def med_history(conn, cursor, file_number, table):
from breast_cancer_tables import med_history_table
from ask_y_n_statement import ask_y_n
from add_update_sql import update_multiple, review_input
check = False
while not check:
medical_history_y_n = ask_y_n("Other Medical History ?")
if medical_history_y_n:
med_hist = med_history_table(conn, cursor, file_number)
medical_history_y_n = "Previous medical history present"
else:
medical_history_y_n = "No previous medical history present"
med_hist = ("NA", ) * 3
condition_hist, diagnosis_date_hist, treatment_hist = med_hist
data_list = [
medical_history_y_n, condition_hist, diagnosis_date_hist,
treatment_hist
]
columns_list = [
"Any_Other_Medical_History_y_n", "Type_Any_Other_Medical_History",
"Diagnosis_Date_Any_Other_Medical_History",
"Treatment_Any_Other_Medical_History"
]
check = review_input(file_number, columns_list, data_list)
data = medical_history_y_n, condition_hist, diagnosis_date_hist, treatment_hist
columns = "Any_Other_Medical_History_y_n", "Type_Any_Other_Medical_History", "Diagnosis_Date_Any_Other_Medical_History", "Treatment_Any_Other_Medical_History"
update_multiple(conn, cursor, table, columns, file_number, data)
def node_block(conn, cursor, file_number, table):
from ask_y_n_statement import ask_option
from add_update_sql import update_multiple
sent_data = node_details("Sentinel")
sentinel, sent_number_rem, sent_number_pos, sent_number = sent_data
print("Sentinel Node " + sent_number)
ax_data = node_details("Axillary")
ax, ax_number_rem, ax_number_pos, ax_number = ax_data
print("Axillary Node " + ax_number)
ap_data = node_details("Apical")
ap, ap_number_rem, ap_number_pos, ap_number = ap_data
print("Apical Node " + ap_number)
category = "Perinodal Spread"
options = ["Yes", "No"]
per_spread = ask_option(category, options)
category = "Supraclavicular Node Involvment"
options = ["Yes", "No"]
supra_inv = ask_option(category, options)
data = sentinel, sent_number_rem, sent_number_pos, sent_number, ax, ax_number_rem, ax_number_pos, ax_number, ap, \
ap_number_rem, ap_number_pos, ap_number, per_spread, supra_inv
columns = "Sentinel_Node_Block_Report", "Sentinel_Node_Number_Removed", "Sentinel_Node_Number_Positive", \
"Sentinel_Node_Block_Report_Number", "Axillary_Node_Block_Report", "Axillary_Node_Number_Removed", \
"Axillary_Node_Number_Positive", "Axillary_Node_Block_Report_Number", "Apical_Node_Block_Report", \
"Apical_Node_Number_Removed", "Apical_Node_Number_Positive", "Apical_Node_Block_Report_Number", \
"Perinodal_Spread_Node_Block_Report", "Supraclavicular_Involved_Node_Block_Report"
update_multiple(conn, cursor, table, columns, file_number, data)
def breast_symptoms(conn, cursor, file_number, table):
from ask_y_n_statement import get_symptom, get_rb_lb, ask_y_n
from add_update_sql import update_multiple
from breast_cancer_tables import other_symp
symp_state = "Pain or tenderness", "Lumps", "Nipple Discharge", "Nipple Retraction", "Dimpling", \
"Discolouration", "Ulceration", "Eczema"
symptoms = get_symptom(symp_state)
rb = get_rb_lb(symptoms, 0)
rb_symp = list(filter(None, get_rb_lb(rb, 0)))
rb_dur = list(filter(None, get_rb_lb(rb, 1)))
lb = get_rb_lb(symptoms, 1)
lb_symp = list(filter(None, get_rb_lb(lb, 0)))
lb_dur = list(filter(None, get_rb_lb(lb, 1)))
data = [rb_symp, rb_dur, lb_symp, lb_dur]
for index in range(0, len(data)):
if not data[index]:
data[index] = ["NA"]
else:
data[index] = ["; ".join(data[index])]
data_flat = [item for sublist in data for item in sublist]
new_data = tuple(data_flat)
columns = "RB_symptoms", "RB_symptoms_duration", "LB_symptoms", "LB_symptoms_duration"
update_multiple(conn, cursor, table, columns, file_number, new_data)
other_symptom = ask_y_n("Other Symptoms?", True, False)
if other_symptom:
other_symp(conn, cursor, file_number, table)
else:
other_symptom = "No other symptoms"
other_symp_dur = "NA"
data = (other_symptom, other_symp_dur, other_symptom, other_symp_dur)
columns = "RB_Other_Symptoms", "RB_Other_Symptoms_duration", "LB_Other_Symptoms", "RB_Other_Symptoms_duration"
update_multiple(conn, cursor, table, columns, file_number, data)
def cancer_history(conn, cursor, file_number, table):
from breast_cancer_tables import cancer_table
from add_update_sql import update_multiple, review_input
from ask_y_n_statement import ask_y_n
check = False
while not check:
previous_cancer_history_y_n = ask_y_n("Previous history of cancer ?")
if previous_cancer_history_y_n:
previous_cancer = cancer_table(conn, cursor, file_number)
previous_cancer_history_y_n = "Previous history of cancer"
else:
previous_cancer_history_y_n = "No previous history of cancer"
previous_cancer = ("NA", ) * 5
type_of_cancer_list, year_diagnosis_list, treat_all, type_all, duration_all = previous_cancer
data_list = [
previous_cancer_history_y_n, type_of_cancer_list,
year_diagnosis_list, treat_all, type_all, duration_all
]
columns_list = ["Previous_Cancer_History_y_n", "Type_Previous_Cancer", "Year_Diagnosed_Previous_Cancer", \
"Treatment_Previous_Cancer", "Treatment_Type_Previous_Cancer",
"Treatment_Duration_Previous_Cancer"]
check = review_input(file_number, columns_list, data_list)
data = previous_cancer_history_y_n, type_of_cancer_list, year_diagnosis_list, treat_all, type_all, duration_all
columns = "Previous_Cancer_History_y_n", "Type_Previous_Cancer", "Year_Diagnosed_Previous_Cancer", \
"Treatment_Previous_Cancer", "Treatment_Type_Previous_Cancer", "Treatment_Duration_Previous_Cancer"
update_multiple(conn, cursor, table, columns, file_number, data)
def family_details(conn, cursor, file_number, table):
from add_update_sql import update_multiple, review_input
from ask_y_n_statement import ask_y_n
check = False
while not check:
marital_status = input('Marital Status :')
siblings = ask_y_n('Siblings')
if siblings:
siblings_number = input("Number of siblings: ")
sisters = input('Sisters :')
brothers = input('Brothers :')
else:
siblings_number, sisters, brothers = "No Siblings", "0", "0"
children_y_n = ask_y_n('Children')
if children_y_n:
children_number = input("Number of children: ")
daughters = input('Daughters :')
sons = input('Sons :')
else:
children_number, daughters, sons = "No Children", "0", "0"
columns_list = ["Marital_Status", "Siblings", "Sisters", "Brothers", "Children", "Daughters", "Sons"]
data_list = [marital_status, siblings_number, sisters, brothers, children_number, daughters, sons]
check = review_input(file_number, columns_list, data_list)
columns = "Marital_Status", "Siblings", "Sisters", "Brothers", "Children", "Daughters", "Sons"
new_data = marital_status, siblings_number, sisters, brothers, children_number, daughters, sons
update_multiple(conn, cursor, table, columns, file_number, new_data)
def breast_symptoms(conn, cursor, file_number, table, symp_state):
from ask_y_n_statement import get_symptom, get_rb_lb
from add_update_sql import update_multiple
from breast_cancer_tables import other_symp
symptoms = get_symptom(symp_state)
rb = get_rb_lb(symptoms, 0)
rb_symp = list(filter(None, get_rb_lb(rb, 0)))
rb_dur = list(filter(None, get_rb_lb(rb, 1)))
lb = get_rb_lb(symptoms, 1)
lb_symp = list(filter(None, get_rb_lb(lb, 0)))
lb_dur = list(filter(None, get_rb_lb(lb, 1)))
data = [rb_symp, rb_dur, lb_symp, lb_dur]
for index in range(0, len(data)):
if not data[index]:
data[index] = ["NA"]
else:
data[index] = ["; ".join(data[index])]
data_flat = [item for sublist in data for item in sublist]
new_data = tuple(data_flat)
columns = "RB_symptoms", "RB_symptoms_duration", "LB_symptoms", "LB_symptoms_duration"
update_multiple(conn, cursor, table, columns, file_number, new_data)
other_symptom = input("Other Symptoms? (y/n) ")
if str.lower(other_symptom) == "y":
other_symp(conn, cursor, file_number, table)
else:
other_symptom = "No other symptoms"
other_symp_dur = "NA"
data = (other_symptom, other_symp_dur, other_symptom, other_symp_dur)
columns = "RB_Other_Symptoms", "RB_Other_Symptoms_duration", "LB_Other_Symptoms", "RB_Other_Symptoms_duration"
update_multiple(conn, cursor, table, columns, file_number, data)
def surgery_info(conn, cursor, file_number, table):
from ask_y_n_statement import ask_option, ask_y_n
from add_update_sql import update_multiple
surg_block_id = input("Surgical Block ID: ")
surg_location = input("Location of surgery block id " + surg_block_id)
surg_no_block = input("Number of Blocks: ")
surg_block_source = input("Surgery Block Source: ")
surg_tumour_block = input("Tumour Block Reference: ")
surg_node_block = input("Nodes Block Reference: ")
surg_normal_block = input("Adjacent Normal Block Reference: ")
surg_red_block = input("Reduction Tissue Block Reference: ")
surg_date = input("Date of Surgery: ")
surg_name = input("Name of surgeon: ")
surg_hosp_id = input("Hospital ID: ")
#can add review statement here.
lesion_side = ()
lesion_side_rb_y_n = ask_y_n("Lesion Side RB")
if lesion_side_rb_y_n:
category = "Lesion Side RB"
options = ["UOQ", "UIQ", "C", "UCQ", "LCQ", "LOQ", "LIQ"]
lesion_side_rb = ask_option(category, options)
lesion_side_rb_data = "RB-" + lesion_side_rb
lesion_side_lb_y_n = ask_y_n("Lesion Side LB")
if lesion_side_lb_y_n:
category = "Lesion Side LB"
options = ["UOQ", "UIQ", "C", "UCQ", "LCQ", "LOQ", "LIQ"]
lesion_side_lb = ask_option(category, options)
lesion_side_lb_data = "LB-" + lesion_side_lb
if lesion_side_rb_y_n and lesion_side_lb_y_n:
lesion_side = lesion_side_rb_data + "; " + lesion_side_lb_data
elif lesion_side_rb_y_n:
lesion_side = lesion_side_rb_data
elif lesion_side_lb_y_n:
lesion_side = lesion_side_lb_data
print("Lesion side " + lesion_side)
category = "Type Surgery"
options = [
"Reconstruction", "Breast Conservation Surgery (BCS)",
"Therapeutic Mammoplasty", "Reduction Mammoplasty",
"Wide Local Excision", "Other"
]
surg_type = ask_option(category, options)
if surg_type == "Reconstruction":
category = "Type Reconstruction"
options = ["Mastectomy/Modified Radical Mastectomy", "Implant"]
surg_type = ask_option(category, options)
category = "Response to Surgery"
options = [
"Complete_Remission/No Residual Tumor", "Progressing", "Partial",
"Static", "Other"
]
surg_response = ask_option(category, options)
data = surg_block_id, surg_no_block, surg_block_source, surg_tumour_block, surg_node_block, surg_normal_block, \
surg_red_block, surg_date, surg_name, surg_hosp_id, lesion_side, surg_type, surg_response
surgery_info = "Surgical_Block_ID", "Surgery_Block_Location", "Surgery_No_of_blocks", "Block_Source", "Tumor_block_ref", "Nodes_block_ref", \
"Ad_Normal_block_ref", "Reduction_tissue_block_ref", "Date_of_Surgery", "Name_Surgeon", "Hospital_ID", \
"Lesion_Side", "Type_surgery", "Response_surgery"
update_multiple(conn, cursor, table, surgery_info, file_number, data)
def repro_details(conn, cursor, file_number, table):
from add_update_sql import update_multiple
menarche = input('Age at menarche (yrs): ')
menopause = input('Menopausal status (pre/peri/post): ')
menopause_age = menopause + " menopausal"
if str.lower(menopause) == "post":
menopause_age = input('Age at menopause (yrs): ')
lmp = "Last menstrual period " + menopause_age + " yrs"
menopause = menopause + " menopausal"
else:
menopause = menopause + " menopausal"
lmp = input("Date of last menstrual period: ")
number_pregnancy = input("Number of pregnancies: ")
number_term = input(
"Pregnancy carried to term (include abortion after 6 months): )")
number_abortion = input("Number of abortions: ")
sql = (
'SELECT Children FROM Patient_Information_History WHERE File_number = \''
+ file_number + "'")
cursor.execute(sql)
kids = cursor.fetchall()
children_number = kids[0][0]
if children_number == 'No Children':
age_first = 'No Children'
age_last = 'No Children'
else:
age_first = input("Age of first child: ")
if int(children_number) > 1:
age_last = input("Age of last child: ")
else:
age_last = age_first
age_first_preg = input("Age at first pregnancy: ")
age_last_preg = input("Age at last pregnancy: ")
twice_birth = input("Two births in a year (not twins) y/n: ")
if str.lower(twice_birth) == "y":
twice_birth = "Two births in a year"
else:
twice_birth = "No two births in a year"
breast_feeding = input("Breast feeding y/n: ")
if str.lower(breast_feeding) == "y":
breast_feeding = "Breast feeding"
feeding_details = input("Feeding from right, left or both breasts? ")
else:
breast_feeding = "No breast feeding"
feeding_details = "NA"
type_birth_control = input("Type of birth control used: ")
detail_birth_control = input("Details of birth control used: ")
duration_birth_control = input("Duration of birth control use: ")
new_data = menarche, menopause, menopause_age, lmp, number_pregnancy, number_term, number_abortion, \
age_first, age_first_preg, age_last,age_last_preg, twice_birth, breast_feeding, feeding_details, \
type_birth_control,detail_birth_control, duration_birth_control
columns = "Menarche_yrs", "Menopause_Status", "Age_at_Menopause_yrs", "Date_last_menstrual_period", \
"Number_pregnancies", "Pregnancy_to_term", "Number_abortions", "Age_first_child", "Age_first_pregnancy", \
"Age_last_child", "Age_last_pregnancy", "Two_births_in_year", "Breast_feeding_y_n", "Breast_usage_feeding",\
"Type_birth_control_used", "Details_birth_control", "Duration_birth_control"
update_multiple(conn, cursor, table, columns, file_number, new_data)
def block_report_info (conn, cursor, file_number, table):
from add_update_sql import update_multiple
block_sr = input("Block Serial Number: ")
block_id = input ("Biopsy Block ID: ")
block_number = input("No of blocks: ")
block_date = input("Date of Biopsy: ")
lab_id = input("Lab ID: ")
biopsy_type = input("Biopsy Type: ")
columns = "Block_SR_Number", "Biopsy_Block_ID", "No_of_blocks", "Date_of_Biopsy", "Lab_ID", "Biopsy_Type"
data = block_sr, block_id, block_number, block_date, lab_id,biopsy_type
update_multiple(conn, cursor, table, columns, file_number, data)
def bio_info(conn, cursor, file_number, table):
import add_update_sql
import ask_y_n_statement
check = False
while not check:
mr_number = input('MR_number :')
name = input('Name :')
consent = ask_y_n_statement.ask_y_n(
"Is consent form with signature present in file", "Consent Taken",
"Consent form not present")
aadhaar_card = input("Aadhaar card number (if available): ")
date_first = input("Date of first visit: ")
permanent_address = input('Permanent_Address :')
current_address = input('Current_Address :')
phone = input('Phone :')
email_id = input('Email_ID :')
gender = input('Gender :')
age_yrs = input('Age (yrs) :')
date_of_birth = input('Date of Birth :')
place_birth = input('Place of Birth :')
height = ask_y_n_statement.ask_option("Height unit",
["cm", "feet/inches"])
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 = str(height_inch * 2.54)
weight_kg = input('Weight (kg) :')
height = float(height_cm) / 100
weight = float(weight_kg)
BMI = str(round(weight / (height * height)))
columns_list = [
"MR_number", "Name", "Consent", "Aadhaar_Card", "FirstVisit_Date",
"Permanent_Address", "Current_Address", "Phone", "Email_ID",
"Gender", "Age_yrs", "Date_of_Birth", "Place_Birth", "Height_cm",
"Weight_kg", "BMI"
]
new_data = [
mr_number, name, consent, aadhaar_card, date_first,
permanent_address, current_address, phone, email_id, gender,
age_yrs, date_of_birth, place_birth, height_cm, weight_kg, BMI
]
check = add_update_sql.review_input(file_number, columns_list,
new_data)
columns = "MR_number", "Name", "Consent", "Aadhaar_Card", "FirstVisit_Date", "Permanent_Address", "Current_Address", \
"Phone", "Email_ID", "Gender", "Age_yrs", "Date_of_Birth", "Place_Birth", "Height_cm", "Weight_kg", "BMI"
data = mr_number, name, consent, aadhaar_card, date_first, permanent_address, current_address, phone, email_id, \
gender, age_yrs, date_of_birth, place_birth, height_cm, weight_kg, BMI
add_update_sql.update_multiple(conn, cursor, table, columns, file_number,
data)
def det_by(conn, cursor, table, file_number):
from add_update_sql import update_multiple
from ask_y_n_statement import ask_option
category = "Current Breast Cancer"
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 = "Current_Breast_Cancer_Detected_By", "Current_Breast_Cancer_Detected_Date"
data = determined_by, det_date
update_multiple(conn, cursor, table, columns, file_number, data)
def tumour_biopsy_data(conn, cursor, file_number, table):
from ask_y_n_statement import ask_option, ask_y_n
from add_update_sql import update_multiple
category = "Tumour biopsy diagnosis"
options = [
'Benign', "Ductal carcinoma in situ(DCIS) with microinvasion",
"Ductal carcinoma in situ(DCIS) without microinvasion",
"Lobular Carcinoma in Situ (LCS)", "Invasive Ductal Carcinoma (IDC)",
"Invasive Lobular Carcinoma (ILC)", "Granulamatous Mastitis",
"Papillary Carcinoma", "Phylloid Carcinoma",
"Invasive Mammary Carcinoma", "Invasive Breast Carcinoma", "Other"
]
tumour_diagnosis = ask_option(category, options)
category = "Tumour Biopsy Diagnosis"
options = ["Grade 1", "Grade 2", "Grade 3", "Other"]
tumour_grade = ask_option(category, options)
category = "ER Status"
options = ["Positive", "Negative"]
tumour_er = ask_option(category, options)
if (tumour_er == "Positive"):
tumour_er_percent = input("ER Percent: ")
else:
tumour_er_percent = "NA"
category = "PR Status"
options = ["Positive", "Negative"]
tumour_pr = ask_option(category, options)
if (tumour_pr == "Positive"):
tumour_pr_percent = input("PR Percent: ")
else:
tumour_pr_percent = "NA"
category = "HER2 Status"
options = ["Positive", "Equivocal", "Negative"]
tumour_her2 = ask_option(category, options)
if tumour_her2 == "Negative":
tumour_her2_grade = "NA"
tumour_fish = "NA"
else:
tumour_her2_grade = input("HER2 Grade: ")
category = "FISH"
options = ["Positive", "Negative"]
tumour_fish = ask_option(category, options)
tumour_ki67 = input("Ki67 Percent: ")
data = tumour_diagnosis, tumour_grade, tumour_er ,tumour_er_percent ,tumour_pr, tumour_pr_percent, tumour_her2, tumour_her2_grade,\
tumour_fish, tumour_ki67
columns = "Tumour_biopsy_diagnosis", "Tumour_biopsy_diagnosis_grade", "Tumour_biopsy_ER", "Tumour_biopsy_ER_Percent",\
"Tumour_biopsy_PR", "Tumour_biopsy_PR_Percent", "Tumour_biopsy_HER2", "Tumour_biopsy_HER2_Grade", \
"Tumour_biopsy_FISH", "Tumour_biopsy_Ki67_Percent"
update_multiple(conn, cursor, table, columns, file_number, data)
def block_report_info(conn, cursor, file_number, table):
from add_update_sql import update_multiple
from ask_y_n_statement import ask_option, ask_y_n
block_sr = input("Block Serial Number: ")
block_id = input("Biopsy Block ID: ")
block_number = input("No of blocks: ")
block_date = input("Date of Biopsy: ")
lab_id = input("Lab ID: ")
category = "Biopsy Type"
options = [
"Direct", "USG Guided", "VAB", "True-cut", "Steriotactic", "Other"
]
biopsy_type = ask_option(category, options)
columns = "Block_SR_Number", "Biopsy_Block_ID", "No_of_blocks", "Date_of_Biopsy", "Lab_ID", "Biopsy_Type"
data = block_sr, block_id, block_number, block_date, lab_id, biopsy_type
update_multiple(conn, cursor, table, columns, file_number, data)
def nipple_cytology(conn, cursor, file_number, table):
import ask_y_n_statement
import add_update_sql
cyto = ask_y_n_statement.ask_option("Nipple Cytology",
["Done", "Not Done"])
if cyto == "Not Done":
cyto_date, cyto_number, cyto_report = "NA", "NA", "NA"
else:
cyto_date = input("Date of nipple cytology: ")
cyto_number = input("Nipple Cytology number: ")
cyto_report = ask_y_n_statement.ask_option(
"Nipple Cytology report and interpretation",
["Normal", "Suspicious", "Diagnostic for Cancer", "Other"])
data = cyto, cyto_date, cyto_number, cyto_report
columns = "Nipple_Cytology", "Date_Nipple_Cytology", "Number_Nipple_Cytology", "Report_Nipple_Cytology"
add_update_sql.update_multiple(conn, cursor, table, columns, file_number,
data)
def habits(conn, cursor, file_number, table):
from add_update_sql import update_multiple, update_single
from ask_y_n_statement import ask_option, ask_y_n
category = "Diet"
options = ["Vegetarian", "Non-Vegetarian", "Ovo-Vegetarian", "Other"]
diet = ask_option(category, options)
alcohol = ask_y_n("Alcohol consumption")
if alcohol:
alcohol_consump = "Alcohol Consumption"
alcohol_age = input("Consumption of alcohol from which age (yrs): ")
alcohol_quant = input("Quantity of alcohol consumed per week: ")
alcohol_duration = input("Duration of alcohol consumption: ")
alcohol_comments = input(
"Additional comments for alcohol consumption: ")
else:
alcohol_consump = "No Alcohol Consumption"
alcohol_age = "NA"
alcohol_quant = "NA"
alcohol_duration = "NA"
alcohol_comments = "NA"
columns = "Diet", "Alcohol_y_n", "Alcohol_Consumption_age_yrs", "Quantity_alcohol_per_week", "Duration_alcohol", "Comments_alcohol"
new_data = diet, alcohol_consump, alcohol_age, alcohol_quant, alcohol_duration, alcohol_comments
update_multiple(conn, cursor, table, columns, file_number, new_data)
tobacco = ask_y_n("Tobacco consumption")
if tobacco:
tobacco = "Tobacco consumption"
tobacco_type = input("Type of tobacco consumption: ")
tobacco_age = input("Consumption of tobacco from which age (yrs): ")
tobacco_quant = input("Quantity of tobacco consumed per week: ")
tobacco_duration = input("Duration of tobacco consumption: ")
tobacco_comments = input(
"Additional comments for tobacco consumption: ")
else:
tobacco = "No Tobacco Consumption"
tobacco_type = "NA"
tobacco_age = "NA"
tobacco_quant = "NA"
tobacco_duration = "NA"
tobacco_comments = "NA"
columns = "Tobacco_y_n", "Type_tobacco", "Tobacco_consumption_age_yrs", "Quantity_tobacco_per_week", "Duration_tobacco", "Comments_tobacco"
new_data = tobacco, tobacco_type, tobacco_age, tobacco_quant, tobacco_duration, tobacco_comments
update_multiple(conn, cursor, table, columns, file_number, new_data)
other_del_habits = input(
"Other Deleterious Habits (if present give details): ")
update_single(conn, cursor, table, "Other_Deleterious_Habits", file_number,
other_del_habits)
def other_symp(conn, cursor, file_number, table):
from add_update_sql import update_multiple
from ask_y_n_statement import get_rb_lb
#data = file_number, mr_number, name
add_symp = "y"
all_data = []
while str.lower(add_symp) == "y":
other_symp = input("Type of symptom: ")
symp_breast_right = input("Right Breast y/n: ")
if str.lower(symp_breast_right) == "y":
symp_breast_right = other_symp
symp_duration_right = input(
"Duration of symptoms in right breast: ")
else:
symp_breast_right = None
symp_duration_right = None
symp_breast_left = input("Left Breast y/n: ")
if str.lower(symp_breast_left) == "y":
symp_breast_left = other_symp
symp_duration_left = input("Duration of symptoms in left breast: ")
else:
symp_breast_left = None
symp_duration_left = None
RB = [symp_breast_right, symp_duration_right]
LB = [symp_breast_left, symp_duration_left]
data = [RB, LB]
all_data.append(data)
print("Include more symptoms?")
add_symp = input("y/n: ")
rb = get_rb_lb(all_data, 0)
rb_symp = list(filter(None, get_rb_lb(rb, 0)))
rb_dur = list(filter(None, get_rb_lb(rb, 1)))
lb = get_rb_lb(all_data, 1)
lb_symp = list(filter(None, get_rb_lb(lb, 0)))
lb_dur = list(filter(None, get_rb_lb(lb, 1)))
data = [rb_symp, rb_dur, lb_symp, lb_dur]
data = [rb_symp, rb_dur, lb_symp, lb_dur]
for index in range(0, len(data)):
if not data[index]:
data[index] = ["No other symptoms"]
else:
data[index] = ["; ".join(data[index])]
data_flat = [item for sublist in data for item in sublist]
new_data = tuple(data_flat)
columns = "RB_Other_Symptoms", "RB_Other_Symptoms_duration", "LB_Other_Symptoms", "RB_Other_Symptoms_duration"
update_multiple(conn, cursor, table, columns, file_number, new_data)
def tumour_biopsy_data(conn, cursor, file_number, table):
from ask_y_n_statement import ask_option
from add_update_sql import update_multiple
category = "Tumour biopsy diagnosis"
options = ['Benign', "Ductal carcinoma in situ(DCIS) with microinvasion",
"Ductal carcinoma in situ(DCIS) without microinvasion", "Lobular Carcinoma in Situ (LCS)",
"Invasive Ductal Carcinoma (IDC)", "Invasive Lobular Carcinoma (ILC)", "Granulamatous Mastitis",
"Papillary Carcinoma", "Phylloid Carcinoma", "Other"]
tumour_diagnosis = ask_option(category, options)
if tumour_diagnosis == 'Other':
tumour_diagnosis = input ('Detail of other diagnosis: ')
check = False
while not check:
tumour_grade = input("Tumour_biopsy_diagnosis_grade (1, 2 or 3): ")
val = ["1", "2", "3"]
check = tumour_grade in val
category = "ER Status"
options = ["Positive", "Negative"]
tumour_er= ask_option(category, options)
if (tumour_er == "Positive"):
tumour_er_percent = input ("ER Percent: ")
else:
tumour_er_percent = "NA"
category = "PR Status"
options = ["Positive", "Negative"]
tumour_pr = ask_option(category, options)
if (tumour_pr == "Positive"):
tumour_pr_percent = input ("PR Percent: ")
else:
tumour_pr_percent = "NA"
category = "HER2 Status"
options = ["Positive", "Negative"]
tumour_her2 = ask_option(category, options)
if (tumour_her2 == "Positive"):
tumour_her2_percent = input ("HER2 Percent: ")
else:
tumour_her2_percent = "NA"
category = "FISH"
options = ["Positive", "Negative"]
tumour_fish = ask_option(category, options)
tumour_ki67 = input("Ki67 Percent")
data = tumour_diagnosis,tumour_er ,tumour_er_percent ,tumour_pr, tumour_pr_percent, tumour_her2, tumour_her2_percent,\
tumour_fish, tumour_ki67
columns = "Tumour_biopsy_diagnosis", "Tumour_biopsy_diagnosis_grade", "Tumour_biopsy_ER", "Tumour_biopsy_ER_Percent", "Tumour_biopsy_PR", "Tumour_biopsy_PR_Percent", "Tumour_biopsy_HER2", "Tumour_biopsy_HER2_Grade", "Tumour_biopsy_FISH", "Tumour_biopsy_Ki67_Percent"
update_multiple(conn, cursor, table, columns, file_number, data)
def family_details(conn, cursor, file_number, table):
from add_update_sql import update_multiple
marital_status = input('Marital_Status :')
siblings = input('Siblings y/n:')
siblings_number, sisters, brothers = "No Siblings", "0", "0"
if (str.lower(siblings) == "y"):
siblings_number = input("Number of siblings: ")
sisters = input('Sisters :')
brothers = input('Brothers :')
children_y_n = input('Children_y_n :')
children_number, daughters, sons = "No Children", "0", "0"
if str.lower(children_y_n) == "y":
children_number = input("Number of children: ")
daughters = input('Daughters :')
sons = input('Sons :')
columns = "Marital_Status", "Siblings", "Sisters", "Brothers", "Children", "Daughters", "Sons"
new_data = marital_status, siblings_number, sisters, brothers, children_number, daughters, sons
update_multiple(conn, cursor, table, columns, file_number, new_data)
def family_cancer(conn, cursor, file_number, table):
from add_update_sql import update_multiple, review_input
from breast_cancer_tables import family_cancer_table
from ask_y_n_statement import ask_y_n
check = False
while not check:
family_cancer_history_y_n = ask_y_n('Cancer history in Family')
if family_cancer_history_y_n:
family_cancer = family_cancer_table(conn, cursor, file_number)
family_cancer_history_y_n = "Family History of Cancer"
else:
family_cancer_history_y_n = "No Family History of Cancer"
family_cancer = "NA"
data_list = [family_cancer_history_y_n, family_cancer]
columns_list = ["FamilyCancer_history_y_n", "Type_DegreeRelation_TypeRelation_Age_FamilyCancer"]
check = review_input(file_number, columns_list, data_list)
data = family_cancer_history_y_n, family_cancer
columns = "FamilyCancer_history_y_n", "Type_DegreeRelation_TypeRelation_Age_FamilyCancer"
update_multiple(conn, cursor, table, columns, file_number, data)
def lymphnode_biopsy(conn, cursor, file_number, table):
from ask_y_n_statement import ask_option
from add_update_sql import update_multiple
category = "Lymph Node biopsy FNAC"
options = ["Done", "Not Done"]
fnac = ask_option(category, options)
if fnac == "Done":
category = "Lymph Node biopsy location"
options = ["Right", "Left", "Both"]
fnac_location = ask_option(category, options)
category = "Lymph Node biopsy diagnosis"
options = ["Normal", "Benign", "Malignant"]
fnac_diagnosis = ask_option(category, options)
else:
fnac_location = "NA"
fnac_diagnosis = "NA"
data = fnac, fnac_location, fnac_diagnosis
columns = "Lymph_Node_biopsy_FNAC", "Lymph_Node_biopsy_location", "Lymph_Node_biopsy_diagnosis"
update_multiple(conn, cursor, table, columns, file_number, data)
def phys_act(conn, cursor, file_number, table):
from breast_cancer_tables import physical_activity_table
from add_update_sql import update_multiple, review_input
from ask_y_n_statement import ask_y_n
check = False
while not check:
phys_act = ask_y_n("Any Physical Activities ?")
if phys_act:
phys = physical_activity_table(conn, cursor, file_number)
phys_act = "Physical Activities Performed"
phys_act_done, phys_act_freq = phys
else:
phys_act = "No Physical Activities"
phys_act_done, phys_act_freq = ("NA",) * 2
data_list = [phys_act, phys_act_done, phys_act_freq]
columns_list = ["Physical_Activity_y_n", "Type_Physical_Activity", "Frequency_Physical_Activity"]
check = review_input(file_number, columns_list, data_list)
data = phys_act, phys_act_done, phys_act_freq
columns = "Physical_Activity_y_n", "Type_Physical_Activity", "Frequency_Physical_Activity"
update_multiple(conn, cursor, table, columns, file_number, data)
def habits(conn, cursor, file_number, table):
from add_update_sql import update_multiple, update_single
alcohol = input("Alcohol consumption (y/n): ")
alcohol_consump = "No Alcohol Consumption"
alcohol_age = "No Alcohol Consumption"
alcohol_quant = "No Alcohol Consumption"
alcohol_duration = "No Alcohol Consumption"
alcohol_comments = "No Alcohol Consumption"
if str.lower(alcohol) == "y":
alcohol_consump = "Alcohol Consumption"
alcohol_age = input("Consumption of alcohol from which age (yrs): ")
alcohol_quant = input("Quantity of alcohol consumed per week: ")
alcohol_duration = input("Duration of alcohol consumption: ")
alcohol_comments = input(
"Additional comments for alcohol consumption: ")
columns = "Alcohol_y_n", "Alcohol_Consumption_age_yrs", "Quantity_alcohol_per_week", "Duration_alcohol", "Comments_alcohol"
new_data = alcohol_consump, alcohol_age, alcohol_quant, alcohol_duration, alcohol_comments
update_multiple(conn, cursor, table, columns, file_number, new_data)
tobacco = input("Tobacco consumption (y/n)")
tobacco_type = "No Tobacco Consumption"
tobacco_age = "No Tobacco Consumption"
tobacco_quant = "No Tobacco Consumption"
tobacco_duration = "No Tobacco Consumption"
tobacco_comments = "No Tobacco Consumption"
if str.lower(tobacco) == "y":
tobacco = ("Tobacco consumption")
tobacco_type = input("Type of tobacco consumption: ")
tobacco_age = input("Consumption of tobacco from which age (yrs): ")
tobacco_quant = input("Quantity of tobacco consumed per week: ")
tobacco_duration = input("Duration of tobacco consumption: ")
tobacco_comments = input(
"Additional comments for tobacco consumption: ")
else:
tobacco = "No Tobacco Consumption"
columns = "Tobacco_y_n", "Type_tobacco", "Tobacco_consumption_age_yrs", "Quantity_tobacco_per_week", "Duration_tobacco", "Comments_tobacco"
new_data = tobacco, tobacco_type, tobacco_age, tobacco_quant, tobacco_duration, tobacco_comments
update_multiple(conn, cursor, table, columns, file_number, new_data)
other_del_habits = input("Other Deleterious Habits: ")
update_single(conn, cursor, table, "Other_Deleterious_Habits", file_number,
other_del_habits)
def surgery_block(conn, cursor, file_number, table):
from ask_y_n_statement import ask_option, ask_y_n
from add_update_sql import update_multiple
print("Surgery Block Report")
tumour_size = input("Tumour size: ")
category = "Tumour Grade"
options = ["I", "II", "III", "Other"]
tumour_grade = ask_option(category, options)
category = "Surgery Diagnosis"
options = [
"Ductal carcinoma in situ(DCIS)", "Invasive Ductal Carcinoma", "Other"
]
surg_diag = ask_option(category, options)
if (surg_diag == "Ductal carcinoma in situ(DCIS)"):
dcis_percent = input("Percent DCIS: ")
category = "DCIS Invasion"
options = ['Microinvasion', 'Macroinvasion']
dcis_invasion = ask_option(category, options)
else:
dcis_percent = "NA"
dcis_invasion = "NA"
per_inv = ask_y_n("Perineural Invasion", "Perineural Invasion Present",
"Perineural Invasion Absent")
necrosis = ask_y_n("Necrosis", "Necrosis Present", "Necrosis Absent")
lymph_invasion = ask_y_n("Lymphovascular invasion",
"Lymphovascular invasion Present",
"Lymphovascular invasion Absent")
category = "Margins"
options = ["Involved", "Free"]
margin = ask_option(category, options)
print("Surgery Block Report")
category = "Pathological Complete Remission"
options = ["Yes", "No", "Other"]
report = ask_option(category, options)
data = tumour_size, tumour_grade, surg_diag, dcis_percent, dcis_invasion, per_inv, necrosis, lymph_invasion, margin, report
columns = "Tumour_size_Surgery_Block_Report", "Grade_Surgery_Block_Report", "Diagnosis_Surgery_Block_Report", \
"DCIS_Percent_Surgery_Block_Report", "DCIS_Invasion_Surgery_Block_Report", \
"Perineural_Invasion_Surgery_Block_Report", "Necrosis_Surgery_Block_Report", \
"Lymphovascular_Invasion_Surgery_Block_Report", "Margins_Surgery_Block_Report", "Surgery_Block_Report"
update_multiple(conn, cursor, table, columns, file_number, data)
def nut_supplements(conn, cursor, file_number, table):
from add_update_sql import update_multiple, review_input
from breast_cancer_tables import nut_supp_table
from ask_y_n_statement import ask_y_n
check = False
while not check:
nut_supplements = ask_y_n("Nutritional supplements taken")
if nut_supplements:
nuts = nut_supp_table(conn, cursor, file_number)
nut_supplements = "Nutritional supplements taken"
else:
nut_supplements = "No nutritional supplements taken"
nuts = ("NA",) * 3
nuts_type, nuts_quant, nuts_dur = nuts
data_list = [nut_supplements, nuts_type, nuts_quant, nuts_dur]
columns_list = ["Nutritional_supplements_y_n", "Type_Nutritional_supplements",
"Quantity_Nutritional_supplements", \
"Duration_Nutritional_supplements"]
check = review_input(file_number, columns_list, data_list)
data = nut_supplements, nuts_type, nuts_quant, nuts_dur
columns = "Nutritional_supplements_y_n", "Type_Nutritional_supplements", "Quantity_Nutritional_supplements", \
"Duration_Nutritional_supplements"
update_multiple(conn, cursor, table, columns, file_number, data)
def surgery_info (conn, cursor, file_number, table):
from ask_y_n_statement import ask_option
from add_update_sql import update_multiple
surg_block_id = input("Surgical Block ID: ")
surg_no_block = input("Number of Blocks: ")
surg_block_source = input ("Surgery Block Source: ")
surg_tumour_block = input ("Tumour Block Reference: ")
surg_node_block = input ("Nodes Block Reference: ")
surg_normal_block = input ("Adjacent Normal Block Reference: ")
surg_red_block = input ("Reduction Tissue Block Reference: ")
surg_date = input ("Date of Surgery: ")
surg_name = input ("Name of surgeon: ")
surg_hosp_id = input ("Hospital ID: ")
category = "Lesion Side"
options = ["RB-UOQ", "RB-UIQ", "RB-C", "RB-LOQ", "RB-LIQ", "LB-UOQ", "LB-UIQ", "LB-C", "LB-LOQ", "LB-LIQ"]
lesion_side = ask_option(category, options)
category = "Type Surgery"
options = ["Reconstruction", "Breast Conservation Surgery (BCS)", "Therapeutic Mammoplasty"]
surg_type = ask_option (category, options)
if (surg_type == "Reconstruction"):
category = "Type Reconstruction"
options = ["Mastectomy/Modified Radical Mastectomy", "Implant"]
surg_type = ask_option(category, options)
elif (surg_type == "Breast Conservation Surgery"):
category = "Type Breast Conservation Surgery"
options = ["Therapeutic Mammoplasty/Reduction Mammoplasty", "Wide Local Excision"]
surg_type = ask_option(category, options)
category = "Response to Surgery"
options = ["Complete_Remission/No Residual Tumor", "Progressing", "Partial", "Static"]
surg_response = ask_option(category, options)
data = surg_block_id, surg_no_block, surg_block_source, surg_tumour_block, surg_node_block, surg_normal_block, \
surg_red_block, surg_date, surg_name, surg_hosp_id, lesion_side, surg_type, surg_response
columns = "Surgical_Block_ID", "Surgery_No_of_blocks", "Block_Source", "Tumor_block_ref", "Nodes_block_ref", \
"Ad_Normal_block_ref", "Reduction_tissue_block_ref", "Date_of_Surgery", "Name_Surgeon", "Hospital_ID", \
"Lesion_Side", "Type_surgery", "Response_surgery"
update_multiple(conn, cursor, table, columns, file_number, data)
def repro_details(conn, cursor, file_number, table):
from add_update_sql import update_multiple
from breast_cancer_tables import feed_duration
from ask_y_n_statement import ask_option, ask_y_n
menarche = input('Age at menarche (yrs): ')
category = "Menopausal Status"
options = ["Pre-menopausal", "Peri-menopausal", "Post-Menopausal", "Other"]
menopause = ask_option(category, options)
menopause_age = menopause
if menopause == "Post-Menopausal":
menopause_age = input('Age at menopause (yrs): ')
lmp = "Last menstrual period " + menopause_age + " yrs"
period_type = "NA"
else:
lmp = input("Date of last menstrual period: ")
category = "Period"
options = ["Regular", "Irregular", "Other"]
period_type = ask_option(category, options)
number_pregnancy = input("Number of pregnancies: ")
number_term = input(
"Pregnancy carried to term (include abortion after 6 months): )")
number_abortion = input("Number of abortions: ")
sql = (
'SELECT Children FROM Patient_Information_History WHERE File_number = \''
+ file_number + "'")
cursor.execute(sql)
kids = cursor.fetchall()
children_number = kids[0][0]
sql = (
'SELECT Age_yrs FROM Patient_Information_History WHERE File_number = \''
+ file_number + "'")
cursor.execute(sql)
age = cursor.fetchall()
age_mother = age[0][0]
if children_number == 'No Children':
age_first = 'NA'
age_last = 'NA'
else:
age_first = input("Age of first child: ")
if int(children_number) > 1:
age_last = input("Age of last child: ")
else:
age_last = age_first
age_first_preg = input("Age at first pregnancy: ")
if str.lower(age_first_preg) == "na":
age_first_preg = str(int(age_mother) - int(age_first))
age_last_preg = input("Age at last pregnancy: ")
if str.lower(age_first_preg) == "na":
age_last_preg = str(int(age_mother) - int(age_last))
twice_birth = ask_y_n("Two births in a year (not twins) y/n: ",
"Two births in a year", "No two births in a year")
breast_feeding = ask_y_n("Breast feeding?")
if breast_feeding:
breast_feeding = "Breast feeding"
feed_duration(conn, cursor, file_number, children_number)
else:
breast_feeding = "No Breast feeding"
type_birth_control = input("Type of birth control used: ")
if str.lower(type_birth_control) == "na":
detail_birth_control = "NA"
duration_birth_control = "NA"
else:
detail_birth_control = input("Details of birth control used: ")
duration_birth_control = input("Duration of birth control use: ")
new_data = menarche, menopause, menopause_age, lmp, period_type, number_pregnancy, number_term, number_abortion, \
age_first, age_first_preg, age_last,age_last_preg, twice_birth, breast_feeding, \
type_birth_control,detail_birth_control, duration_birth_control
columns = "Menarche_yrs", "Menopause_Status", "Age_at_Menopause_yrs", "Date_last_menstrual_period", "Period_Type", \
"Number_pregnancies", "Pregnancy_to_term", "Number_abortions", "Age_first_child", "Age_first_pregnancy",\
"Age_last_child", "Age_last_pregnancy", "Two_births_in_year", "Breast_feeding", \
"Type_birth_control_used", "Details_birth_control", "Duration_birth_control"
update_multiple(conn, cursor, table, columns, file_number, new_data)
def breast_symptoms(conn, cursor, file_number, table):
from ask_y_n_statement import ask_y_n
from add_update_sql import update_multiple, review_input
import textwrap
check = False
while not check:
note = ("Pain or tenderness; Lumps, Nipple Discharge - Milky/water discharge on pressing nippple, Nipple Retraction - nipple reagion goes inside, Dimpling small pits anwywhere on breast, Discolouration, Ulceration (small boils on surface), Eczema - Reddish spots with without itching")
wrapper = textwrap.TextWrapper(width=100)
string = wrapper.fill(text=note)
print(string)
symp_state = ["Pain or tenderness", "Lumps", "Nipple Discharge", "Nipple Retraction", "Dimpling",\
"Discolouration", "Ulceration", "Eczema"]
rb_symp_list = []
rb_dur_list= []
lb_symp_list = []
lb_dur_list = []
for index in symp_state:
symp = ask_y_n("Is "+ index +" present")
if symp:
RB = ask_y_n(index + " in Right Breast?")
if RB:
rb_symp = index
rb_dur = input ("Duration of "+ index+": ")
rb_symp_list.append(rb_symp)
rb_dur_list.append(rb_dur)
LB = ask_y_n(index + " in Left Breast?")
if LB:
lb_symp = index
lb_dur = input ("Duration of "+ index+": ")
lb_symp_list.append(lb_symp)
lb_dur_list.append(lb_dur)
rb_symps = "; ".join(rb_symp_list)
rb_duration = "; ".join(rb_dur_list)
lb_symps = "; ".join(lb_symp_list)
lb_duration = "; ".join(lb_dur_list)
data_list = [rb_symps, rb_duration, lb_symps, lb_duration]
for index in range(0, len(data_list)):
if data_list[index] == '':
data_list[index] = "NA"
columns_list = ["RB_symptoms", "RB_symptoms_duration", "LB_symptoms", "LB_symptoms_duration"]
check = review_input(file_number, columns_list, data_list)
data = tuple(data_list)
columns = "RB_symptoms", "RB_symptoms_duration", "LB_symptoms", "LB_symptoms_duration"
update_multiple(conn,cursor, table, columns, file_number, data)
check = False
while not check:
rb_symp_list = []
rb_dur_list = []
lb_symp_list = []
lb_dur_list = []
other_symptom = ask_y_n("Other Symptoms?")
if other_symptom:
check = True
while check:
type = input("Other Symptoms type? ")
RB = ask_y_n(type + " in Right Breast?")
if RB:
rb_symp = type
rb_dur = input("Duration of " + type)
rb_symp_list.append(rb_symp)
rb_dur_list.append(rb_dur)
LB = ask_y_n(type + " in Left Breast?")
if LB:
lb_symp = type
lb_dur = input("Duration of " + type)
lb_symp_list.append(lb_symp)
lb_dur_list.append(lb_dur)
check = ask_y_n("Additional Symptoms?")
rb_symps_other = "; ".join(rb_symp_list)
rb_duration_other = "; ".join(rb_dur_list)
lb_symps_other = "; ".join(lb_symp_list)
lb_duration_other = "; ".join(lb_dur_list)
data_list = [rb_symps_other, rb_duration_other , lb_symps_other , lb_duration_other]
for index in range(0, len(data_list)):
if data_list[index] == '':
data_list[index] = "NA"
columns_list = ["RB_Other_Symptoms", "RB_Other_Symptoms_duration", "LB_Other_Symptoms", "LB_Other_Symptoms_duration"]
check = review_input(file_number, columns_list, data_list)
data = tuple(data_list)
columns = "RB_Other_Symptoms", "RB_Other_Symptoms_duration", "LB_Other_Symptoms", "LB_Other_Symptoms_duration"
update_multiple(conn, cursor, table, columns, file_number, data)
def cancer_table(conn, cursor, file_number):
from add_update_sql import insert, update_multiple
from ask_y_n_statement import ask_y_n
table_cancer = "Previous_Cancer_History"
type_of_cancer_list = []
year_diagnosis_list = []
treat_all = []
type_all = []
duration_all = []
data_return = []
add_cancer = True
while add_cancer:
type_of_cancer = input("Type of Cancer: ")
type_of_cancer_list.append(type_of_cancer)
year_diagnosis = input("Year of diagnosis: ")
year_diagnosis_list.append(year_diagnosis)
columns = ("File_number, Type_Cancer, Year_diagnosis")
data = file_number, type_of_cancer, year_diagnosis
insert(conn, cursor, table_cancer, columns, data)
print("Please enter the type of treatment used: ")
treatment = [
"Surgery", "Radiation", "Chemotherapy", "Hormone", "Alternative",
"HomeRemedy"
]
treat_list = []
type_list = []
duration_list = []
treated, type, duration = ("NA", ) * 3
for index in treatment:
treat = ask_y_n(index)
if treat:
treat_list.append(index)
type_treat = input("Type of " + index)
type_list.append(type_treat)
duration_treat = input("Duration of " + index)
duration_list.append(duration_treat)
data = index, type_treat, duration_treat
columns = [index, ("Type_" + index), ("Duration_" + index)]
treated = "; ".join(treat_list)
type = "; ".join(type_list)
duration = "; ".join(duration_list)
update_multiple(conn, cursor, table_cancer, columns,
file_number, data)
elif not treat:
index_no = "No " + index
type_treat, duration_treat = ("NA", ) * 2
data = index_no, type_treat, duration_treat
columns = [index, ("Type_" + index), ("Duration_" + index)]
update_multiple(conn, cursor, table_cancer, columns,
file_number, data)
treat_all.append(treated)
type_all.append(type)
duration_all.append(duration)
add_cancer = ask_y_n("Additional cancer history")
all_data = [
type_of_cancer_list, year_diagnosis_list, treat_all, type_all,
duration_all
]
for index in all_data:
data_joint = "|".join(index)
data_return.append(data_joint)
return tuple(data_return)
def habits(conn, cursor, file_number, table):
from add_update_sql import update_multiple, review_input
from ask_y_n_statement import ask_option, ask_y_n
check = False
while not check:
category = "Diet"
print ("Note Ovo-Vegetarian is Egg + Veg eating. If eating patterms are only fish etc enter in Others")
options = ["Vegetarian", "Non-Vegetarian", "Ovo-Vegetarian", "Other"]
diet = ask_option(category, options)
alcohol = ask_y_n("Alcohol consumption")
if alcohol:
alcohol_consump = "Alcohol Consumption"
alcohol_age = input("Consumption of alcohol from which age (yrs): ")
alcohol_quant = input("Quantity of alcohol consumed per week: ")
alcohol_duration = input("Duration of alcohol consumption: ")
alcohol_comments = input("Additional comments for alcohol consumption: ")
else:
alcohol_consump = "No Alcohol Consumption"
alcohol_age, alcohol_quant, alcohol_duration, alcohol_comments = ("NA",) * 4
columns_list = ["Diet", "Alcohol_y_n", "Alcohol_Consumption_age_yrs", "Quantity_alcohol_per_week",
"Duration_alcohol", "Comments_alcohol"]
data_list = [diet, alcohol_consump, alcohol_age, alcohol_quant, alcohol_duration, alcohol_comments]
check = review_input(file_number, columns_list, data_list)
columns = "Diet", "Alcohol_y_n", "Alcohol_Consumption_age_yrs", "Quantity_alcohol_per_week", "Duration_alcohol", "Comments_alcohol"
new_data = diet, alcohol_consump, alcohol_age, alcohol_quant, alcohol_duration, alcohol_comments
update_multiple(conn, cursor, table, columns, file_number, new_data)
check = False
while not check:
print ("Note this question includes Gutkha, Pan Masala, Jarda/Maava, Hookah, Nicotine Patch, Mishri consumption")
tobacco = ask_y_n("Tobacco exposure (Passive and/or Active)")
if tobacco:
tobacco = "Tobacco consumption"
exposure_type = ask_option("Mode of exposure to Tobacco", ["Passive", "Active", "Other"])
if exposure_type =="Passive":
tobacco_type_partic = ask_option("Mode of passive consumption", ["Home", "Work", "Commute", "Social Interactions"])
if tobacco_type_partic == "Home":
tobacco_type_who = input ("What is the specific source?")
tobacco_passive = tobacco_type_partic + (" : ") + tobacco_type_who
else:
tobacco_passive = tobacco_type_partic
else:
tobacco_passive = "NA"
tobacco_type = ask_option("Type of tobacco use", ["Cigarette", "Beedi", "Gutkha", "Pan Masala", "Jarda/Maava", "Hookah", "Nicotine Patch", "Mishri", "Other"])
tobacco_age = input("Consumption of tobacco from which age (yrs): ")
tobacco_freq = input ("Frequency of tobacco consumption: ")
tobacco_quant = input("Quantity of tobacco consumed per week: ")
tobacco_duration = input("Duration of tobacco consumption: ")
tobacco_comments = input("Additional comments for tobacco consumption: ")
else:
tobacco = "No Tobacco Consumption"
exposure_type, tobacco_passive, tobacco_type, tobacco_age, tobacco_freq, tobacco_quant, tobacco_duration, \
tobacco_comments = ("NA",) * 8
other_del_habits = input("Other Deleterious Habits (if present give details): ")
columns_list = ["Tobacco_y_n", "Exposure_Mode", "Type_Passive", "Type_tobacco","Tobacco_consumption_age_yrs", "Tobacco_Frequency","Quantity_tobacco_per_week",
"Duration_tobacco", "Comments_tobacco", "Other_Deleterious_Habits"]
data_list = [tobacco, exposure_type, tobacco_passive,tobacco_type, tobacco_age, tobacco_freq, tobacco_quant,
tobacco_duration, tobacco_comments, other_del_habits]
check = review_input(file_number, columns_list, data_list)
columns = "Tobacco_y_n", "Exposure_Mode", "Type_Passive", "Type_tobacco","Tobacco_consumption_age_yrs", \
"Tobacco_Frequency","Quantity_tobacco_per_week", "Duration_tobacco", "Comments_tobacco",\
"Other_Deleterious_Habits"
data = tobacco, exposure_type,tobacco_passive, tobacco_type, tobacco_age, tobacco_freq, tobacco_quant, \
tobacco_duration, tobacco_comments, other_del_habits
update_multiple(conn, cursor, table, columns, file_number, data)
def path_stage(conn, cursor, file_number, table):
from add_update_sql import update_multiple
from ask_y_n_statement import ask_option, ask_y_n
category = "pT"
options = ["is", "0", "1", "2", "3", "4", "Other"]
pT = ask_option(category, options)
category = "pN"
options = ["0", "1", "2", "3", "4", "Other"]
pN = ask_option(category, options)
category = ("M")
options = ["0", "x", "Present", "Other"]
M = ask_option(category, options)
path_stage = "pT" + pT + "N" + pN + "M" + M
print("Pathological Stage: " + path_stage)
check = input("Is patholgicial stage correct (y/n): ")
if str.lower(check) == "n":
path_stage = input("Please enter correct pathological stage: ")
if M == "1":
clinical_stage = "IV"
elif M == "0":
if pN == "3":
clinical_stage = "IIIC"
elif pN == "2":
if pT == "4":
clinical_stage = "IIIB"
else:
clinical_stage = "IIIA"
elif pN == "1mi":
clinical_stage = "IB"
elif pN == "1":
if (pT == "0" or pT == "1"):
clinical_stage = "IIA"
elif pT == "2":
clinical_stage = "IIB"
elif pT == "3":
clinical_stage = "IIIA"
elif pT == "4":
clinical_stage = "IIIC"
else:
clinical_stage = input("Clinical Staging: ")
elif pN == "0":
if pT == "is":
clinical_stage = "0"
elif pT == "1":
clinical_stage = "IA"
elif pT == "2":
clinical_stage = "IIA"
elif pT == "3":
clinical_stage = "IIB"
elif pT == "4":
clinical_stage = "IIIB"
else:
clinical_stage = input("Clinical Staging: ")
else:
clinical_stage = input("Clinical Staging: ")
print("Clinical stage " + clinical_stage)
print(
"Based on TNM status", path_stage,
"and data at https://emedicine.medscape.com/article/2007112-overview")
check = ask_y_n("Is clinical stage correct", True, False)
if not check:
clinical_stage = input("Please enter correct clinical stage: ")
data = pT, pN, M, path_stage, clinical_stage
columns = "Pathological_Staging_pT", "Pathological_Staging_pN", "Pathological_Staging_M", \
"Pathological_Staging_P_Stage", "Clinical_Staging"
update_multiple(conn, cursor, table, columns, file_number, data)
