def report(self):
data_list = ask.default_data_list(self.col_list_all)
check = False
while not check:
reason_report = ask.ask_option(
"What is the purpose of this report"
"?", MultiTest.test_reason_imaging)
report_date = ask.check_date("Date of examination of ABVS: ")
abvs_acc = input("Accession number of ABVS: ")
abvs_lesion = ask.ask_option("Location of lesion",
MultiTest.breast_cancer)
if abvs_lesion in {MultiTest.breast_cancer}:
abvs_lesion_data = radio_tables.lesion_location(abvs_lesion)
else:
abvs_lesion_data = "NA"
abvs_size = ask.ask_option("Size of lesion",
["<2 cm", "2-5 cm", ">5 cm", "Other"])
abvs_dist = ask.ask_option("Distance from Skin (cm)",
["<0.5 cm", ">0.5 cm", "Other"])
abvs_pect = input("Distance from Pectoralis Major (cm): ")
abvs_diagnosis = ask.ask_option("ABVS Diagnosis", Radio.diagnosis)
data_list = [
self.file_number, reason_report, report_date, abvs_acc,
abvs_lesion, abvs_lesion_data, abvs_size, abvs_dist, abvs_pect,
abvs_diagnosis
]
check = sql.review_input(self.file_number, self.col_list_all[:-2],
data_list)
data_list = data_list + [self.user_name, sql.last_update()]
return data_list
def mammo_mass(self, mass_id):
print(self.table, mass_id)
check = False
data_list = ask.default_data_list(self.col_list)
while not check:
mass_location = self.mammo_breast
if self.mammo_breast == "bilateral":
mass_location = ask.ask_option("Location of mass "
+ str(mass_id),
RadioTables.breast)
mass_quadrant = ask.ask_list('Quadrant location of lesion',
Radio.lesion_quadrant)
mammo_mass_shape = ask.ask_option("Shape of mass",
RadioTables.mass_shape)
mammo_mass_margin = ask.ask_option("Margins of mass",
RadioTables.mass_margin)
mass_nipple = input("Distance from nipple (cm): ")
mass_dimension,
mass_size_unit,
mass_longest_dimension = self.lesion_size()
modality = self.table
data_list = [self.file_number, mass_location, mass_name,
mass_quadrant, mammo_mass_shape, mammo_mass_margin,
mass_nipple, mass_dimension, mass_longest_dimension,
mass_size_unit, modality]
check = sql.review_input(self.file_number, columns=self.col_list,
data=data_list)
data_list = data_list + [self.user_name, sql.last_update()]
return data_list
def node_excision (file_number):
check = False
while not check:
surgery_guide, frozen, gross_tumour, skin, nodes, number_lymph, level_lymph, sentinel_method, sentinel_blue, \
sentinel_hot, sentinel_blue_hot, sentinel_non_blue_hot, sentinel_palpable = (" ",)*13
guide_add = True
guide = []
while guide_add:
surgery_guide = ask_option("Excision guided by",
["Palpation", "USG guided", "Wire placement guided", 'Gamma camera guided',
'Clipped node'])
guide.append(surgery_guide)
guide_add = ask_y_n("Add another method to guide?")
surgery_guide = "; ".join(guide)
frozen_samples = ask_option_y_n("Any samples sent for histopathology (frozen)?")
if frozen_samples == 'Yes':
frozen_samples = []
sn_frozen = ask_y_n("Sentinel Node sent for histopathology (frozen)?", yes_ans="Sentinel Node")
if sn_frozen == 'Sentinel Node':
frozen_samples.append(sn_frozen)
specimen_frozen = ask_y_n_na("Specimen sent for histopathology (frozen)?")
if specimen_frozen == 'Yes':
nipple_frozen = ask_y_n_na("Under Nipple Surface sent for histopathology (frozen)?",
yes_ans='Under Nipple Surface')
if nipple_frozen == 'Under Nipple Surface':
frozen_samples.append(nipple_frozen)
other_frozen = ask_y_n_na("Any other specimen sent for histopathology (frozen)?")
if other_frozen == 'Yes':
other_frozen = input("Type of tissue sent for histopathology (frozen): ")
frozen_samples.append(other_frozen)
frozen = "; ".join(frozen_samples)
else:
frozen = "NA"
gross_tumour = input ("Size of tumour on cross section (cm): ")
skin = ask_option_y_n("Skin involved", yes_ans="Skin involved", no_ans="Skin not involved")
nodes = ask_option("Nodes excised", ["Sentinel Node", "Sentinel and Axillary Nodes", "Axillary Nodes only",
"Other"])
number_lymph = input("Number of lymph nodes excised (if available): ")
level_lymph = ask_option("Level of lymph node excised", ["I", "II", "III", "Data not available", "Other"])
if nodes == 'Axillary Nodes only':
sentinel_method, sentinel_blue, sentinel_hot, sentinel_blue_hot, sentinel_non_blue_hot, sentinel_palpable = \
('No Sentinel Node excised', )*6
else:
sentinel_method = ask_option("Method of labelling Sentinel Node", ["Isotope", "Blue Dye", "Isotope + Blue Dye",
"Not done", "Other"])
sentinel_blue = ask_option_y_n("Blue Node", yes_ans="Blue Node", no_ans="No Blue Node")
sentinel_hot = ask_option_y_n("Hot Node", yes_ans="Hot Node", no_ans="No Hot Node")
sentinel_blue_hot = ask_option_y_n("Blue Hot Node", yes_ans="Blue Hot Node", no_ans="No Blue Hot Node")
sentinel_non_blue_hot = ask_option_y_n("Non Blue, Hot Node", yes_ans= "Non Blue, Hot Node",
no_ans="No Non Blue, Hot Node")
sentinel_palpable = ask_option_y_n("Palpable Node", yes_ans="Palpable Node", no_ans="No Palpable Node")
data_list = [surgery_guide, frozen, gross_tumour, skin, nodes, number_lymph, level_lymph, sentinel_method,
sentinel_blue, sentinel_hot, sentinel_blue_hot, sentinel_non_blue_hot, sentinel_palpable]
col_list = names("node_excision")
check = add_update_sql.review_input(file_number, col_list, data_list)
return data_list
def bio_info(self):
module_name = "bio_info"
new_data = ['NA'] * 16
check = False
while not check:
mr_number = input('MR number :')
name = input('Name :')
aadhaar_card = input("Aadhaar card number (if available): ")
date_first = check_date("Date of first visit: ")
permanent_address = input('Permanent Address :')
current_address_check = ask_option(
'Current Address', ["Same as Permanent", "Different"])
if current_address_check == "Different":
current_address = input("Current Address: ")
else:
current_address = permanent_address
phone = input('Phone :')
email_id = input('Email_ID :')
gender = ask_option('Gender', ["Female", "Male", "Other"])
age_yrs = input('Age at first visit (yrs) :')
age_diag = input('Age at diagnosis (yrs): ')
date_of_birth = check_date('Date of Birth (dd/mm/yyyy):')
place_birth = input('Place of Birth :')
height = ask_option("Height unit",
["cm", "feet/inches", "Height not available"])
height_cm, height_feet, height_inch, weight, bmi = ['NA'] * 5
if height == "Height not available":
height_cm = "NA"
weight_kg = input('Weight (kg) (if available else enter NA) :')
bmi = "NA"
else:
if height == "cm":
height_cm = input('Height (cm) :')
else:
height_feet = float(input("Height (feet)"))
height_inch = float(input("Height (inches)"))
height_inch = height_inch + 12 * height_feet
height_cm = height_inch * 2.54
weight_kg = input('Weight (kg) (if available else enter NA) :')
try:
weight = float(weight_kg)
height = float(height_cm) / 100
bmi = str(round(weight / (height * height)))
except ValueError:
bmi = 'NA'
columns_list = pccm_names.names_info(module_name)
new_data = [
mr_number, name, aadhaar_card, date_first, permanent_address,
current_address, phone, email_id, gender, age_yrs, age_diag,
date_of_birth, place_birth, height_cm, weight_kg, bmi
]
check = review_input(self.file_number, columns_list, new_data)
return new_data
def tox_table(file_number, drug_cyc, tox_all):
tox_index = 0
check_tox = False
while not check_tox:
tox = ask.ask_y_n(
"Were there any toxic effects in administration of " + drug_cyc)
if tox:
add_tox = True
while add_tox:
check = False
while not check:
tox_present = ask.ask_option("Toxic effects of type",
chemo.toxicity())
tox_grade = ask.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.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.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
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.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 patient_status():
status = ask.ask_option("Status at last follow up", [
"Survivor", "Deceased", "Lost to follow-up",
'Case of Non Malignant Breast Disease', "Other"
])
if status == "Survivor":
type_survivor = ask.ask_list("the Survivor is ",
FollowUpStatus.survivor_status)
status = status + ": " + type_survivor
if status == "Deceased":
type_death = ask.ask_option("Cause of death",
FollowUpStatus.deceased_status)
status = status + ": " + type_death
return status
def review_data_key(conn, cursor, table, key_name, key_value, columns, col_name, col_value):
if 'file_number' in columns:
# remove 1st position from column names (assumes it is file_number)
col_list = columns[1:]
else:
col_list = columns
sql_statement = 'SELECT ' + ", ".join(col_list) + ' FROM ' + table + " WHERE " + key_name + "= '" + key_value + "'"
data = cursor.execute(sql_statement)
data_list = data.fetchall()
if not data_list:
print("This " + col_name + ' ' + col_value + ' has not been entered in ' + table)
enter = ask.ask_y_n("Do you want to enter now")
if enter:
add_pk_fk_to_table(conn, cursor, table, col_name=key_name, pk=key_value)
print('added new row for this ' + key_name)
return enter
else:
data_list = list(data_list[0])
col_number = len(col_list)
if data_list == [None]*len(data_list):
print("This section of the database has not been entered")
enter = ask.ask_y_n("Do you want to enter now")
return enter
elif None in set(data_list):
print("Some entries are missing from the database: ")
for index in range(0, col_number):
print(col_list[index] + " : " + str(data_list[index]))
enter = ask.ask_option("Do you want to proceed?", ["Edit all", "Add new data only"])
if enter == "Edit all":
return True
else:
enter = edit_few(conn, cursor, table, col_list, key_value, data_list)
return enter
else:
print("Entries present in database are as follows : ")
for index in range(0, col_number):
print(col_list[index] + " : " + str(data_list[index]))
enter = ask.ask_option("Do you want to", ["Edit all", "Edit some entries", "Edit None"])
if enter == "Edit some entries":
for index in range(0, col_number):
print(col_list[index] + " : " + str(data_list[index]))
edit = ask.ask_y_n("Edit")
if edit:
data = input("Data for " + col_list[index] + ": ")
update_single_pk(conn, cursor, table, col_list[index], pk_value=key_name, pk=key_value, var=data)
return False
elif enter == "Edit all":
return True
else:
return False
def edit_table(df, pk_col, df_col):
import helper_function.ask_y_n_statement as ask
rows = (df.shape)[0]
for row in range(0,rows):
print(df.iloc[row].to_string()+'\n')
to_correct = ask.ask_y_n("Are entries correct?")
if not to_correct:
to_correct = ask.ask_y_n("Re-enter entire table?")
if to_correct:
return to_correct, df
else:
change_row = True
while change_row:
pk_list = list(df[pk_col])
print(pk_list)
pk = input("Enter " + pk_col + " to change: ")
index = pk_list.index(id)
to_do = True
while to_do:
print(df.loc[index, :])
col_change = ask.ask_option("Name of column to change", df_col)
old_val = df.loc[index, col_change]
print(old_val + '\n')
new_val = input("Enter correct value for " + col_change + ' for ' + pk + ": ")
df.loc[index, col_change] = new_val
print(df.iloc[index].to_string() + '\n')
to_do = ask.ask_y_n("Make more changes to " + pk_col + ' ' + pk + '?')
print_df(df)
change_row = ask.ask_y_n("Change another row?")
to_correct = False
return to_correct, df
def family_cancer_table(conn, cursor, file_number):
add_family = True
type_cancer_list, relation_degree_list, type_relation_list, age_detect_list = [], [], [], []
all_data = []
while add_family:
type_of_cancer = input("Type of Cancer: ")
type_cancer_list.append(type_of_cancer)
relation_to_patient = ask_option("Relation to patient",
PatientInfo.family)
relation_degree_list.append(relation_to_patient)
type_relation = input("Specific Relationship:")
type_relation_list.append(type_relation)
age_at_detection_yrs = input('Age at detection (yrs) :')
age_detect_list.append(age_at_detection_yrs)
family_history = file_number, type_of_cancer, relation_to_patient, type_relation, age_at_detection_yrs
family_history_list = "; ".join([
type_of_cancer, relation_to_patient, type_relation,
age_at_detection_yrs
])
all_data.append(family_history_list)
columns = 'file_number, type_cancer, relation_to_patient, type_relation, age_at_detection_yrs'
table = "family_cancer_history"
sql.insert(conn, cursor, table, columns, family_history)
add_family = ask_y_n("Add more family cancer history? ")
all_data_flat = "|".join(all_data)
return (all_data_flat)
def check_path_report_entry(conn, cursor, file_number, table_to_check, pk,
block_id, number_of_blocks, user_name):
from reports.biopsy_report import BiopsyData
from reports.surgery_block import SurgeryBlockData
table_data = BiopsyData(conn, cursor, file_number, pk, block_id,
number_of_blocks, user_name)
col_name = 'pk'
if 'surgery' in table_to_check:
table_data = SurgeryBlockData(conn, cursor, file_number, pk, block_id,
number_of_blocks, user_name)
col_filter = 'fk'
pk_fk_present = sql.check_pk_fk_exist(cursor, col_name, pk, table_to_check)
if not pk_fk_present:
sql.add_pk_fk_to_table(conn, cursor, table_to_check, col_name, pk)
print("This block_id -'" + block_id + "' for " + file_number +
" does not exist in table " + table_to_check +
". Enter new record")
table_data.add_data()
else:
todo = ask.ask_option(
file_number + " already exists in table " + table_to_check + ".",
["Edit record", "Edit None"])
if todo == "Edit record":
table_data.edit_data()
return
def mri_mass(self, mass_id):
check = False
data_list = ask.default_data_list(self.col_list)
while not check:
if self.mammo_breast == "bilateral":
mass_location = ask.ask_option("Location of mass " + str(
mass_id), RadioTables.breast)
else:
mass_location = self.mammo_breast
check_t1_t2 = ask.ask_y_n('Are both T1 and T2 image analysis'
'available for this mass?')
type_of_imaging = ['T1', 'T2']
if not check_t1_t2:
type_of_imaging = ask.ask_list('Observation of this mass is a'
'result of which type of'
'imaging? ',
RadioTables.mri_image_type)
data_list = self.mri_mass_detail(type_of_imaging, mass_id)
if type_of_imaging in {'T1', 'T2'}:
data_list = [('{0}_{1}'.format(type_of_imaging, data)) for
data in data_list]
mass_name = "Lesion " + str(mass_id)
data_list = [self.file_number, mass_location, mass_name]+data_list
check = sql.review_input(self.file_number, columns=self.col_list,
data=data_list)
data_list = [data_list] + [self.user_name, sql.last_update()]
data_list = data_list + [self.user_name, sql.last_update()]
return data_list
def metastasis(file_number, user_name):
check = False
while not check:
met_has = ask.ask_y_n(
"Has the patient been examined for metastatic disease?")
if not met_has:
met_has = "Not examined for metastatic disease"
else:
met_has = "Examined for metastatic disease"
date_last = ask.check_date("Date of last follow-up: ")
recur = ask.ask_y_n("Has the patient experienced a recurrence?")
if recur:
time_recur = input("Time to disease recurrence: ")
nature_recur = ask.ask_option("Nature of recurrence",
["Distant", "Local", "Other"])
if nature_recur == "Distant":
distant_site = input("Site of distant recurrence: ")
else:
distant_site = "NA"
else:
time_recur, nature_recur, distant_site = ("NA", ) * 3
status = patient_status()
data_list = [
met_has, date_last, time_recur, nature_recur, distant_site, status,
user_name,
last_update()
]
col_list = names.names_longterm("metastasis")
check = review_input(file_number, col_list, data_list)
return data_list
def lesion_location(lesion, option=MultiTest.breast_cancer):
lesion_data = {}
category = ["Location on right_breast", "Location on left_breast",
'Other Location']
if lesion in {"right_breast", "bilateral"}:
lesion_rb = ask.ask_option(category[0], )
lesion_rb_data = "RB-" + lesion_rb
lesion_data.append(lesion_rb_data)
if lesion in {"right_breast", "bilateral"}:
lesion_lb = ask.ask_option(category[1], option)
lesion_lb_data = "LB-" + lesion_lb
lesion_data.append(lesion_lb_data)
if lesion not in {MultiTest.breast_cancer}:
lesion_other = str.lower(str.replace(lesion, ' ', '_'))
lesion_data.append(lesion_other)
lesion_data = "|".join(lesion_data)
return lesion_data
def view_multiple(conn, table, col_list, file_number):
import pandas as pd
from helper_function.ask_y_n_statement import ask_option
sql_statement = ('SELECT '+ ", ".join(col_list) +' FROM '+ table + " WHERE file_number = '" +file_number+"'")
df = pd.read_sql(sql_statement, conn)
print_df(df)
enter = ask_option("Do you want to add or edit data", ["Add data", 'Edit data', 'Do not add or edit'])
return enter
def usg_mass(self, mass_id):
print(self.table, mass_id)
check = False
data_list = ask.default_data_list(self.col_list)
while not check:
mass_location = self.mammo_breast
if self.mammo_breast == "bilateral":
mass_location = ask.ask_option("Location of mass "
+ str(mass_id),
RadioTables.breast)
location_clock = ask.check_number_input("What is the clock"
"position of mass "
+ str(mass_id) + "?",
'Please enter only numbers'
' additional paramters '
'can be entered '
'next')
location_add = input('Additional parameters for clock position')
location_clock = location_clock + location_add + " o'clock"
mass_quadrant = 'data_not_available'
quad = ask.ask_y_n('Is the quadrant location given?')
if quad:
mass_quadrant = ask.ask_list('what is the quadrant location',
Radio.lesion_quadrant)
mass_shape = ask.ask_list("Shape of mass " + str(mass_id),
RadioTables.mass_shape)
mass_name = "lesion_" + str(mass_id)
mass_dimension,
mass_size_unit,
mass_longest_dimension = self.lesion_size()
mass_margin = ask.ask_option("Margin of mass " + str(mass_id),
RadioTables.mass_margin_usg)
mass_echo = ask.ask_option("Echo pattern of mass " + str(mass_id),
RadioTables.mass_echo)
mass_id = "Mass " + str(mass_id)
modality = self.table
data_list = [self.file_number, mass_name, mass_location,
location_clock, mass_quadrant, mass_shape,
mass_margin, mass_echo, mass_dimension,
mass_longest_dimension, mass_size_unit, modality]
check = sql.review_input(self.file_number, columns=self.col_list,
data=data_list)
data_list = data_list + [self.user_name, sql.last_update()]
return data_list
def nipple_cytology(file_number):
module_name = "nipple_cytology"
check = False
while not check:
cyto = ask.ask_option("Nipple Cytology", ["Done", "Not Done"])
if cyto == "Not Done":
cyto_date, cyto_number, cyto_report = ("NA", ) * 3
else:
cyto_date = input("Date of nipple cytology: ")
cyto_number = input("Nipple Cytology number: ")
cyto_report = ask.ask_option(
"Nipple Cytology report and interpretation",
["Normal", "Suspicious", "Diagnostic for "
"Cancer", "Other"])
data_list = [cyto, cyto_date, cyto_number, cyto_report]
columns_list = pccm_names.name_clinical(module_name)
check = add_update_sql.review_input(file_number, columns_list,
data_list)
return (tuple(data_list))
def ffpe_csv():
folder_name, file_name, database_folder_name, database_name = (
'D:/repos/pccm_db/main/DB', "FFPE_new_blocks.csv",
'D:/repos/pccm_db/main/DB',
'PCCM_BreastCancerDB_FFPE_dk_2018-11-20.db')
check_folder = None
while check_folder != 'All are correct':
print('\nFolder location of FFPE new blocks data is set as: \n' +
folder_name + '\n')
print('File name of FFPE new blocks data is set as: \n' + file_name +
'\n')
print('Database file folder is set as \n' + database_folder_name +
'\n')
print('Database file name is set as \n' + database_name + '\n')
check_folder = ask_option("Do you want to change any options?", [
'FFPE File Folder', 'FFPE File Name', 'Database Folder',
'Database Name', 'All are correct'
])
if check_folder == 'FFPE File Folder':
print('Folder location of FFPE new blocks data is set as \n' +
folder_name + '\n')
folder_name = input(
"Please enter folder location of FFPE new blocks data: ")
elif check_folder == 'FFPE File Name':
print('File name of FFPE new blocks data is set as: \n' +
file_name + '\n')
file_name = input(
"Please input correct File name of FFPE new blocks data (with .csv extension): "
)
elif check_folder == 'Database Folder':
print('Database file folder is set as: \n' + database_folder_name +
'\n')
database_folder_name = input(
"Please input correct database file destination: ")
elif check_folder == 'Database Name':
print('Database file name is set as: \n' + database_name + '\n')
database_name = input(
"Please input correct database file name (with .db extension): "
)
conn_path = os.path.join(database_folder_name, database_name)
conn = sqlite3.connect(conn_path)
cursor = conn.cursor()
ffpe_data = FFPECSVData(conn, cursor, folder_name, file_name)
ffpe_df = ffpe_data.read_file()
n_rows = ffpe_df.shape[1]
print(str(n_rows) + ' block entries read from file uploaded')
ffpe_str = ffpe_df.astype(dtype='str')
ffpe_data.write_file(ffpe_str)
print(
str(n_rows) + ' block entries added to ' + database_name + ' database')
output_file_name = 'Uploaded_Database_' + file_name + str(
date.today()) + '.xlsx'
file_information = database_folder_name, database_name, folder_name, output_file_name
print_file = OutputData(file_information)
print_file.output_data()
def birads():
check = False
while not check:
birad_list = [i for i in Radio.birads]
mammo_birads = ask.ask_option("BI-RADS Category", birad_list)
mammo_birads_det = Radio.birads.get(mammo_birads)
birad = mammo_birads + ": " + mammo_birads_det
print(birad)
check = ask.ask_y_n("Is this correct?")
data_list = birad
return data_list
def surgery_block_information_0(self):
module_name = self.module_list[0]
check = False
data_list = ['NA']*17
surgery_block_data_type = 'primary'
while not check:
data_type = ask.ask_y_n("Is surgery type: '" + surgery_block_data_type + "'")
if not data_type:
surgery_block_data_type = ask.ask_option("Type of surgery", ['revision', 'recurrence'])
block_list_table = BlockInformation(self.conn, self.cursor, self.file_number)
block_data = ['block_sr_number', 'block_location', 'current_block_location', 'block_series']
block_sr_number, block_location, current_block_location, surgery_block_series = \
block_list_table.get_block_information(self.surgery_block_id, block_data)
surgery_block_source = ask.ask_option("Pathology Lab (source of block)", PathReports.path_labs)
breast_cancer_yes_no = ask.ask_y_n('Is this a case of breast cancer (Unilateral OR Bilateral)',
yes_ans="breast_cancer_yes", no_ans="breast_cancer_no")
pathology_report_available_yes_no = ask.ask_y_n('Is the pathology report available', yes_ans="yes",
no_ans="no")
nat = ask.ask_y_n('Has Neo-Adjuvant therapy been administered to the patient (NACT or NAHT)?')
if nat:
nact = ask.ask_list('What type of therapy has been givent to the patient?',
['NACT', 'NAHT', 'NACT_and_NAHT'])
neoadjuvant_therapy = nact.lower() + '_yes'
surgery_block_primary_tissue = 'treated_tissue'
else:
neoadjuvant_therapy = 'nact_no'
surgery_block_primary_tissue = 'primary_tissue'
date_of_surgery = ask.check_date("Date of Surgery: ")
surgeon_s = ask.ask_option("Name of the Surgeon/s", PathReports.surgeon)
surgery_hospital_id = input("Hospital ID: ")
surgery_lesion_site = ask.ask_list("Lesion on", ["right_breast", "left_breast", "bilateral"])
surgery_type = self.bilateral_treatment(surgery_lesion_site, 'Type of surgery', PathReports.surgery_type)
data_list = [self.file_number, surgery_block_data_type, block_sr_number, block_location,
current_block_location, self.surgery_block_id, self.surgery_number_of_blocks,
surgery_block_series, breast_cancer_yes_no, pathology_report_available_yes_no,
neoadjuvant_therapy, str(surgery_block_primary_tissue).lower(), surgery_block_source,
date_of_surgery, surgeon_s, surgery_hospital_id, surgery_lesion_site, surgery_type]
columns_list = names(module_name)
check = sql.review_input(self.file_number, columns_list, data_list)
return data_list
def pet_report_identifier(self):
module_name = self.module_list[0]
check = False
report_identifier = ['NA'] * 12
while not check:
pet_scan_date = ask.check_date('Please enter PET report date: ')
pet_scan_number = input(
'Please enter PET scan number as given on the report: ')
pet_scan_source = input(
'Please enter the facility at which PET scan was done: ')
pet_scan_reg_number = input(
"Please enter PET report registration number: ")
pet_scan_history = input(
'Please input patient history as given on report: ')
pet_carcinoma_status = ask.ask_option(
'Please enter breast cancer status',
MultiTest.carcinoma_status)
pet_cancer_location = ask.ask_list(
'What is the location of the cancer', MultiTest.breast_cancer)
pet_recurrence = ask.ask_y_n(
'Does the patient have a previously detected recurrence/mets?')
if pet_recurrence:
pet_recurrence_known = input(
'Please describe the recurrence/metastasis: ')
else:
pet_recurrence_known = 'no_known_recurrence_or_metastasis'
pet_procedure_body_region = ask.ask_list(
"Region of body monitored by PET scan", PetReport.body_region)
pet_procedure_fdg_dose_mci = ask.check_number_input(
"Please enter dose of 18F-FDG used in mCi. ",
"(Please enter only dose. If given in other units "
"enter under additional notes.): ")
pet_procedure_bsl = input(
"Please enter basal sugar level with units as given: ")
pet_scanner_name = ask.ask_list('Please enter name of scanner',
PetReport.machine_name)
pet_procedure_additional_notes = input(
'Please enter additional notes, if any for PET scan and patient '
'conditions: ')
report_identifier = [
self.file_number, pet_scan_date, pet_scan_number,
pet_scan_source, pet_scan_reg_number, pet_scan_history,
pet_carcinoma_status, pet_cancer_location,
pet_recurrence_known, pet_procedure_body_region,
pet_procedure_fdg_dose_mci, pet_procedure_bsl,
pet_scanner_name, pet_procedure_additional_notes
]
columns_list = names(module_name)
check = sql.review_input(self.file_number, columns_list,
report_identifier)
return report_identifier
def abvs(file_number):
module_name = "abvs"
check = False
while not check:
abvs = ask.ask_y_n("Automated Breast Volume Scanner (ABVS) done?")
if abvs:
abvs = "Automated Breast Volume Scanner done"
abvs_date = input("Date of examination of ABVS: ")
abvs_acc = input("Accession number of ABVS: ")
abvs_lesion = ask.ask_option(
"Location of lesion",
["Right Breast", "Left Breast", "Both", "Not present"])
if abvs_lesion in {"Right Breast", "Left Breast", "Both"}:
abvs_lesion_data = radio_tables_old.lesion_location(
abvs_lesion)
else:
abvs_lesion_data = "NA"
abvs_size = ask.ask_option("Size of lesion",
["<2 cm", "2-5 cm", ">5 cm", "Other"])
abvs_dist = ask.ask_option("Distance from Skin (cm)",
["<0.5 cm", ">0.5 cm", "Other"])
abvs_pect = input("Distance from Pectoralis Major (cm): ")
abvs_diagnosis = ask.ask_option(
"ABVS Diagnosis",
["Normal", "Benign", "Suspicious", "Diagnostic for Cancer"])
else:
abvs = "Automated Breast Volume Scanner done"
abvs_date, abvs_acc, abvs_lesion, abvs_lesion_data, abvs_size, abvs_dist, abvs_pect, \
abvs_diagnosis = ("NA",) * 8
data_list = [
abvs, abvs_date, abvs_acc, abvs_lesion, abvs_lesion_data,
abvs_size, abvs_dist, abvs_pect, abvs_diagnosis
]
columns_list = names(module_name)
check = add_update_sql.review_input(file_number, columns_list,
data_list)
return (tuple(data_list))
def mri_mass_detail(self, image_type, mass_id):
print(self.table, mass_id)
data_list = ask.default_data_list(self.col_list)
check = False
while not check:
non_mass = ask.ask_y_n('Is the enhancement non-mass?')
enhancement_type = 'mass'
if non_mass:
enhancement_type = 'non_mass'
location_clock = input("What is the clock position of mass "
+ str(mass_id) + "? (Enter NA if clock"
"position not available)")
if location_clock != 'NA':
location_clock = location_clock + " o'clock"
mass_quadrant = ask.ask_option('Quadrant location of mass',
Radio.lesion_quadrant)
mass_shape = ask.ask_option("Shape of mass " + str(mass_id),
RadioTables.mass_shape)
mass_margin = ask.ask_option("Margin of mass " + str(mass_id),
RadioTables.mass_margin_mri)
mass_dimension,
mass_size_unit,
mass_longest_dimension = self.lesion_size()
mass_echo = ask.ask_option("Internal enhancement characteristics"
" " + str(mass_id),
RadioTables.mass_iec)
mass_id = "Mass " + str(mass_id)
modality = self.table
data_list = [mass_id, image_type, enhancement_type, location_clock,
mass_quadrant, mass_shape, mass_margin,
mass_echo, mass_dimension,
str(mass_longest_dimension), mass_size_unit, modality]
col_list = self.col_list[3:]
check = sql.review_input(self.file_number, columns=col_list,
data=data_list)
data_list = data_list + [self.user_name, sql.last_update()]
return data_list
def review_data(self):
sql = ('SELECT ' + ", ".join(self.columns) + ' FROM ' + self.table + " WHERE file_number = '" +
self.file_number + "'")
data = self.cursor.execute(sql)
data_list = data.fetchall()
data_list = list(data_list[0])
col_number = len(self.columns)
if data_list == [None]*len(data_list):
print("This section of the database has not been entered")
enter = ask.ask_y_n("Do you want to enter now")
return enter
if None in set(data_list):
print("Some entries are missing from the database: ")
for index in range(0, col_number):
print(self.columns[index] + " : " + str(self.data[index]))
enter = ask.ask_option("Do you want to proceed?", ["Edit all", "Add new data only"])
if enter == "Edit all":
return True
else:
edit_few(self.conn, self.cursor, self.table, self.columns, self.file_number, self.data)
else:
print("Entries present in database are as follows : ")
for index in range(0, col_number):
print(self.columns[index] + " : " + str(self.data[index]))
enter = ask.ask_option("Do you want to", ["Edit all", "Edit some entries", "Edit None"])
if enter == "Edit some entries":
for index in range(0, col_number):
print(self.columns[index] + " : " + str(self.data[index]))
edit = ask.ask_y_n("Edit")
if edit:
data = input("Data for " + self.columns[index] + ": ")
update_single(self.conn, self.cursor, self.table, self.columns, self.file_number, data)
return False
elif enter == "Edit all":
return True
else:
return False
def bilateral_treatment(surgery_lesion_site, data_type_statement, data_type_options):
if data_type_options != 'input':
if surgery_lesion_site.lower == "bilateral":
print("Right Breast")
data_type = ask.ask_option(data_type_statement, data_type_options)
data_type_rb = "rb_" + data_type
print("Left Breast")
data_type = ask.ask_option(data_type_statement, data_type_options)
data_type_lb = "lb_" + data_type
data = data_type_rb + "; " + data_type_lb
else:
data = ask.ask_option(data_type_statement, data_type_options)
else:
if surgery_lesion_site.lower == "bilateral":
print("Right Breast")
data_type = input(data_type_statement)
data_type_rb = "rb_" + data_type
print("Left Breast")
data_type = input(data_type_statement)
data_type_lb = "lb_" + data_type
data = data_type_rb + "; " + data_type_lb
else:
data = input(data_type_statement)
return data
def det_by(file_number):
module_name = "det_by"
check = False
while not check:
category = "Current Breast Cancer Detected by"
options = ["Self", "Physician", "Screening Camp", "Other"]
determined_by = ask_option(category, options)
if determined_by == "Screening Camp":
sc_id = input("Screening Camp ID: ")
determined_by = "Screening Camp ID " + sc_id
det_date = input("Date of current breast cancer detection: ")
columns_list = pccm_names.names_info(module_name)
data_list = [determined_by, det_date]
check = review_input(file_number, columns_list, data_list)
return (tuple(data_list))
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 hormone_therapy_chemo():
hormone_therapy = ask.ask_y_n_na("Was hormone therapy given?")
if hormone_therapy == 'Yes':
hormone_therapy = "Hormone therapy given"
therapy_type = ask.ask_option("Hormone therapy type",
["Sequential", "Concurrent"])
therapy_duration = input("What was the duration of therapy? ")
therapy_side = ask.ask_y_n_na("Were any side effects observed ?")
if therapy_side == 'Yes':
therapy_side = input(
"Please give details of side effects observed: ")
elif hormone_therapy == 'No':
hormone_therapy = "No hormone therapy given"
therapy_type, therapy_duration, therapy_side = (hormone_therapy, ) * 3
else:
therapy_type, therapy_duration, therapy_side = (hormone_therapy, ) * 3
return hormone_therapy, therapy_type, therapy_duration, therapy_side
def output_data(self):
cursor = self.conn.cursor()
tables_to_print = []
summary_df = pd.DataFrame(columns=["table_name", "number_entries"])
output_name = self.output_name
if self.research:
output_name = 'Research_' + self.output_name
output_path = os.path.join(self.output_folder, output_name)
for table in print_db_tables():
check = table_check(cursor, table)
if check:
tables_to_print.append(table)
if not tables_to_print:
print(
"Selected Database has no tables. Please re-start and edit database file"
)
return
else:
writer = pd.ExcelWriter(output_path, engine='xlsxwriter')
print('This database contains the following tables:')
i = 1
for table in tables_to_print:
print(str(i) + ". " + table)
i = i + 1
to_print = ask_option(
"Do you want to print all tables or only select tables?",
["All tables", "Select tables"])
if to_print == "All tables":
index = 0
for table in tables_to_print:
self.print_table(writer, table)
number = self.print_table(writer, table)
summary_df.loc[index] = [table, number]
index = index + 1
elif to_print == "Select tables":
for table in tables_to_print:
to_print = ask_y_n("Do you want to print " + table)
if to_print:
self.print_table(writer, table)
number = self.print_table(writer, table)
summary_df.loc[table] = [table, number]
self.print_summary(summary_df)
print("Data file " + output_name + " has been created at " +
self.output_folder + '\n')
writer.save()
def check_file(conn, cursor, table, file_number, user_name, folders):
sql_statement = "SELECT rowid FROM " + table + " WHERE file_number = ?"
cursor.execute(sql_statement, (file_number, ))
data = cursor.fetchall()
if len(data) == 0:
if table != "Follow_up_Data":
cursor.execute("INSERT INTO " + table + "(file_number) VALUES ('" + file_number + "')")
print(file_number + " does not exist in table " + table + ". Enter new record")
add_new.add_new(conn, cursor, file_number, table, user_name,folders)
else:
todo = ask.ask_option(file_number + " already exists in table " + table + ".",
["Edit record", "Add new record for same file number", "Edit None"])
if todo == "Edit record":
edit_record.edit_record(conn, cursor, file_number, table, user_name, folders)
elif todo == "Add new record for same file number":
print("Add additional record module TBD")
ask_table = ask.ask_y_n("Add another table?")
return ask_table
def feed_duration(conn, cursor, file_number, children_number):
table = "breast_feeding"
child_list, feeding_duration_list, feeding_details_list = [], [], []
child_number = int(children_number)
for index in range(0, child_number):
kid = str(index + 1)
kid_add = "Child " + kid
child_list.append(kid_add)
feeding_duration = input("Breast feeding duration for " + kid_add +
" (months) ?")
feeding_duration_list.append(feeding_duration)
feeding_details = ask_option("Breast feeding for child " + kid,
PatientInfo.breast_feeding)
feeding_details_list.append(feeding_details)
columns = 'file_number, child_number, feeding_duration, breast_usage_feeding'
data = file_number, kid, feeding_duration, feeding_details
sql.insert(conn, cursor, table, columns, data)
data_list = [child_list, feeding_duration_list, feeding_details_list]
data_return = join_lists(data_list, "; ")
return (data_return)