def drug_table_enter(file_number, drug_table):
drug_add = True
drug_index = 0
while drug_add:
check_drug= False
while not check_drug:
drug = ask_y_n_statement.ask_option("Drug used for therapy", chemo.drug_list())
try:
dose = input("Dose of " + drug +" (actual dose ammount without unit, numbers only): ")
dose_x = float(dose)
except:
print ('ERROR: enter numbers only')
dose = input("Dose of " + drug +" (actual dose ammount without unit, numbers only): ")
dose_unit = input("Dose unit: ")
cyc_freq_week = input("Cycle Frequency (frequency per week, so three weekly is 3 and weekly is 1): ")
try:
number_cycle = input("Number of cycles actually given: ")
dose_x = int(number_cycle)
except:
print('ERROR: enter numbers only')
number_cycle = input("Number of cycles actually given: ")
try:
drug_dose = float(dose) * int(number_cycle)
except:
drug_dose = 'PLEASE RE-ENTER DATA, DOSE AND NUMBER OF CYCLES MUST BE DIGITS ONLY'
data_drug = [file_number, number_cycle, drug, str(drug_dose), dose_unit, cyc_freq_week]
drug_table.loc[drug_index] = data_drug
check_drug, drug_table = review_df_row(drug_table)
drug_index = drug_index + 1
drug_add = ask_y_n_statement.ask_y_n("Add another drug")
return drug_table
def tox_table(file_number, drug_cyc, tox_all):
tox_index = 0
check_tox = False
while not check_tox:
tox = ask_y_n_statement.ask_y_n(
"Were there any toxic effects in administration of " + drug_cyc)
if tox:
add_tox = True
while add_tox:
tox_present = ask_y_n_statement.ask_option(
"Toxic effects of type", chemo.toxicity())
tox_grade = ask_y_n_statement.ask_option(
("the grade of " + tox_present + "? "),
["Mild", "Moderate", "Severe", "Other"])
treatment = input("Treatment given for " + tox_grade + " " +
tox_present + " (include all details): ")
resp_treatment = ask_y_n_statement.ask_option(
("Response to treatment given for " + tox_grade + " " +
tox_present),
["Partial", "Complete", "No Effect", "Other"])
cyc_tox = input("Cycle at which toxicity occurred: ")
change_tox = ask_y_n_statement.ask_option(
"Changes to treatment", [
"No change", "Therapy changed due to toxicity",
"Therapy stopped due to toxicity",
"Therapy changed due to other reasons",
"Therapy stopped due to other reasons"
])
if change_tox == "Therapy changed due to toxicity" or change_tox == "Therapy changed due to other "\
"reasons":
change = input("Please describe changes to Therapy: ")
change_tox = change_tox + ": " + change
check = False
while not check:
data = [
file_number, drug_cyc, tox_present, tox_grade,
treatment, resp_treatment, cyc_tox, change_tox
]
tox_all.loc[tox_index] = data
check = review_df_row(tox_all)
tox_index = tox_index + 1
add_tox = ask_y_n_statement.ask_y_n(
'Add another toxicity type?')
else:
tox_present, tox_grade, treatment, resp_treatment, cyc_tox, change_tox = (
"No Toxicity", ) * 6
data = [
file_number, drug_cyc, tox_present, tox_grade, treatment,
resp_treatment, cyc_tox, change_tox
]
tox_all.loc[tox_index] = data
check_tox = review_df(tox_all)
return tox_all
def drug_table_enter(file_number, drug_table):
drug_add = True
drug_index = 0
while drug_add:
check_drug = False
while not check_drug:
drugs_administered = ask.ask_option("Drug used for therapy",
chemo.drug_list())
dose_check = ask.ask_y_n('Is the drug dose available?')
if dose_check:
dose = ask.check_number_input(
"Dose of " + drugs_administered + ':',
'Please input dose amount'
'without unit')
if dose == 'NA':
dose_unit = 'NA'
else:
dose_unit = input("Dose unit: ")
else:
dose, dose_unit = [
'NA',
] * 2
cycle_check = ask.ask_y_n('Is the drug cycle available?')
if cycle_check:
cycle_frequency_per_week = ask.check_number_input(
"Cycle Frequency: ", 'Please enter frequency per '
'week, so three weekly is 3 and '
'weekly is 1')
number_cycle = ask.check_number_input(
"Number of cycles actually given: ",
'Please enter numbers only')
else:
cycle_frequency_per_week, number_cycle = [
'NA',
] * 2
drug_dose = 'NA'
if number_cycle != 'NA' and dose != 'NA':
drug_dose = float(dose) * int(number_cycle)
data_drug = [
file_number, drugs_administered, number_cycle,
cycle_frequency_per_week,
str(drug_dose), dose_unit
]
drug_table.loc[drug_index] = data_drug
check_drug, drug_table = review_df_row(drug_table)
drug_index = drug_index + 1
drug_add = ask.ask_y_n("Add another drug")
return drug_table
def update_block_id(self, file_number, block_type):
block_df = self.block_data
pk = uuid.uuid4().hex
data_list = self.columns
check = False
while not check:
patient_name = sql.get_value_no_error(col_name='patient_name',
table=self.table_name,
pk=file_number,
pk_name='file_number',
cursor=self.cursor)
mr_number = sql.get_value_no_error(col_name='mr_number',
table=self.table_name,
pk=file_number,
pk_name='file_number',
cursor=self.cursor)
date_of_birth = sql.get_value_no_error(col_name='date_of_birth',
table=self.table_name,
pk=file_number,
pk_name='file_number',
cursor=self.cursor)
date_first_visit = sql.get_value_no_error(
col_name='date_first_visit',
table=self.table_name,
pk=file_number,
pk_name='file_number',
cursor=self.cursor)
block_sr_number = sql.get_value_no_error(
col_name='block_sr_number',
table=self.table_name,
pk=file_number,
pk_name='file_number',
cursor=self.cursor)
block_location = sql.get_value_no_error(col_name='block_location',
table=self.table_name,
pk=file_number,
pk_name='file_number',
cursor=self.cursor)
blocks_received_at_pccm = sql.get_value_no_error(
col_name='blocks_received_at_pccm',
table=self.table_name,
pk=file_number,
pk_name='file_number',
cursor=self.cursor)
consent_discussed = sql.get_value_no_error(
col_name='consent_discussed',
table=self.table_name,
pk=file_number,
pk_name='file_number',
cursor=self.cursor)
consent = sql.get_value_no_error(col_name='consent',
table=self.table_name,
pk=file_number,
pk_name='file_number',
cursor=self.cursor)
block_id = self.check_block_value_in_db(
input_statement='Please enter block id: ',
value_name='block_id',
integer=False)
if blocks_received_at_pccm == 'NA':
number_of_blocks, block_series, current_block_location = [
'NA',
] * 3
else:
number_of_blocks = ask.check_number_input(
'Please enter number of blocks recieved at PCCM: ',
'Number of blocks has to be a whole number or NA')
block_series = input(
"Series of blocks recieved (Please enter series in the form A-B and separate "
"series by '|' e.g, A-B|E): ")
current_block_location = ask.ask_list(
'Current location of block',
BlockList.edit_values['current_block_location'])
data_list = [
pk, file_number, patient_name, mr_number, date_of_birth,
date_first_visit, block_sr_number, block_location, block_type,
block_id, current_block_location, blocks_received_at_pccm,
number_of_blocks, block_series,
str(consent_discussed), consent, self.user_name,
sql.last_update()
]
# print(data_list, self.columns_db)
block_df.loc[pk] = data_list
check, block_df = sql.review_df_row(block_df)
return data_list[1:], pk
def add_block_id(self, file_number):
block_df = self.block_data
pk = uuid.uuid4().hex
data_list = self.columns
check = False
while not check:
check_name = False
while not check_name:
patient_name = input('Please enter patient name: '),
print('Patient name: ' + str(patient_name))
check_name = ask.ask_y_n('Is name correct')
mr_number = self.check_block_value_in_db(
input_statement='Please enter MR number: ',
value_name='mr_number',
integer=True)
date_of_birth = self.get_value_and_check_value(
col_name='date_of_birth',
file_number=file_number,
input_statement='Please input patient date of birth '
'(format: dd.mm.yyyy): ',
integer=False)
date_first_visit = ask.check_date(
'Please enter date of first visit: ')
block_sr_number = self.check_block_value_in_db(
input_statement='Please enter block serial number: ',
value_name='block_sr_number',
integer=True)
block_pccm = ask.ask_y_n(
'Have these blocks been recieved at PCCM?')
block_location, blocks_received_at_pccm = [
'NA',
] * 2
if block_pccm:
block_location_check = False
while not block_location_check:
block_location = block_location_format()
block_location_check = sql.check_value_not_exist(
self.cursor,
value_name='block_location',
value=block_location,
table=self.table_name)
blocks_received_at_pccm = ask.check_date_or_today(
'Please enter date blocks recieved at PCCM (or '
'today): ')
consent_discussed, consent = self.get_consent(file_number)
block_id = self.check_block_value_in_db(
input_statement='Please enter block id: ',
value_name='block_id',
integer=False)
block_type = ask.ask_list('Block type', ['biopsy', 'surgery'])
if blocks_received_at_pccm == 'NA':
number_of_blocks, block_series, current_block_location = [
'NA',
] * 3
else:
number_of_blocks = ask.check_number_input(
'Please enter number of blocks recieved at PCCM: ',
'Number of blocks has to be a whole number or NA')
block_series = input(
"Series of blocks recieved (Please enter series in the form A-B and separate "
"series by '|' e.g, A-B|E): ")
current_block_location = ask.ask_list(
'Current location of block',
BlockList.edit_values['current_block_location'])
data_list = [
pk, file_number, patient_name, mr_number, date_of_birth,
date_first_visit, block_sr_number, block_location, block_type,
block_id, current_block_location, blocks_received_at_pccm,
number_of_blocks, block_series,
str(consent_discussed), consent, self.user_name,
sql.last_update()
]
block_df.loc[pk] = data_list
check, block_df = sql.review_df_row(block_df)
return data_list[1:], pk
def update_patient(self, file_number, block_id):
block_df = self.block_data
check = False
while not check:
print('update_patient')
pk = uuid.uuid4().hex
patient_name = self.get_value_and_check_value(
col_name='patient_name',
file_number=file_number,
input_statement='Please enter patient name: ',
integer=False)
block_sr_number = self.get_value_and_check_value(
col_name='block_sr_number',
file_number=file_number,
input_statement='Please enter block serial number: ',
integer=True)
if block_sr_number != 'block_not_available':
block_location_check = sql.get_value_no_error(
'block_location', self.table_name, file_number,
'file_number', self.cursor)
block_location = block_location_check
print('block_location: ' + str(block_location))
block_location_check = ask.ask_y_n('Is this correct?')
while not block_location_check:
block_location = block_location_format()
block_location_check = self.check_block_value_not_exist(
value_name='block_location',
value=block_location,
table=self.table_name)
blocks_received_at_pccm = sql.check_db_value(
col_name='blocks_received_at_pccm',
table=self.table_name,
file_number=file_number,
cursor=self.cursor,
error_statement='Please enter date blocks recieved at PCCM'
' (dd.mm.yyyy): ')
block_type = ask.ask_list('Block type', ['biopsy', 'surgery'])
if block_id == 'block_id':
block_id = self.check_block_value_in_db(
input_statement='Please enter block id: ',
value_name='block_id',
integer=False)
number_of_blocks = ask.check_number_input(
'Please enter number of blocks recieved at PCCM: ',
'Number of blocks has to be a whole number or NA')
block_series = input(
"Series of blocks recieved (Please separate series by ';'): "
)
current_block_location = ask.ask_list(
'Current location of block', names.block_list('location'))
consent_discussed, consent = self.get_consent(file_number)
else:
block_type = ask.ask_list('Block type', ['biopsy', 'surgery'])
if block_id == 'block_id':
block_id = self.check_block_value_in_db(
input_statement='Please enter block id: ',
value_name='block_id',
integer=False)
block_location, blocks_received_at_pccm, number_of_blocks, block_series, current_block_location, \
consent_discussed, consent = (block_sr_number, )*7
data_list = [
pk, file_number, patient_name, block_sr_number, block_location,
block_type, block_id, current_block_location,
blocks_received_at_pccm, number_of_blocks, block_series,
consent_discussed, consent, self.user_name,
sql.last_update()
]
block_df.loc[pk] = data_list
check, block_df = sql.review_df_row(block_df)
print("error check in update_patient")
sql.print_df(block_df)
return block_df
def add_update_patient(self):
block_df = self.block_data
file_number = 'test'
check_file = False
while not check_file:
print('add_update_patient')
file_number = input("Enter File Number: ")
print("File Number: " + file_number)
check_file = ask.ask_y_n("Is this file number correct")
check = False
while not check:
if sql.check_file_number_exist(self.cursor, file_number,
self.table_name):
print('add_update_patient_not_checck')
pk = uuid.uuid4().hex
patient_name = self.get_value_and_check_value(
col_name='patient_name',
file_number=file_number,
input_statement='Please enter patient name: ',
integer=False)
block_sr_number = self.get_value_and_check_value(
col_name='block_sr_number',
file_number=file_number,
input_statement='Please enter block serial number: ',
integer=True)
# block_location = 'block_location'
block_location_check = sql.get_value_no_error(
col_name='block_location',
table=self.table_name,
pk=file_number,
pk_name='file_number',
cursor=self.cursor)
if not block_location_check:
print(
'Block location already exists for another file_number'
)
while not block_location_check:
block_location = block_location_format()
block_location_check = sql.check_value_not_exist(
self.cursor,
value_name='block_location',
value=block_location,
table=self.table_name)
else:
block_location = block_location_check
blocks_received_at_pccm = sql.get_value_no_error(
col_name='blocks_received_at_pccm',
table=self.table_name,
pk=file_number,
pk_name='file_number',
cursor=self.cursor)
if not blocks_received_at_pccm:
blocks_received_at_pccm = ask.check_date_or_today(
'Please enter date blocks recieved at PCCM (or '
'today): ')
consent_discussed, consent = self.get_consent(file_number)
else:
pk = uuid.uuid4().hex
patient_name = input('Please enter patient name: ')
block_sr_number = self.check_block_value_in_db(
input_statement='Please enter block serial number: ',
value_name='block_sr_number',
integer=True)
block_pccm = ask.ask_y_n(
'Have these blocks been recieved at PCCM?')
block_location, blocks_received_at_pccm = [
'NA',
] * 2
if block_pccm:
block_location_check = False
while not block_location_check:
block_location = block_location_format()
block_location_check = sql.check_value_not_exist(
self.cursor,
value_name='block_location',
value=block_location,
table=self.table_name)
blocks_received_at_pccm = ask.check_date_or_today(
'Please enter date blocks recieved at PCCM (or '
'today): ')
consent_discussed, consent = self.get_consent(file_number)
block_type = ask.ask_list('Block type', ['biopsy', 'surgery'])
block_id = self.check_block_value_in_db(
input_statement='Please enter block id: ',
value_name='block_id',
integer=False)
number_of_blocks = ask.check_number_input(
'Please enter number of blocks recieved at PCCM: ',
'Number of blocks has to be a whole number or NA')
block_series = input(
"Series of blocks recieved (Please separate series by ';'): ")
current_block_location = ask.ask_list('Current location of block',
names.block_list('location'))
data_list = [
pk, file_number, patient_name, block_sr_number, block_location,
block_type, block_id, current_block_location,
blocks_received_at_pccm, number_of_blocks, block_series,
str(consent_discussed), consent, self.user_name,
sql.last_update()
]
# error check
print("error check in loop 1")
sql.print_df(block_df)
block_df.loc[pk] = data_list
print("error check in loop 2")
sql.print_df(block_df)
check, block_df = sql.review_df_row(block_df)
# error check
print("error check out of loop_to_db")
sql.print_df(block_df)
return block_df
def multiple_mass(table, mammo_breast="Right Breast"):
import modules.ask_y_n_statement as ask_y_n_statement
import sql.add_update_sql as add_update_sql
import modules.pccm_names as pccm_names
import pandas as pd
number_mass = input("Number of masses detected: ")
try:
mass_number = int(number_mass)
except:
mass_number = 1
col_list = pccm_names.names_radio_df(table)
mass_df = pd.DataFrame(columns=col_list)
for index in range(0, mass_number):
mass_id = index + 1
if table == "Mammography_Mass":
check = False
while not check:
if mammo_breast == "Bilateral":
mass_location = ask_y_n_statement.ask_option(
"Location of mass " + str(mass_id),
["Right Breast", "Left Breast"])
else:
mass_location = mammo_breast
location_quad = lesion_location(mass_location)
mammo_mass_shape = ask_y_n_statement.ask_option(
"Shape of mass", ["Oval", "Round", "Irregular", "Other"])
mammo_mass_margin = ask_y_n_statement.ask_option(
"Margins of mass", [
"Circumscribed", "Obscured", "Microlobulated",
"Indistinct", "Spiculated", "Other"
])
mass_nipple = input("Distance from nipple (cm): ")
mass_size = input("Mass dimensions (without unit): ")
mass_size_unit = input("Mass dimensions unit")
mass_id = "Mass " + str(index + 1)
data_list = [
mass_id, location_quad, mammo_mass_shape,
mammo_mass_margin, mass_nipple, mass_size, mass_size_unit
]
mass_df.loc[index] = data_list
check, mass_df = add_update_sql.review_df_row(mass_df)
data_list = []
for index in col_list:
data_mass = "; ".join(list(mass_df.loc[:, index]))
data_list.append([data_mass])
data_df = ask_y_n_statement.join_lists(data_list, "; ")
mass_id_, location_quad, mammo_mass_shape, mammo_mass_margin, mass_nipple, \
mass_size, mass_size_unit = data_df
data_return = number_mass, location_quad, mammo_mass_shape, mammo_mass_margin, mass_nipple, mass_size, mass_size_unit
elif table == "SonnoMammography_Mass":
check = False
while not check:
if mammo_breast == "Bilateral":
mass_location = ask_y_n_statement.ask_option(
"Location of mass " + str(mass_id),
["Right Breast", "Left Breast"])
else:
mass_location = mammo_breast
location_clock = input("What is the clock position of mass " +
str(mass_id) + "?")
location_clock = location_clock + " o'clock"
mass_shape = ask_y_n_statement.ask_option(
"Shape of mass " + str(mass_id),
["Oval", "Round", "Irregular", "Other"])
mass_size = input("Mass dimensions (without unit: ")
mass_size_unit = input("Mass dimensions unit")
mass_margin = ask_y_n_statement.ask_option(
"Margin of mass " + str(mass_id), [
"Circumscribed", "Indistinct", "Angular",
"Microlobulated"
])
mass_echo = ask_y_n_statement.ask_option(
"Echo pattern of mass " + str(mass_id), [
"Anechoic", "Hyperechoic", "Complex cystic "
"and solid", "Hypoechoic", "Isoechoic",
"Heterogeneous", "Other"
])
mass_id = "Mass " + str(index + 1)
data_list = [
mass_id, mass_location, location_clock, mass_shape,
mass_margin, mass_echo, mass_size, mass_size_unit
]
mass_df.loc[index] = data_list
check, mass_df = add_update_sql.review_df_row(mass_df)
data_list = []
for index in col_list:
data_mass = "; ".join(list(mass_df.loc[:, index]))
data_list.append([data_mass])
data_df = ask_y_n_statement.join_lists(data_list, "; ")
mass_id_, mass_location, location_clock, mass_shape, mass_margin, mass_echo, mass_size, mass_size_unit = data_df
if mammo_breast != 'Bilateral':
mass_location = mammo_breast
data_return = number_mass, mass_location, location_clock, mass_shape, mass_margin, mass_echo, mass_size, mass_size_unit
elif table == "MRI_Mass":
check = False
while not check:
if mammo_breast == "Bilateral":
mass_location = ask_y_n_statement.ask_option(
"Location of mass " + str(mass_id),
["Right Breast", "Left Breast"])
else:
mass_location = mammo_breast
mri_mass_shape = ask_y_n_statement.ask_option(
"Shape of mass", ["Oval", "Round", "Irregular", "Other"])
mri_mass_margin = ask_y_n_statement.ask_option(
"Margins of mass",
["Circumscribed", "Irregular", "Spiculated"])
mri_mass_internal = ask_y_n_statement.ask_option(
"Internal enhancement characteristics", [
"Homogeneous", "Heterogeneous", "Rim enhancement",
"Dark internal septations"
])
mass_id = "Mass " + str(index + 1)
data_list = [
str(mass_id), mass_location, mri_mass_shape,
mri_mass_margin, mri_mass_internal
]
mass_df.loc[index] = data_list
check, mass_df = add_update_sql.review_df_row(mass_df)
data_list = []
for index in col_list:
data_mass = "; ".join(list(mass_df.loc[:, index]))
data_list.append([data_mass])
data_df = ask_y_n_statement.join_lists(data_list, "; ")
mass_id_, mass_location, mri_mass_shape, mri_mass_margin, mri_mass_internal = data_df
if mammo_breast != 'Bilateral':
mass_location = mammo_breast
data_return = number_mass, mass_location, mri_mass_shape, mri_mass_margin, mri_mass_internal
else:
data_return = "Table does not exist"
return data_return
def follow_up(self):
follow = True
follow_index = 0
col_list = ["file_number"] + names()
follow_up_data = pd.DataFrame(columns=col_list)
while follow:
check = False
while not check:
time_follow = ask.ask_option("Follow-up Period", [
"3 months", "6 months", "9 months", "1 year",
"1 year, 3 months", "1 year, 6 months", "1 year, 9 months",
"2 years", "2 years, 6 months", "3 years",
"3 years, 6 months", "4 years", "4 years, 6 months",
"5 years", "6 years", "7 years", "8 years", "9 years",
"10 years", "Other"
])
follow_status = patient_status()
follow_mammo, follow_mammo_date, follow_usg, follow_usg_date = (
"NA", ) * 4
is_mammo = ask.ask_y_n('Is follow up mammogramm present?')
if is_mammo:
follow_mammo_date = ask.check_date(
'Date of follow-up Mammograph? ')
follow_mammo = input(
"Results of Mammography (Please enter in the format (Observation(mass/calc/lesion "
"etc)/Location/BIRADs)): ")
is_usg = ask.ask_y_n(
'Is follow up USG abdomen/Pelvis present?')
if is_usg:
follow_usg_date = ask.check_date(
'Date of follow-up USG abdomen/Pelvis? ')
follow_usg = input(
"Results of USG abdomen/Pelvis (Please enter in the format (Observation"
"(mass/calc/lesion etc)/Location/BIRADs)): ")
other_type_date, other_type, other_result = ("NA", ) * 3
follow_other = ask.ask_y_n(
"Are there other reports in follow-up?")
if follow_other:
other_type_date_list = []
other_type_list = []
other_result_list = []
while follow_other:
other_type_date = ask.check_date(
'Date of other test: ')
other_type = input("Type of other report: ")
other_result = input("Result of " + other_type + ": ")
other_type_date_list.append(other_type_date)
other_type_list.append(other_type)
other_result_list.append(other_result)
follow_other = ask.ask_y_n("Add more reports?")
all_data = [
other_type_date_list, other_type_list,
other_result_list
]
all_data = ask.join_lists(all_data, "; ")
other_type_date, other_type, other_result = all_data
follow_up_treatment = ask.ask_y_n(
'Was any oncological treatment given after follow up?')
if not follow_up_treatment:
follow_up_treatment, follow_up_treatment_result = [
'no_treatment_given',
] * 2
else:
follow_up_treatment = input(
'What follow up treatment was given?')
follow_up_treatment_result = input(
'What was the result of follow-up treatment ' +
follow_up_treatment + '?')
data_list = [
self.file_number, time_follow, follow_status,
follow_mammo_date, follow_mammo, follow_usg_date,
follow_usg, other_type, other_type_date, other_result,
follow_up_treatment, follow_up_treatment_result,
self.user_name,
sql.last_update()
]
follow_up_data.loc[follow_index] = data_list
check, follow_up_data = sql.review_df_row(follow_up_data)
follow_index = follow_index + 1
follow_up_period = list(follow_up_data.loc[:, "follow_up_period"])
print("\n Follow up periods added: " +
"; ".join(follow_up_period) + '\n')
follow = ask.ask_y_n("Add another follow-up period?")
return follow_up_data
