive, apical_node_number_removed, apical_node_number_positive = node_details
surgery_perinodal_spread = ask.ask_list('Perinodal Spread',
ask.create_yes_no_options
('Perinodal Spread', not_cancer='requires_follow_up'))
pathological_pt = input('Pathological T Status (Enter T0/T1/T2 etc as given in report): ')
pathological_pn = input('Pathological N Status (Enter N0/N1/N2 etc as given in report): ')
metastasis = ask.ask_y_n('Did the patient have metastasis at diagnosis?')
nat = sql.get_value(col_name='neoadjuvant_therapy', table=self.table_name, pk=self.fk, cursor=self.cursor,
pk_name='fk', error_statement='what is the nact status?')
if nat != 'nact_no':
prefix = 'yp'
else:
prefix = 'p'
pathological_stage, clinical_stage = BlockDescription.stage(pathological_pt, pathological_pn, metastasis,
prefix)
data_list = [surgery_er, surgery_er_percent, surgery_pr, surgery_pr_percent, surgery_her2,
surgery_her2_grade, surgery_fish, surgery_ki67, surgery_subtype, sentinel_node_number_removed,
sentinel_node_number_positive, axillary_node_number_removed, axillary_node_number_positive,
apical_node_number_removed, apical_node_number_positive, surgery_perinodal_spread,
pathological_pt, pathological_pn, str(metastasis).lower(), pathological_stage, clinical_stage,
self.user_name, sql.last_update()]
columns_list = names(module_name)
check = sql.review_input(self.file_number, columns_list[:-2], data_list[:-2])
return data_list
def ihc_biopsy_data(self):
col_list = names.names_biopsy('ihc_biopsy_data')
try:
columns = names.names_biopsy('biopsy_report_info')
biopsy_ihc_report_pccm = sql.extract_select_column_key(
conn=self.conn,
columns=columns,
table=self.table_name,
key_name='pk',
key_value=self.pk,
col_select='biopsy_ihc_report_pccm')
except ValueError:
biopsy_ihc_report_pccm = ask.ask_list(
"Is the biopsy IHC report available?", [
"biopsy_ihc_report_pccm_yes", "biopsy_ihc_report_pccm_no",
'doctors_notes_available', 'path_history_notes_'
'available', 'requires_specialist_input'
])
data_list = ['NAv'] * 11
try:
columns = names.names_biopsy('biopsy_details')
benign = sql.extract_select_column_key(conn=self.conn,
columns=columns,
table=self.table_name,
key_name='pk',
key_value=self.pk,
col_select='benign')
# print('Diagnosis is :', benign)
if benign.lower() == 'false':
benign = False
elif benign.lower() == 'true':
benign = True
else:
benign = ask.ask_y_n("Is the diagnosis for this block benign?")
except ValueError:
benign = ask.ask_y_n("Is the diagnosis for this block benign?")
check = False
while not check:
if benign:
# print(str(benign))
print('Diagnosis is benign so IHC has not been considered')
biopsy_er, biopsy_er_percent, biopsy_pr, biopsy_pr_percent, biopsy_her2, biopsy_her2_grade, biopsy_fish,\
biopsy_ki67, biopsy_subtype = ['NA'] * 9
else:
print('biopsy_ihc_report_pccm: ' + biopsy_ihc_report_pccm)
if biopsy_ihc_report_pccm[0] != 'biopsy_ihc_report_pccm_no':
print('Please input all data for ' + self.biopsy_block_id +
' block only')
biopsy_er, biopsy_er_percent, biopsy_pr, biopsy_pr_percent, biopsy_her2, biopsy_her2_grade, \
biopsy_fish, biopsy_ki67 = BlockDescription.ihc_report('biopsy')
else:
biopsy_er, biopsy_er_percent, biopsy_pr, biopsy_pr_percent, biopsy_her2, biopsy_her2_grade, \
biopsy_fish, biopsy_ki67 = ['NAv'] * 8
biopsy_subtype = breast_cancer_subtype('biopsy', biopsy_er,
biopsy_pr, biopsy_her2,
biopsy_her2_grade,
biopsy_fish)
fnac_lymph_node = ask.ask_list(
"Lymph Node FNAC",
ask.create_yes_no_options('Lymph Node FNAC'))
fnac_lymph_node_location, fnac_lymph_node_diagnosis = (
fnac_lymph_node, ) * 2
if fnac_lymph_node == "lymph_node_fnac_yes":
fnac_lymph_node_location = input(
"Please enter lymph node biopsy location: ")
fnac_lymph_node_diagnosis = ask.ask_list(
"Lymph Node FNAC diagnosis",
ask.create_yes_no_options('Lymph Node FNAC '
'diagnosis',
yes='malignant',
no='non_malignant'))
data_list = [
biopsy_er, biopsy_er_percent, biopsy_pr, biopsy_pr_percent,
biopsy_her2, biopsy_her2_grade, biopsy_fish, biopsy_ki67,
biopsy_subtype, fnac_lymph_node, fnac_lymph_node_location,
fnac_lymph_node_diagnosis
]
check = sql.review_input(self.file_number, col_list[:-2],
data_list)
data = data_list + [self.user_name, sql.last_update()]
return data