def add_gen_info(conn, cursor, file_number, user_name):
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 and family 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)
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)
def print_info(cursor, file_number, folders):
import docx
from datetime import date
import helper_function.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 bio_info(file_number):
module_name = "bio_info"
mr_number = gf.get_number_lt(500, 2000)
name = names.get_full_name(gender='female')
aadhaar_card = 'data_not_available'
date_first = gf.gen_date(base_date='2010-12-12')
permanent_address = 'data_not_available'
current_address = permanent_address
phone = gf.get_number_lt(900000000, 999999999)
email_id = 'data_not_available'
gender = gf.get_choice(["Female", "Male"])
date_of_birth = gf.get_dob()
age_yrs = gf.get_age(date_of_birth)
age_diag = gf.get_years(date_of_birth, date_first)
place_birth = 'data_not_available'
height_cm = gf.get_number_lt(140, 180)
weight_kg = gf.get_number_lt(50, 90)
weight = float(weight_kg)
height = float(height_cm) / 100
bmi = str(round(weight / (height * height)))
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
]
return (age_diag, tuple(new_data))
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 edit_data(conn, cursor, file_number, user_name):
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 and family medical history")
col_list = pccm_names.names_info("med_history") + pccm_names.names_info(
"cancer_history") + pccm_names.names_info("family_cancer")
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_fam = family_cancer(conn, cursor, file_number)
data = data_med + data_can + data_fam
update_multiple(conn, cursor, table, col_list, file_number, data)
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)
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 family_cancer(file_number):
module_name = "family_cancer"
family_cancer_history_y_n = gf.get_yes_no_na()
if family_cancer_history_y_n == 'yes':
family_cancer = bct.family_cancer_table(file_number)
family_cancer_history_y_n = "Family History of Cancer"
elif family_cancer_history_y_n == 'no':
family_cancer_history_y_n = "No Family History of Cancer"
family_cancer = "No Family History of Cancer"
else:
family_cancer = family_cancer_history_y_n
data_list = [family_cancer_history_y_n, family_cancer]
columns_list = pccm_names.names_info(module_name)
return (tuple(data_list))
def nut_supp_table(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"))
nut_supplements_type = 'data_not_available'
type_nut_list.append(nut_supplements_type)
nut_supplements_quant = str(gf.get_number(1000))
quant_nut_list.append(nut_supplements_quant)
nut_supplements_duration = str(gf.get_number(4))
duration_nut_list.append(nut_supplements_duration)
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)
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 nut_supplements(file_number):
module_name = "nut_supplements"
nut_supplements = gf.get_yes_no_na()
if nut_supplements == 'yes':
nuts = bct.nut_supp_table(file_number)
nut_supplements = "Nutritional supplements taken"
elif nut_supplements == 'no':
nut_supplements = "No nutritional supplements taken"
nuts = ("No nutritional supplements taken", ) * 3
else:
nuts = (nut_supplements, ) * 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)
return (tuple(data_list))
def phys_act(file_number):
module_name = "phys_act"
phys_act = gf.get_yes_no_na()
if phys_act == 'yes':
phys = bct.physical_activity_table(file_number)
phys_act = "Physical Activities Performed"
phys_act_done, phys_act_freq = phys
elif phys_act == 'no':
phys_act = "No Physical Activities"
phys_act_done, phys_act_freq = ("No Physical Activities", ) * 2
else:
phys_act_done, phys_act_freq = (phys_act, ) * 2
data_list = [phys_act, phys_act_done, phys_act_freq]
columns_list = pccm_names.names_info(module_name)
return (tuple(data_list))
def other_test(self):
data_list = [
'data_to_be_entered',
] * 14 + [self.user_name, last_update()]
module_name = "other_test"
check = False
while not check:
print(
'In this module please enter data for tests done at the time of diagnosis before the start of '
'treatment')
data = clinical_tests()
data_list = data + [self.user_name, last_update()]
col_list = pccm_names.names_info(module_name)
check = review_input(self.file_number, col_list, data_list)
return data_list
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(file_number):
# def physical_activity_table(file_number):
table_act = "physical_activity"
columns = ", ".join(pccm_names.names_info("phys_act_table"))
type_phys_list, freq_phys_list = [], []
type_phys_act = gf.get_choice(options=PatientInfo.phys_act)
type_phys_list.append(type_phys_act)
freq_phys_act = gf.get_choice(options=PatientInfo.frequency)
freq_phys_list.append(freq_phys_act)
type_phys_act = gf.get_choice(options=PatientInfo.phys_act)
type_phys_list.append(type_phys_act)
freq_phys_act = gf.get_choice(options=PatientInfo.frequency)
freq_phys_list.append(freq_phys_act)
type_phys = '; '.join(type_phys_list)
freq_phys = '; '.join(freq_phys_list)
return (type_phys, freq_phys)
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 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
sql.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 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 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 med_history(file_number):
module_name = "med_history"
medical_history_y_n = gf.get_yes_no_na()
if medical_history_y_n == 'yes':
med_hist = bct.med_history_table(file_number)
medical_history_y_n = "Previous medical history present"
elif medical_history_y_n == 'no':
medical_history_y_n = "No previous medical history present"
med_hist = ("No previous medical history present", ) * 3
else:
med_hist = (medical_history_y_n, ) * 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)
return (tuple(data_list))
def family_cancer(self):
module_name = "family_cancer"
check = False
while not check:
family_cancer_history_y_n = ask_y_n_na('Cancer history in Family')
if family_cancer_history_y_n == 'Yes':
family_cancer = family_cancer_table(self.conn, self.cursor,
self.file_number)
family_cancer_history_y_n = "Family History of Cancer"
elif family_cancer_history_y_n == 'No':
family_cancer_history_y_n = "No Family History of Cancer"
family_cancer = "No Family History of Cancer"
else:
family_cancer = family_cancer_history_y_n
data_list = [family_cancer_history_y_n, family_cancer]
columns_list = pccm_names.names_info(module_name)
check = review_input(self.file_number, columns_list, data_list)
return 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 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 nut_supplements(self):
module_name = "nut_supplements"
data_list = ['NA'] * 4
check = False
while not check:
nutrition = ask_y_n_na("Nutritional supplements taken")
if nutrition == 'Yes':
nuts = nut_supp_table(self.conn, self.cursor, self.file_number)
nutrition = "Nutritional supplements taken"
elif nutrition == 'No':
nutrition = "No nutritional supplements taken"
nuts = ("No nutritional supplements taken", ) * 3
else:
nuts = (nutrition, ) * 3
nuts_type, nuts_quant, nuts_dur = nuts
data_list = [nutrition, nuts_type, nuts_quant, nuts_dur]
columns_list = pccm_names.names_info(module_name)
check = review_input(self.file_number, columns_list, data_list)
return data_list
def phys_act(self):
module_name = "phys_act"
check = False
data_list = ['NA'] * 3
while not check:
activity = ask_y_n_na("Any Physical Activities ?")
if activity == 'Yes':
phys = physical_activity_table(self.conn, self.cursor,
self.file_number)
activity = "Physical Activities Performed"
phys_act_done, phys_act_freq = phys
elif activity == 'No':
activity = "No Physical Activities"
phys_act_done, phys_act_freq = ("No Physical Activities", ) * 2
else:
phys_act_done, phys_act_freq = (activity, ) * 2
data_list = [activity, phys_act_done, phys_act_freq]
columns_list = pccm_names.names_info(module_name)
check = review_input(self.file_number, columns_list, data_list)
return data_list
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
sql.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)
def med_history(self):
module_name = "med_history"
check = False
while not check:
medical_history_y_n = ask_y_n_na("Any Other Medical History ?")
if medical_history_y_n == 'Yes':
med_hist = med_history_table(self.conn, self.cursor,
self.file_number)
medical_history_y_n = "Previous medical history present"
elif medical_history_y_n == 'No':
medical_history_y_n = "No previous medical history present"
med_hist = ("No previous medical history present", ) * 3
else:
med_hist = (medical_history_y_n, ) * 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(self.file_number, columns_list, data_list)
return data_list
def cancer_history(self):
module_name = "cancer_history"
data_list = ['NA'] * 6
check = False
while not check:
previous_cancer_history_y_n = ask_y_n_na(
"Previous history of cancer ?")
if previous_cancer_history_y_n == 'Yes':
previous_cancer = cancer_table(self.conn, self.cursor,
self.file_number)
previous_cancer_history_y_n = "Previous history of cancer"
elif previous_cancer_history_y_n == 'No':
previous_cancer_history_y_n = "No previous history of cancer"
previous_cancer = ("No previous history of cancer", ) * 5
else:
previous_cancer = (previous_cancer_history_y_n, ) * 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(self.file_number, columns_list, data_list)
return data_list
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:
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))
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('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"
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: ")
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 = ('NA',) * 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: ")
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]
if children_number == 'No Children':
age_first, age_last, twice_birth, breast_feeding_data, kid_feeding, \
duration_feeding, breast_usage = ('NA',) * 7
else:
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
fert_treat_y_n = ask_y_n(
"Have any fertility treatments ever been used")
if fert_treat_y_n:
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")
else:
fert_treat = "No Fertility Treatment used"
type_fert, detail_fert, cycles_fert, success_fert = ("NA", ) * 4
type_birth_control = input("Type of birth control used: ")
if str.lower(type_birth_control) == "na":
type_birth_control, detail_birth_control, duration_birth_control = (
"NA", ) * 3
else:
detail_birth_control = input("Details of birth control used: ")
duration_birth_control = input("Duration of birth control use: ")
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))
