def add_data(self):
block_list_table = BlockInformation(self.conn, self.cursor,
self.file_number)
enter = ask.ask_y_n("Enter Biopsy Report information?")
if enter:
data = self.biopsy_report_info()
sql.update_multiple_key(self.conn,
self.cursor,
self.table_name,
names.names_biopsy("biopsy_report_info"),
key_name='pk',
key_value=self.pk,
data=data)
enter = ask.ask_y_n("Enter Biopsy data?")
if enter:
data = self.biopsy_details()
sql.update_multiple_key(self.conn,
self.cursor,
self.table_name,
names.names_biopsy("biopsy_details"),
key_name='pk',
key_value=self.pk,
data=data)
data = self.ihc_biopsy_data()
sql.update_multiple_key(self.conn,
self.cursor,
self.table_name,
names.names_biopsy("ihc_biopsy_data"),
key_name='pk',
key_value=self.pk,
data=data)
data = self.review_biopsy()
sql.update_multiple_key(self.conn,
self.cursor,
self.table_name,
names.names_biopsy("review_biopsy"),
key_name='pk',
key_value=self.pk,
data=data)
is_surgery = ask.ask_y_n(
'Is a surgery associated with this biopsy?')
if is_surgery:
surgery_block_id, surgery_number_of_blocks = block_list_table.get_block_id(
'surgery')
else:
surgery_block_id = 'NA'
sql.update_single_key(self.conn,
self.cursor,
self.table_name,
'surgery_block_id',
key_name='pk',
key_value=self.pk,
var=surgery_block_id)
def review_biopsy(self):
review_biopsy_date, review_biopsy_source, review_biopsy_diagnosis, review_biopsy_diagnosis_comment, \
review_biopsy_block_id, review_biopsy_er, review_biopsy_er_percent, review_biopsy_pr, review_biopsy_pr_percent, \
review_biopsy_her2, review_biopsy_her2_grade, review_biopsy_fish, review_biopsy_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 biopsy block?'
)
if review:
review_biopsy_date = ask.check_date(
'Date of review biopsy (if multiple dates?): ')
review_biopsy_source = input(
'Name of Review Biopsy Laboratory (Enter multiple if required Lab_test): '
)
review_biopsy_diagnosis = input(
'Enter diagnosis of review biopsy: ')
review_biopsy_diagnosis_comment = input(
'Additional comments for biopsy review diagnosis: ')
review_biopsy_block_id = self.biopsy_block_id
block_id = ask.ask_y_n(
'Has the block been relabelled in the review biopsy?')
if block_id:
old_block_id = input('Please enter old block id: ')
new_block_id = input('Please enter new block id: ')
review_biopsy_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_biopsy_er, review_biopsy_er_percent, review_biopsy_pr, review_biopsy_pr_percent, \
review_biopsy_her2, review_biopsy_her2_grade, review_biopsy_fish, review_biopsy_ki67 = \
BlockDescription.ihc_report('review_biopsy')
data_list = [
review_biopsy_date, review_biopsy_source,
review_biopsy_diagnosis, review_biopsy_diagnosis_comment,
review_biopsy_block_id, review_biopsy_er,
review_biopsy_er_percent, review_biopsy_pr,
review_biopsy_pr_percent, review_biopsy_her2,
review_biopsy_her2_grade, review_biopsy_fish,
review_biopsy_ki67
]
col_list = names.names_biopsy('review_biopsy')
check = sql.review_input(self.file_number, col_list[:-2],
data_list)
data = data_list + [self.user_name, sql.last_update()]
return data
def db_dict(table, module):
db_tables = {
"patient_information_history": names.names_info(module),
"radiology": names.names_radio(module),
'pet_reports': names.names_pet(module),
'biopsy_path_report_data': names.names_biopsy(module),
"neo_adjuvant_therapy": names.names_nact(module),
"surgery_report": names.names_surgery_information(module),
'surgery_path_report_data': names.names_surgery(module),
"adjuvant_chemotherapy": names.names_chemotherapy(module),
"radiotherapy": names.names_radiation(),
"hormonetherapy_survival": names.names_longterm(module),
"follow_up_data": names.name_follow_up(),
'block_list': names.block_list(module)
}
cols = db_tables.get(table)
return cols
col_list = ["File_number"] + col_list_bio + names.names_info("phys_act") + names.names_info("habits") + \
names.names_info("nut_supplements") + names.names_info("family_details") + names.names_info("med_history") + \
names.names_info("cancer_history") + names.names_info("family_cancer") + names.names_info("breast_symptoms")
sql = ('SELECT ' + ", ".join(col_list) + " FROM '" + table + "'")
df = pd.read_sql(sql, conn)
df.to_excel(writer, sheet_name=table)
writer.save()
#######################################33
table = "Biopsy_Report_Data"
module_names = ["biopsy_report_info", "tumour_biopsy_data", "lymphnode_biopsy"]
col_list = ["File_number"]
for index in module_names:
col_list = col_list + names.names_biopsy(index)
sql = ('SELECT ' + ", ".join(col_list) + " FROM '" + table + "'")
df = pd.read_sql(sql, conn)
df.to_excel(writer, sheet_name=table, index=False)
#writer.save()
table = "Surgery_Block_Report_Data"
module_names = [
"surgery_block_information_1", "surgery_block_information_2",
"surgery_block_information_3", "path_stage"
]
col_list = ["File_number"]
for index in module_names:
col_list = col_list + names.names_surgery(index)
sql = ('SELECT ' + ", ".join(col_list) + " FROM '" + table + "'")
df = pd.read_sql(sql, conn)
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
def edit_data(self):
print("Block Report information")
col_list = names.names_biopsy("biopsy_report_info")
enter = sql.review_data_key(self.conn,
self.cursor,
self.table_name,
key_name='pk',
key_value=self.pk,
columns=col_list,
col_name='biopsy_block_id',
col_value=self.biopsy_block_id)
if enter:
# sql.add_pk_fk_to_table(self.conn, self.cursor, self.table_name, col_filter='pk', pk=self.pk)
data = self.biopsy_report_info()
sql.update_multiple_key(self.conn,
self.cursor,
self.table_name,
col_list,
key_name='pk',
key_value=self.pk,
data=data)
print("Biopsy Tumour data")
col_list = names.names_biopsy("biopsy_details")
enter = sql.review_data_key(self.conn,
self.cursor,
self.table_name,
key_name='pk',
key_value=self.pk,
columns=col_list,
col_name='biopsy_block_id',
col_value=self.biopsy_block_id)
if enter:
data = self.biopsy_details()
sql.update_multiple_key(self.conn,
self.cursor,
self.table_name,
col_list,
key_name='pk',
key_value=self.pk,
data=data)
print("Biopsy IHC data")
col_list = names.names_biopsy("ihc_biopsy_data")
enter = sql.review_data_key(self.conn,
self.cursor,
self.table_name,
key_name='pk',
key_value=self.pk,
columns=col_list,
col_name='biopsy_block_id',
col_value=self.biopsy_block_id)
if enter:
data = self.ihc_biopsy_data()
sql.update_multiple_key(self.conn,
self.cursor,
self.table_name,
col_list,
key_name='pk',
key_value=self.pk,
data=data)
print('Review Biopsy data')
col_list = names.names_biopsy("review_biopsy")
enter = sql.review_data_key(self.conn,
self.cursor,
self.table_name,
key_name='pk',
key_value=self.pk,
columns=col_list,
col_name='biopsy_block_id',
col_value=self.biopsy_block_id)
if enter:
data = self.review_biopsy()
sql.update_multiple_key(self.conn,
self.cursor,
self.table_name,
col_list,
key_name='pk',
key_value=self.pk,
data=data)
surgery_block_id = sql.get_value(
col_name='surgery_block_id',
table=self.table_name,
pk=self.pk,
pk_name='pk',
cursor=self.cursor,
error_statement='Please enter surgery block id associated '
'with this biopsy entry: ')
print('Surgery block id associated with this biopsy is ' +
str(surgery_block_id))
block = ask.ask_y_n('Is this block id correct?')
if not block:
surgery_block_id = input(
'Please enter surgery block id associated with this biopsy entry: '
)
sql.update_single_key(self.conn,
self.cursor,
self.table_name,
'surgery_block_id',
key_name='pk',
key_value=self.pk,
var=surgery_block_id)
def biopsy_report_info(self):
module = 'biopsy_report_info'
col_list = names.names_biopsy(module)
check = False
data_list = [self.file_number] + (['To be done'] * 18)
while not check:
block_list_table = BlockInformation(self.conn, self.cursor,
self.file_number)
block_data = [
'block_sr_number', 'block_location', 'current_block_location',
'blocks_received_at_pccm', 'block_series'
]
block_sr_number, block_location, current_block_location, blocks_received_at_pccm, biopsy_block_series = \
block_list_table.get_block_information(block_id=self.biopsy_block_id, block_data=block_data)
fnac = ask.ask_list('FNAC done for breast lesion?',
['fnac_breast_yes', 'fnac_breast_no'])
if fnac == 'fnac_breast_no':
fnac_breast, fnac_breast_date, fnac_slide_id, fnac_diagnosis, fnac_diagnosis_comments = (
fnac, ) * 5
else:
fnac_breast = ask.ask_list('FNAC location', [
'left_breast', 'right_breast', 'requires_specialist_input'
])
fnac_breast_date = ask.check_date('Date of FNAC test: ')
fnac_slide_id = input('Enter FNAC slide ID: ')
fnac_diagnosis = input(
'Enter diagnosis for FNAC breast as given in report: ')
fnac_diagnosis_comments = input(
'Enter additional comments for FNAC diagnosis: ')
biopsy_date = ask.check_date('Date of Biopsy: ')
reason_path_report = ask.ask_list('Reason for pathology report', [
'diagnosis', 'bilateral_diagnosis', 'review_biopsy',
'nact_follow up', 'recurrence_diagnosis', 'revision_surgery',
'requires_specialist_input'
])
biopsy_site = ask.ask_list('Biopsy_site', [
'left_breast', 'right_breast', 'left_axilla', 'right_axilla',
'requires_specialist_input'
])
biopsy_report_pccm = ask.ask_list(
"Is the biopsy report available?", [
"biopsy_report_pccm_yes", "biopsy_report_pccm_no",
'doctors_notes_available', 'path_history_notes',
'requires_specialist_input'
])
if biopsy_report_pccm != 'biopsy_report_pccm_no':
biopsy_block_source = ask.ask_option('Source of Biopsy Block',
PathReports.path_labs)
biopsy_lab_id = input("Biopsy Lab ID/SID: ")
else:
biopsy_block_source, biopsy_lab_id = ('NAv', ) * 2
biopsy_ihc_report_pccm = ask.ask_list(
"Is the 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 = [
self.file_number, block_sr_number, block_location,
current_block_location, blocks_received_at_pccm, fnac_breast,
fnac_breast_date, fnac_slide_id, fnac_diagnosis,
fnac_diagnosis_comments, reason_path_report, biopsy_site,
biopsy_report_pccm, biopsy_ihc_report_pccm,
self.biopsy_block_id, self.biopsy_number_of_blocks,
biopsy_block_series, biopsy_date, biopsy_block_source,
biopsy_lab_id
]
print(data_list)
check = sql.review_input(self.file_number, col_list, data_list)
data = data_list
return data
def biopsy_details(self):
col_list = names.names_biopsy('biopsy_details')
try:
columns = names.names_biopsy('biopsy_report_info')
biopsy_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_report_pccm')
except ValueError:
biopsy_report_pccm = ask.ask_list(
"Is the biopsy report available?", [
"biopsy_report_pccm_yes", "biopsy_report_pccm_no",
'doctors_notes_available', 'path_history_notes',
'requires_specialist_input'
])
data_list = ['NAv'] * 3 + ['False'] + ['NAv'] * 3
if biopsy_report_pccm != 'biopsy_report_pccm_no':
check = False
while not check:
print('Please input all data for ' + self.biopsy_block_id +
' report only')
biopsy_type = ask.ask_list("Biopsy Type",
PathReports.biopsy_type)
biopsy_diagnosis = ask.ask_list("Biopsy Diagnosis: ",
PathReports.diagnosis)
biopsy_comments = input(
'Enter any additional comments on the diagnosis: ')
benign = ask.ask_y_n('Is the diagnosis of ' +
str(biopsy_diagnosis) +
' describing a benign condition ('
'If diagnosis is not available '
'enter NO here)')
if benign:
biopsy_tumour_grade, biopsy_lymph_emboli, dcis_biopsy = [
'benign condition'
] * 3
else:
biopsy_tumour_grade = ask.ask_option(
"Tumour Biopsy Grade", PathReports.grade)
biopsy_lymph_emboli = ask.ask_list(
"Are Lymphovascular emboli seen?",
ask.create_yes_no_options(
'Lymphovascular emboli Biopsy',
not_cancer='requires_follow_up'))
dcis_biopsy = ask.ask_list(
"Does the biopsy show DCIS",
ask.create_yes_no_options(
'dcis biopsy', not_cancer='requires_follow_up'))
data_list = [
biopsy_type, biopsy_diagnosis, biopsy_comments,
str(benign), biopsy_tumour_grade, biopsy_lymph_emboli,
dcis_biopsy
]
check = sql.review_input(self.file_number, col_list, data_list)
else:
print(
'\nBiopsy report is not available. Data for biopsy_type, biopsy_diagnosis, biopsy_comments, '
'tumour_grade, lymph_emboli, dcis_biopsy has been entered as NAv\n'
)
return data_list
def makedb(self):
db_create = CreateTable(self.cursor)
file_number = "file_number"
table = "patient_information_history"
module_list = [
"bio_info", "phys_act", "habits", "nut_supplements",
"family_details", "med_history", "cancer_history", 'family_cancer',
'det_by', "breast_symptoms", 'other_test'
]
col_names = [pccm_names.names_info(module) for module in module_list]
col_list = ask.flatten_nested_list(col_names)
db_create.create_table(table,
file_number=file_number,
col_names=col_list)
table = "biopsy_path_report"
module_list = [
"biopsy_report_info", "biopsy_details", 'ihc_biopsy_data',
'review_biopsy'
]
col_names = [pccm_names.names_biopsy(module) for module in module_list]
col_list = ask.flatten_nested_list(col_names)
db_create.create_table_pk(table, col_list)
table = 'surgery_path_report_data'
module_list = [
"surgery_block_information_0", "surgery_block_information_1",
"surgery_block_information_2", "surgery_block_information_3"
]
col_names = [
pccm_names.names_surgery(module) for module in module_list
]
col_list = ask.flatten_nested_list(col_names)
db_create.create_table_pk(table, col_list, pk='fk')
table = "block_data"
col_names = pccm_names.names_surgery('block_data')[1:]
db_create.create_table_pk(table, col_names, pk='fk')
table = "mammography"
col_names = pccm_names.names_radio(table)
db_create.create_table_pk(table, col_names)
table = 'abvs'
col_names = pccm_names.names_radio(table)
db_create.create_table_pk(table, col_names)
table = 'ultrasound'
col_names = pccm_names.names_radio(table)
db_create.create_table_pk(table, col_names)
table = 'mri'
col_names = pccm_names.names_radio(table)
db_create.create_table_pk(table, col_names)
table = 'pet_reports'
module_list = [
'pet_report_identifier', 'pet_report_findings', 'pet_breast_cancer'
]
col_names = [pccm_names.names_pet(module) for module in module_list]
col_list = ask.flatten_nested_list(col_names)
db_create.create_table_pk(table, col_list)
table = "surgery_report"
module_list = ["surgery_information", "node_excision", "post_surgery"]
col_names = [
pccm_names.names_surgery_information(module)
for module in module_list
]
col_list = ask.flatten_nested_list(col_names)
db_create.create_table(table,
file_number='file_number',
col_names=col_list)
table = "general_medical_history"
col_names = ['condition', 'diagnosis_date', 'treatment']
# col_list = ask.flatten_nested_list(col_names)
db_create.create_table(table,
file_number='file_number',
col_names=col_names)
table = "family_cancer_history"
col_names = [
'type_cancer', 'relation_to_patient', 'type_relation',
'age_at_detection_yrs'
]
# col_list = ask.flatten_nested_list(col_names)
db_create.create_table(table,
file_number='file_number',
col_names=col_names)
table = "previous_cancer_history"
col_names = [
'type_cancer', 'year_diagnosis', 'surgery', 'type_surgery',
'duration_surgery', 'radiation', 'type_radiation',
'duration_radiation', 'chemotherapy', 'type_chemotherapy',
'duration_chemotherapy', 'hormone', 'type_hormone',
'duration_hormone', 'alternative', 'type_alternative',
'duration_alternative', 'homeremedy', 'type_homeremedy',
'duration_homeremedy'
]
col_list = ask.flatten_nested_list(col_names)
db_create.create_table(table,
file_number='file_number',
col_names=col_list)
table = "nutritional_supplements"
col_names = [
'type_nutritional_supplements',
'quantity_nutritional_supplements_per_day',
'duration_nutritional_supplements'
]
col_list = ask.flatten_nested_list(col_names)
db_create.create_table(table,
file_number='file_number',
col_names=col_list)
table = "physical_activity"
col_names = ['type_activity', 'frequency_activity']
col_list = ask.flatten_nested_list(col_names)
db_create.create_table(table,
file_number='file_number',
col_names=col_list)
table = "breast_feeding"
col_names = [
'child_number', 'feeding_duration', 'breast_usage_feeding'
]
col_list = ask.flatten_nested_list(col_names)
db_create.create_table(table,
file_number='file_number',
col_names=col_list)
table = "nact_tox_table"
col_names = pccm_names.names_nact(table)
db_create.create_table(table,
file_number='file_number',
col_names=col_names)
table = "nact_drug_table"
col_names = pccm_names.names_nact(table)
db_create.create_table(table,
file_number='file_number',
col_names=col_names)
table = "neo_adjuvant_therapy"
module_list = ["neo_adjuvant_therapy", "clip_information"]
col_names = [pccm_names.names_nact(module) for module in module_list]
col_list = ask.flatten_nested_list(col_names)
db_create.create_table(table,
file_number='file_number',
col_names=col_list)
table = "adjuvant_chemotherapy"
col_names = pccm_names.names_chemotherapy(table)
db_create.create_table(table,
file_number='file_number',
col_names=col_names)
table = "chemo_tox_table"
col_names = pccm_names.names_chemotherapy(table)
db_create.create_table(table,
file_number='file_number',
col_names=col_names)
table = "chemo_drug_table"
col_names = pccm_names.names_chemotherapy(table)
db_create.create_table(table,
file_number='file_number',
col_names=col_names)
table = "radiotherapy"
col_names = pccm_names.names_radiation()
db_create.create_table(table,
file_number='file_number',
col_names=col_names)
table = "follow_up_data"
col_names = pccm_names.name_follow_up()
db_create.create_table(table,
file_number='file_number',
col_names=col_names)
table = "hormonetherapy_survival"
module_list = ["hormone", "metastasis"]
col_names = [
pccm_names.names_longterm(module) for module in module_list
]
col_list = ask.flatten_nested_list(col_names)
db_create.create_table(table,
file_number='file_number',
col_names=col_list)
table = 'block_list'
col_names = pccm_names.block_list('all')
db_create.create_table_pk(table, col_names=col_names, pk='pk')
table = "clinical_exam"
module_list = ['clinical_exam_initial', 'nipple_cytology']
col_names = [
pccm_names.name_clinical(module) for module in module_list
]
col_list = ask.flatten_nested_list(col_names)
db_create.create_table(table,
file_number=file_number,
col_names=col_list)
self.conn.commit()
print(self.path + " file created")
self.conn.close()
#create new table
path_all = 'D:/repos/pccm_db/main/DB/DB_with_real_data/PCCM_BreastCancerDB_all_data.db'
os.path.isfile(path_all)
conn_all = sqlite3.connect(path_all)
cursor_all = conn_all.cursor()
table = "Biopsy_Report_Data"
file_number = "File_number"
if sql.table_check(cursor_all, table) == 0:
cursor_all.execute('CREATE TABLE {tn}({nf})'.format(tn=table,
nf=file_number))
module_names = [
"biopsy_report_info", "tumour_biopsy_data", "lymphnode_biopsy"
]
for index in module_names:
col_name = pccm_names.names_biopsy(index)
sql.add_columns(cursor_all, table, col_name)
#read from excel with same col names and distribution as in table
file_to_read = "D:/Documents/IISER/Prashanti_docs/Breast_Cancer_FFPE_blocks_database_Biopsy_dk08062018.xlsx"
data = pd.read_excel(file_to_read, header=1, dtype='object', usecols='A:AB')
update_by = "dk from ruhi/shaheen data"
module_names = ["biopsy_report_info", "tumour_biopsy_data", "lymphnode_biopsy"]
col_list = ["File_number"]
for index in module_names:
col_list = col_list + pccm_names.names_biopsy(index)
columns = ", ".join(col_list)
for index in range(0, len(data)):
data_list = list(data.loc[index])
data_list.append(update_by)