def add_gen_info(conn, cursor, file_number, user_name, folders):
table = "Patient_Information_History"
#file_row(cursor, file_number)
enter = ask_y_n("Enter Patient Biographical Information")
if enter:
data = bio_info(file_number)
update_multiple(conn, cursor, table, pccm_names.names_info("bio_info"),
file_number, data)
enter = ask_y_n("Enter Patient habits")
if enter:
data = phys_act(conn, cursor, file_number)
update_multiple(conn, cursor, table, pccm_names.names_info("phys_act"),
file_number, data)
data = habits(file_number)
update_multiple(conn, cursor, table, pccm_names.names_info("habits"),
file_number, data)
data = nut_supplements(conn, cursor, file_number)
update_multiple(conn, cursor, table,
pccm_names.names_info("nut_supplements"), file_number,
data)
enter = ask_y_n("Enter Patient family and reproductive details?")
if enter:
data = family_details(conn, cursor, file_number)
update_multiple(conn, cursor, table,
pccm_names.names_info("family_details"), file_number,
data)
enter = ask_y_n("Enter Patient medical history?")
if enter:
data = med_history(conn, cursor, file_number)
update_multiple(conn, cursor, table,
pccm_names.names_info("med_history"), file_number,
data)
data = cancer_history(conn, cursor, file_number)
update_multiple(conn, cursor, table,
pccm_names.names_info("cancer_history"), file_number,
data)
enter = ask_y_n("Enter patient family cancer history")
if enter:
data = family_cancer(conn, cursor, file_number)
update_multiple(conn, cursor, table,
pccm_names.names_info("family_cancer"), file_number,
data)
enter = ask_y_n("Enter Patient Symptoms?")
if enter:
data = det_by(file_number)
update_multiple(conn, cursor, table, pccm_names.names_info("det_by"),
file_number, data)
data = breast_symptoms(file_number, user_name)
update_multiple(conn, cursor, table,
pccm_names.names_info("breast_symptoms"), file_number,
data)
print_info(cursor, file_number, folders)
def edit_data(conn, cursor, file_number, user_name, folders):
table = "Patient_Information_History"
print("Patient Biographical Information")
col_list = pccm_names.names_info("bio_info")
enter = review_data(conn, cursor, table, file_number, col_list)
if enter:
data = bio_info(file_number)
update_multiple(conn, cursor, table, col_list, file_number, data)
col_list = pccm_names.names_info("phys_act") + pccm_names.names_info(
"habits") + pccm_names.names_info("nut_supplements")
print("Patient habits")
enter = review_data(conn, cursor, table, file_number, col_list)
if enter:
data_phys = phys_act(conn, cursor, file_number)
data_hab = habits(file_number)
data_nut = nut_supplements(conn, cursor, file_number)
data = data_phys + data_hab + data_nut
update_multiple(conn, cursor, table, col_list, file_number, data)
print("Patient family and reproductive details")
col_list = pccm_names.names_info("family_details")
enter = review_data(conn, cursor, table, file_number, col_list)
if enter:
data = family_details(conn, cursor, file_number)
update_multiple(conn, cursor, table, col_list, file_number, data)
print("Patient medical history")
col_list = pccm_names.names_info("med_history") + pccm_names.names_info(
"cancer_history")
enter = review_data(conn, cursor, table, file_number, col_list)
if enter:
data_med = med_history(conn, cursor, file_number)
data_can = cancer_history(conn, cursor, file_number)
data = data_med + data_can
update_multiple(conn, cursor, table, col_list, file_number, data)
print("Patient Family Cancer History")
col_list = pccm_names.names_info("family_cancer")
enter = review_data(conn, cursor, table, file_number, col_list)
if enter:
data_fam = family_cancer(conn, cursor, file_number)
update_multiple(conn, cursor, table, col_list, file_number, data_fam)
print("Patient Symptoms")
col_list = pccm_names.names_info("det_by") + pccm_names.names_info(
"breast_symptoms")
enter = review_data(conn, cursor, table, file_number, col_list)
if enter:
data_det = det_by(file_number)
data_symp = breast_symptoms(file_number, user_name)
data = data_det + data_symp
update_multiple(conn, cursor, table, col_list, file_number, data)
print_info(cursor, file_number, folders)
def metastasis_symp(file_number):
module_name = "metastasis_symp"
check = False
while not check:
met_none = ask_y_n("Metastatis Symptoms Present?")
met = []
if not met_none:
met = [["No Metastatis Symptoms"]]
else:
met_bone = ask_y_n("Bone Pain")
if met_bone:
met.append(["Bone Pain"])
met_cough = ask_y_n("Cough")
if met_cough:
met.append(["Cough"])
met_jaundice = ask_y_n("Jaundice")
if met_jaundice:
met.append(["Jaundice"])
met_headache = ask_y_n("Headache")
if met_headache:
met.append(["Headache"])
met_weight = ask_y_n("Weight loss")
if met_weight:
met.append(["WeightLoss"])
met_flat = [item for sublist in met for item in sublist]
data_met = "; ".join(met_flat)
columns_list = pccm_names.names_info(module_name)
check = review_input(file_number, columns_list, [data_met])
return (str(data_met))
def print_info(cursor, file_number, folders):
import docx
from datetime import date
import modules.pccm_names as pccm_names
import os.path
module_name = [
"bio_info", "nut_supplements", "phys_act", "habits", "family_details",
"med_history", "cancer_history", "family_cancer", "det_by",
"breast_symptoms"
]
folder = folders + '/Gen_Info_Docs'
file_name = "Folder_" + (file_number.replace("/", "_")) + ".docx"
path = os.path.join(folder, file_name)
p_date_to_print = date.today().strftime('%d-%b-%Y')
doc = docx.Document()
doc.add_paragraph(("File Number " + file_number), style="Title")
doc.add_paragraph(("Document Created on " + p_date_to_print),
style="Quote")
for index in range(0, len(module_name)):
col_titles = pccm_names.names_info(module_name[index])
columns = ", ".join(col_titles)
sql = 'SELECT ' + columns + ' FROM Patient_Information_History WHERE File_number = \'' + file_number + "'"
data = cursor.execute(sql)
data_file = data.fetchall()
data_print = list(data_file[0])
text_titles = pccm_names.info_print_all(module_name[index])
for i in range(0, len(data_print)):
p = doc.add_paragraph((text_titles[i] + ": "),
style="List Bullet")
(p.add_run(data_print[i])).bold = True
doc.add_paragraph()
doc.save(path)
def habits(file_number):
module_name = "habits"
check = False
while not check:
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, alcohol_quant, alcohol_duration, alcohol_comments = ("NA",) * 4
data_list_alc = [diet, alcohol_consump, alcohol_age, alcohol_quant, alcohol_duration, alcohol_comments]
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_type, tobacco_passive, tobacco_age, tobacco_freq, tobacco_quant, tobacco_duration, \
tobacco_comments = ("NA",) * 8
other_del_habits = input("Other Deleterious Habits (if present give details): ")
data_list_tob = [tobacco, exposure_type, tobacco_passive,tobacco_type, tobacco_age, tobacco_freq,
tobacco_quant, tobacco_duration, tobacco_comments, other_del_habits]
columns_list = pccm_names.names_info(module_name)
data_list = data_list_alc + data_list_tob
check = review_input(file_number, columns_list, data_list)
return (tuple(data_list))
def bio_info(file_number):
module_name = "bio_info"
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"])
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 = str(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(file_number, columns_list, new_data)
return (tuple(new_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 db_dict(table, module):
db_tables = {
"Patient_Information_History": names.names_info(module),
"Biopsy_Report_Data": names.names_biopsy_new(module),
"Radiology": names.names_radio(module),
"Neo_Adjuvant_Therapy": names.names_nact(module),
"Surgery_Report": names.names_surgery_information(module),
"Surgery_Block_Report_Data": names.names_surgery(module),
"Adjuvant_ChemoTherapy": names.names_chemotherapy(module),
"Radiotherapy": names.names_radiation(),
"HormoneTherapy_Survival": names.names_longterm(module),
"Follow_up_Data": names.name_follow_up()
}
cols = db_tables.get(table)
return cols
def family_cancer(conn, cursor, file_number):
module_name = "family_cancer"
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 = pccm_names.names_info(module_name)
check = review_input(file_number, columns_list, data_list)
return (tuple(data_list))
def physical_activity_table(conn, cursor, file_number):
table_act = "Physical_Activity"
columns = ", ".join(pccm_names.names_info("phys_act_table"))
add_act = True
type_phys_list, freq_phys_list = [], []
while add_act:
type_phys_act = input("Type of physical activity: ")
type_phys_list.append(type_phys_act)
freq_phys_act = input("Frequency of physical activity: ")
freq_phys_list.append(freq_phys_act)
data = file_number, type_phys_act, freq_phys_act
insert(conn, cursor, table_act, columns, data)
add_act = ask_y_n("Add further activities?")
type_phys = '; '.join(type_phys_list)
freq_phys = '; '.join(freq_phys_list)
return (type_phys, freq_phys)
def med_history(conn, cursor, file_number):
module_name = "med_history"
check = False
while not check:
medical_history_y_n = ask_y_n("Any 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 = pccm_names.names_info(module_name)
check = review_input(file_number, columns_list, data_list)
return (tuple(data_list))
def phys_act(conn, cursor, file_number):
module_name = "phys_act"
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 = pccm_names.names_info(module_name)
check = review_input(file_number, columns_list, data_list)
return (tuple(data_list))
def nut_supplements(conn, cursor, file_number):
module_name = "nut_supplements"
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 = pccm_names.names_info(module_name)
check = review_input(file_number, columns_list, data_list)
return (tuple(data_list))
def cancer_history(conn, cursor, file_number):
module_name = "cancer_history"
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 = pccm_names.names_info(module_name)
check = review_input(file_number, columns_list, data_list)
return (tuple(data_list))
def db_dict(table, module):
db_tables = {
"patient_information_history": names.names_info(module),
"radiology": names.names_radio(module),
'pet_reports': names.names_pet(module),
'biopsy_path_report_data': names.names_biopsy(module),
"neo_adjuvant_therapy": names.names_nact(module),
"surgery_report": names.names_surgery_information(module),
'surgery_path_report_data': names.names_surgery(module),
"adjuvant_chemotherapy": names.names_chemotherapy(module),
"radiotherapy": names.names_radiation(),
"hormonetherapy_survival": names.names_longterm(module),
"follow_up_data": names.name_follow_up(),
'block_list': names.block_list(module)
}
cols = db_tables.get(table)
return cols
def nut_supp_table(conn, cursor, file_number):
type_nut_list, quant_nut_list, duration_nut_list = [], [], []
add_supp = True
table_nut = "Nutritional_Supplements"
columns = ", ".join(pccm_names.names_info("nut_sup"))
while add_supp:
nut_supplements_type = input("Type of nutritional supplements taken: ")
type_nut_list.append(nut_supplements_type)
nut_supplements_quant = input(
"Quantity of nutritional supplements taken per day: ")
quant_nut_list.append(nut_supplements_quant)
nut_supplements_duration = input(
"Duration of nutritional supplements use: ")
duration_nut_list.append(nut_supplements_duration)
new_data = file_number, nut_supplements_type, nut_supplements_quant, nut_supplements_duration
insert(conn, cursor, table_nut, columns, new_data)
add_supp = ask_y_n('Add more nutritional supplements?')
type_nut = '; '.join(type_nut_list)
quant_nut = '; '.join(quant_nut_list)
duration_nut = "; ".join(duration_nut_list)
return (type_nut, quant_nut, duration_nut)
table = "HormoneTherapy_Recurrence_Survival"
col_list = [
"File_number"
] + names.names_longterm("hormone") + names.names_longterm("metastasis")
sql = ('SELECT ' + ", ".join(col_list[:-2]) + " FROM '" + table + "'")
df = pd.read_sql(sql, conn)
df.to_excel(writer, sheet_name="Hormone_RecurrenceSurvival")
table = "Follow_up_Data"
col_list = ["File_number"] + names.name_follow_up()
sql = ('SELECT ' + ", ".join(col_list[:-2]) + " FROM '" + table + "'")
df = pd.read_sql(sql, conn)
df.to_excel(writer, sheet_name=table)
table = "Patient_Information_History"
col_list_bio = names.names_info("bio_info")
col_list = ["File_number"] + col_list_bio + names.names_info("phys_act") + names.names_info("habits") + \
names.names_info("nut_supplements") + names.names_info("family_details") + names.names_info("med_history") + \
names.names_info("cancer_history") + names.names_info("family_cancer") + names.names_info("breast_symptoms")
sql = ('SELECT ' + ", ".join(col_list) + " FROM '" + table + "'")
df = pd.read_sql(sql, conn)
df.to_excel(writer, sheet_name=table)
writer.save()
#######################################33
table = "Biopsy_Report_Data"
module_names = ["biopsy_report_info", "tumour_biopsy_data", "lymphnode_biopsy"]
col_list = ["File_number"]
for index in module_names:
def family_details(conn, cursor, file_number):
module_name = "family_details"
check = False
while not check:
marital_status = input('Marital Status :')
siblings = ask_y_n_na('Siblings')
if siblings == 'Yes':
siblings_number = input("Number of siblings: ")
sisters = input('Sisters :')
brothers = input('Brothers :')
elif siblings == 'No':
siblings_number, sisters, brothers = "No Siblings", "0", "0"
else:
siblings_number, sisters, brothers = (siblings, ) * 3
children_y_n = ask_y_n_na('Children')
if children_y_n == 'Yes':
children_number = input("Number of children: ")
daughters = input('Daughters :')
sons = input('Sons :')
elif children_y_n == 'No':
children_number, daughters, sons = "No Children", "0", "0"
else:
children_number, daughters, sons = (children_y_n, ) * 3
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 = "Type of Period"
options = ["Regular", "Irregular", "Other"]
period_type = ask_option(category, options)
number_pregnancy = input(
"Number of pregnancies (enter Requires Follow-up if no data given): "
)
if number_pregnancy == "0":
age_first_preg, age_last_preg, number_term, number_abortion, age_first, age_last, twice_birth, \
breast_feeding_data, kid_feeding, duration_feeding, breast_usage = ('No children',) * 11
elif number_pregnancy == "Requires Follow-up":
age_first_preg, age_last_preg, number_term, number_abortion, age_first, age_last, twice_birth, \
breast_feeding_data, kid_feeding, duration_feeding, breast_usage = ('Requires Follow-up',) * 11
else:
number_term = input(
"Pregnancy carried to term (include abortion after 6 months): "
)
number_abortion = input("Number of abortions: ")
age_first_preg = input("Age at first pregnancy: ")
age_last_preg = "NA"
try:
sql = (
'SELECT Age_at_First_Visit_yrs FROM Patient_Information_History WHERE File_number = \''
+ file_number + "'")
cursor.execute(sql)
age = cursor.fetchall()
age_mother = age[0][0]
except:
age_mother = input("Age at first visit to clinic")
if children_number == 'No Children':
age_first, age_last, twice_birth, breast_feeding_data, kid_feeding, \
duration_feeding, breast_usage = (children_number,) * 7
elif children_y_n == 'Yes':
age_first = input("Age of first child: ")
if age_first_preg == "NA":
age_first_preg = str(int(age_mother) - int(age_first))
if int(children_number) > 1:
age_last = input("Age of last child: ")
age_last_preg = input("Age at last pregnancy: ")
if age_last_preg == "NA":
age_last_preg = str(int(age_mother) - int(age_last))
twice_birth = ask_y_n("Two births in a year (not twins)",
"Two births in a year",
"No two births in a year")
else:
age_last = age_first
age_last_preg, twice_birth = ("NA", ) * 2
breast_feeding = ask_y_n("Breast feeding?")
if breast_feeding:
breast_feeding_data = "Breast feeding"
feed_details = feed_duration(conn, cursor, file_number,
children_number)
else:
breast_feeding_data = "No Breast feeding"
feed_details = ("NA", ) * 3
kid_feeding, duration_feeding, breast_usage = feed_details
else:
age_first, age_last, twice_birth, breast_feeding_data, kid_feeding, \
duration_feeding, breast_usage = (children_y_n,) * 7
fert_treat_y_n = ask_y_n_na(
"Have any fertility treatments ever been used")
if fert_treat_y_n == 'Yes':
fert_treat = "Fertility Treatment used"
type_fert = input("Type of fertility treatment used: ")
detail_fert = input("Details of fertility treatment used:")
cycles_fert = input(
"Number of cycles of fertility treatment taken: ")
success_fert = ask_y_n(
"Did fertility treatment result in successful pregnancy? ",
"Pregnancy from Treatment", "No pregnancy from treatment")
elif fert_treat_y_n == "No":
fert_treat = "No Fertility Treatment used"
type_fert, detail_fert, cycles_fert, success_fert = (
"No Fertility Treatment used", ) * 4
else:
fert_treat, type_fert, detail_fert, cycles_fert, success_fert = (
fert_treat_y_n, ) * 5
birth_control = ask_y_n_na("Birth control used?")
if birth_control == 'Yes':
type_birth_control = ask_option("Type of birth control used",
["Birth control pills", "Other"])
detail_birth_control = input("Details of birth control used: ")
duration_birth_control = input("Duration of birth control use: ")
elif birth_control == 'No':
type_birth_control, detail_birth_control, duration_birth_control = (
"No birth control used", ) * 3
else:
type_birth_control, detail_birth_control, duration_birth_control = (
birth_control, ) * 3
data_list = [
marital_status, siblings_number, sisters, brothers,
children_number, daughters, sons, 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_data, kid_feeding,
duration_feeding, breast_usage, fert_treat, type_fert, detail_fert,
cycles_fert, success_fert, type_birth_control,
detail_birth_control, duration_birth_control
]
columns_list = pccm_names.names_info(module_name)
check = review_input(file_number, columns_list, data_list)
return tuple(data_list)
import pandas as pd
folder = "d:/repos/pccm_db/main/DB/DB_with_real_data"
db_name = 'PCCM_BreastCancerDB_all_data.db'
path = os.path.join(folder, db_name)
conn_all = sqlite3.connect(path)
cursor_all = conn_all.cursor()
file_number = "File_number"
table = "Patient_Information_History"
if table_check(cursor_all, table) == 0:
cursor_all.execute('CREATE TABLE {tn}({nf})'\
.format(tn=table, nf=file_number))
module_names = ["bio_info", "phys_act", "habits", "nut_supplements", "family_details", "med_history",
"cancer_history", "family_cancer", "det_by", "breast_symptoms"]
for index in module_names:
col_name = pccm_names.names_info(index)
add_columns(cursor_all, table, col_name)
table = "Radiotherapy"
if table_check(cursor_all, table) == 0:
column = ", ".join(pccm_names.names_radiation())
cols_file = "File_number, "+column
cursor_all.execute('CREATE TABLE {tn}({nf})'.format(tn=table, nf=cols_file))
table = "Follow_up_Data"
if table_check(cursor_all, table) == 0:
column = ", ".join(pccm_names.name_follow_up())
cols_file = "File_number, " + column
cursor_all.execute('CREATE TABLE {tn}({nf})'.format(tn=table, nf=cols_file))
table = "HormoneTherapy_Recurrence_Survival"
if table_check(cursor_all, table) == 0:
def breast_symptoms(file_number, user_name):
module_name = "breast_symptoms"
check = False
while not check:
symp_present = ask_y_n(
"Does the file include on patient symptoms at presentations?")
if symp_present:
# 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 - may occur after surgery, 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_symp = [rb_symps, rb_duration, lb_symps, lb_duration]
for index in range(0, len(data_list_symp)):
if data_list_symp[index] == '':
data_list_symp[index] = "NA"
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_other = [
rb_symps_other, rb_duration_other, lb_symps_other,
lb_duration_other
]
for index in range(0, len(data_list_other)):
if data_list_other[index] == '':
data_list_other[index] = "NA"
met = []
met_bone = ask_y_n("Is Bone Pain present?")
if met_bone:
met.append(["Bone Pain"])
met_cough = ask_y_n("Is Cough present")
if met_cough:
met.append(["Cough"])
met_jaundice = ask_y_n("Is Jaundice present")
if met_jaundice:
met.append(["Jaundice"])
met_headache = ask_y_n("Is Headache present")
if met_headache:
met.append(["Headache"])
met_weight = ask_y_n("Has Weight loss occurred")
if met_weight:
met.append(["WeightLoss"])
met_flat = [item for sublist in met for item in sublist]
data_met = "; ".join(met_flat)
if met_flat == []:
data_met = "No Metastatis Symptoms"
else:
data_list_other = [
"Requires Follow-up",
] * 4
data_list_symp = [
"Requires Follow-up",
] * 4
data_met = "Requires Follow-up"
columns_list = pccm_names.names_info(module_name)
last_update = datetime.now().strftime("%Y-%b-%d %H:%M")
data_list = data_list_symp + data_list_other + [
data_met, user_name, last_update
]
check = review_input(file_number, columns_list, data_list)
return tuple(data_list)
