def edit_data(conn, cursor, file_number, user_name):
table = "Follow_up_Data"
col_list = names.name_follow_up()
enter = view_multiple(conn, table, col_list, file_number)
if enter == "Add data":
data = follow_up(file_number, user_name)
data.to_sql("Follow_up_Data", conn, index=False, if_exists="append")
if enter == "Re-enter data":
table = "Follow_up_Data"
col_list = ["File_number"] + names.name_follow_up()
sql = ('SELECT ' + ", ".join(col_list[:-2]) + " FROM '" + table +
"' WHERE File_number = '" + file_number + "'")
df = pd.read_sql(sql, conn)
follow_up_period = list(df.loc[:, "Follow_up_Period"])
delete_data = True
while delete_data:
check_delete = False
while not check_delete:
col_data = ask_y_n_statement.ask_option(
"Which entry do you want to modify?", follow_up_period)
check_delete = ask_y_n_statement.ask_y_n(
"Are you sure you want to delete data for follow-up period "
+ col_data)
delete_rows(cursor, table, "Follow_up_Period", col_data)
add_data(conn, file_number, user_name)
delete_data = ask_y_n_statement.ask_y_n(
"Do you want to re-enter another follow up period")
def mammo_asym():
import modules.ask_y_n_statement as ask_y_n_statement
asym = ask_y_n_statement.ask_y_n("Is asymmetry present")
if asym:
asym_loc = ask_y_n_statement.ask_option(
"Location of Asymmetry", ["Right Breast", "Left Breast", "Both"])
asym_quad = lesion_location(asym_loc)
asym_depth = ask_y_n_statement.ask_option(
"Depth of Asymmetry", ["Anterior", "Middle", "Posterior", "Other"])
asym_dist = ask_y_n_statement.ask_option(
"Distance from nipple of Asymmetry",
["<0.5 cm", ">0.5 cm", "Other"])
pect_check = ask_y_n_statement.ask_y_n(
"Is distance from Pectoralis Major described for Asymmetry")
if pect_check:
asym_pect = input("Distance from Pectoralis Major (cm): ")
else:
asym_pect = "NA"
mammo_asymm = lesion_location(asym_loc, [
"Type of Asymmetry in Right Breast",
"Type of Asymmetry in Left Breast"
], [
"Asymmetry", "Global asymmetry", "Focal asymmetry",
"Developing asymmetry", "Other"
])
else:
asym_quad, asym_depth, asym_dist, asym_pect, mammo_asymm = ("NA", ) * 5
asym_loc = "Not Present"
data_list = [
asym_loc, asym_quad, asym_depth, asym_dist, asym_pect, mammo_asymm
]
return data_list
def create_block_id(self):
block_id_list = []
block_no = int(self.block_no)
block_id_chunks = list(divmod(block_no, 26))
chunk = block_id_chunks[0]
suffix = [i for i in range(chunk)]
if chunk == 0:
for j in range(block_id_chunks[1]):
alph_list = string.ascii_uppercase[j]
block_id_list.append(alph_list)
else:
for i in range(chunk):
if i == chunk - 1:
for j in range(block_id_chunks[1]):
alph_list = string.ascii_uppercase[j] + str(i)
block_id_list.append(alph_list)
else:
for j in range(26):
alph_list = string.ascii_uppercase[j] + suffix[i]
block_id_list.append(alph_list)
print((", ").join(block_id_list))
check_list = ask.ask_y_n("Is block list correct?")
while not check_list:
block_id_list = []
for i in range(block_no):
id = input('Block id of block number ' + str(i + 1) + ': ')
block_id_list.append(id)
print((", ").join(block_id_list))
check_list = ask.ask_y_n("Is block list correct?")
return block_id_list
def metastasis(file_number, user_name):
check = False
while not check:
met_has = ask_y_n_statement.ask_y_n(
"Has the patient been examined for metastatic disease?")
if not met_has:
met_has = "Not examined for metastatic disease"
else:
met_has = "Examined for metastatic disease"
date_last = input("Date of last follow-up: ")
recur = ask_y_n_statement.ask_y_n(
"Has the patient experienced a recurrence?")
if recur:
time_recur = input("Time to disease recurrence: ")
nature_recur = ask_y_n_statement.ask_option(
"Nature of recurrence", ["Distant", "Local", "Other"])
if nature_recur == "Distant":
distant_site = input("Site of distant recurrence: ")
else:
distant_site = "NA"
else:
time_recur, nature_recur, distant_site = ("NA", ) * 3
status = patient_status()
last_update = datetime.now().strftime("%Y-%b-%d %H:%M")
data_list = [
met_has, date_last, time_recur, nature_recur, distant_site, status,
user_name, last_update
]
col_list = names.names_longterm("metastasis")
check = review_input(file_number, col_list, data_list)
return data_list
def mammo_arch():
import modules.ask_y_n_statement as ask_y_n_statement
mammo_arch = ask_y_n_statement.ask_y_n(
"Is Architectural distortion present")
if mammo_arch:
mammo_arch = "Architectural distortion present"
arch_loc = ask_y_n_statement.ask_option(
"Location of Distortion", ["Right Breast", "Left Breast", "Both"])
arch_quad = lesion_location(arch_loc)
arch_depth = ask_y_n_statement.ask_option(
"Depth of Architectural Distortion",
["Anterior", "Middle", "Posterior", "Other"])
arch_dist = ask_y_n_statement.ask_option(
"Distance from nipple of Architectural Distortion",
["<0.5 cm", ">0.5 cm", "Other"])
pect_check = ask_y_n_statement.ask_y_n(
"Is distance from Pectoralis Major described for "
"Architectural Distortion")
if pect_check:
arch_pect = input("Distance from Pectoralis Major (cm): ")
else:
arch_pect = "NA"
else:
mammo_arch = "Architectural distortion not present"
arch_loc = "Not Present"
arch_quad, arch_depth, arch_dist, arch_pect = ("Not Present", ) * 4
data_list = [
mammo_arch, arch_loc, arch_quad, arch_depth, arch_dist, arch_pect
]
return data_list
def add_data(self):
enter = ask.ask_y_n("Enter Surgery Block information?")
if enter:
data = SurgeryBlockData.surgery_block_information_1(self)
col_list = names(self.module_list[0])
sql.update_multiple(self.conn, self.cursor, self.table, col_list,
self.file_number, data)
enter = ask.ask_y_n(
"Enter Surgery Block information (Tumour Details) ?")
if enter:
col_list = names(self.module_list[1])
data, block_data_df = SurgeryBlockData.surgery_block_information_2(
self)
sql.update_multiple(self.conn, self.cursor, self.table, col_list,
self.file_number, data)
block_data_df.to_sql("block_data",
self.conn,
index=False,
if_exists="append")
enter = ask.ask_y_n("Enter Surgery Block information (Node Details)?")
if enter:
col_list = names(self.module_list[2])
data = SurgeryBlockData.surgery_block_information_3(self)
sql.update_multiple(self.conn, self.cursor, self.table, col_list,
self.file_number, data)
enter = ask.ask_y_n("Enter Pathological Stage?")
if enter:
col_list = names(self.module_list[3])
data = SurgeryBlockData.path_stage(self)
sql.update_multiple(self.conn, self.cursor, self.table, col_list,
self.file_number, data)
def cancer_table(conn, cursor, file_number):
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)
col = ("File_number, Type_Cancer, Year_diagnosis")
data = file_number, type_of_cancer, year_diagnosis
insert(conn, cursor, table_cancer, col, 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 edit_table(df, id_col, df_col):
rows = df.shape[0]
for row in range(0, rows):
print(df.iloc[row].to_string() + '\n')
to_correct = ask.ask_y_n("Are entries correct?")
if not to_correct:
to_correct = ask.ask_y_n("Re-enter entire table?")
if to_correct:
return to_correct, df
else:
change_row = True
while change_row:
id_list = list(df[id_col])
print(id_list)
id_change = input("Enter " + id_col + " to change: ")
index = id_list.index(id)
to_do = True
while to_do:
print(df.loc[index, :])
col_change = ask.ask_option("Name of column to change", df_col)
old_val = df.loc[index, col_change]
print(old_val + '\n')
new_val = input("Enter correct value for " + col_change + ' for ' + id_change + ": ")
df.loc[index, col_change] = new_val
print(df.iloc[index].to_string() + '\n')
to_do = ask.ask_y_n("Make more changes to " + id_col + ' ' + id_change + '?')
ReviewSQL.print_df(df)
change_row = ask.ask_y_n("Change another row?")
to_correct = False
return to_correct, df
def add_data(self):
enter = ask.ask_y_n("Enter Biopsy Block Report information?")
if enter:
data = BiopsyData.biopsy_report_info(self)
sql.update_multiple(self.conn, self.cursor, self.table, names("biopsy_report_info"), self.file_number, data)
enter = ask.ask_y_n("Enter Tumour Biopsy data?")
if enter:
data = BiopsyData.tumour_biopsy_data(self)
sql.update_multiple(self.conn, self.cursor, self.table, names("tumour_biopsy_data"), self.file_number, data)
def tox_table(file_number, drug_cyc, tox_all):
tox_index = 0
check_tox = False
while not check_tox:
tox = ask_y_n_statement.ask_y_n(
"Were there any toxic effects in administration of " + drug_cyc)
if tox:
add_tox = True
while add_tox:
tox_present = ask_y_n_statement.ask_option(
"Toxic effects of type", chemo.toxicity())
tox_grade = ask_y_n_statement.ask_option(
("the grade of " + tox_present + "? "),
["Mild", "Moderate", "Severe", "Other"])
treatment = input("Treatment given for " + tox_grade + " " +
tox_present + " (include all details): ")
resp_treatment = ask_y_n_statement.ask_option(
("Response to treatment given for " + tox_grade + " " +
tox_present),
["Partial", "Complete", "No Effect", "Other"])
cyc_tox = input("Cycle at which toxicity occurred: ")
change_tox = ask_y_n_statement.ask_option(
"Changes to treatment", [
"No change", "Therapy changed due to toxicity",
"Therapy stopped due to toxicity",
"Therapy changed due to other reasons",
"Therapy stopped due to other reasons"
])
if change_tox == "Therapy changed due to toxicity" or change_tox == "Therapy changed due to other "\
"reasons":
change = input("Please describe changes to Therapy: ")
change_tox = change_tox + ": " + change
check = False
while not check:
data = [
file_number, drug_cyc, tox_present, tox_grade,
treatment, resp_treatment, cyc_tox, change_tox
]
tox_all.loc[tox_index] = data
check = review_df_row(tox_all)
tox_index = tox_index + 1
add_tox = ask_y_n_statement.ask_y_n(
'Add another toxicity type?')
else:
tox_present, tox_grade, treatment, resp_treatment, cyc_tox, change_tox = (
"No Toxicity", ) * 6
data = [
file_number, drug_cyc, tox_present, tox_grade, treatment,
resp_treatment, cyc_tox, change_tox
]
tox_all.loc[tox_index] = data
check_tox = review_df(tox_all)
return tox_all
def 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 stage(pt, pn, m):
path_stage = "pT" + pt + "N" + pn + 'M' + m
clinical_stage = 'NA'
print("Pathological Stage: " + path_stage)
check = ask.ask_y_n("Is pathological stage correct")
if not check:
path_stage = input("Please enter correct pathological stage: ")
if m in {"1", "2", "3"}:
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 = "IIIB"
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: ")
print("Clinical stage " + clinical_stage)
print(
"Based on TNM status", path_stage,
"and TABLE 2 of Giuliano et al., 2017, CA CANCER J "
"CLIN 2017;67:290–303")
check = ask.ask_y_n("Is clinical stage correct")
if not check:
clinical_stage = input("Please enter correct clinical stage: ")
return path_stage, clinical_stage
def add_data(conn, cursor, file_number, user_name):
#file_row(cursor, file_number)
table = "HormoneTherapy_Survival"
enter = ask_y_n_statement.ask_y_n("Enter Hormone Therapy Details?")
if enter:
col_list = names.names_longterm(module_name="hormone")
data = hormone(file_number)
update_multiple(conn, cursor, table, col_list, file_number, data)
enter = ask_y_n_statement.ask_y_n("Enter Recurrence and follow-up status?")
if enter:
col_list = names.names_longterm(module_name="metastasis")
data = metastasis(file_number, user_name)
update_multiple(conn, cursor, table, col_list, file_number, data)
def follow_up(file_number, user_name):
follow = True
follow_index = 0
col_list = ["File_number"] + names.name_follow_up()
follow_up_data = pd.DataFrame(columns=col_list)
while follow:
check = False
while not check:
time_follow = ask_y_n_statement.ask_option("Follow-up Period", [
"3 months", "6 months", "9 months", "1 year",
"1 year, 3 months", "1 year, 6 months", "1 year, 9 months",
"2 years", "2 years, 6 months", "3 years", "3 years, 6 months",
"4 years", "4 years, 6 months", "5 years", "6 years",
"7 years", "8 years", "9 years", "10 years", "Other"
])
follow_notes = input("Details of follow up information: ")
follow_report = ask_y_n_statement.ask_y_n(
"Does follow-up contain other reports (USG/Mammography)?")
follow_mammo, follow_usg = ("NA", ) * 2
if follow_report:
follow_mammo = input("Results of Mammography: ")
follow_usg = input("Results of USG abdomen/Pelvis: ")
follow_other = ask_y_n_statement.ask_y_n(
"Are there other reports in follow-up?")
if not follow_other:
other_type, other_result = ("NA", ) * 2
else:
other_type_list = []
other_result_list = []
while follow_other:
other_type = input("Type of other report: ")
other_result = input("Result of " + other_type + ": ")
other_type_list.append(other_type)
other_result_list.append(other_result)
follow_other = ask_y_n_statement.ask_y_n(
"Add more reports?")
all_data = [other_type_list, other_result_list]
all_data = ask_y_n_statement.join_lists(all_data, "; ")
other_type, other_result = all_data
last_update = datetime.now().strftime("%Y-%b-%d %H:%M")
data_list = [
file_number, time_follow, follow_notes, follow_mammo,
follow_usg, other_type, other_result, user_name, last_update
]
follow_up_data.loc[follow_index] = data_list
check = review_df(follow_up_data.loc[follow_index])
follow_index = follow_index + 1
follow_up_period = list(follow_up_data.loc[:, "Follow_up_Period"])
print("Follow up periods added: " + "; ".join(follow_up_period))
follow = ask_y_n_statement.ask_y_n("Add another follow-up period?")
return follow_up_data
def family_cancer_table(conn, cursor, file_number):
add_family = True
type_cancer_list, relation_degree_list, type_relation_list, age_detect_list = [], [], [], []
all_data = []
while add_family:
type_of_cancer = input("Type of Cancer: ")
type_cancer_list.append(type_of_cancer)
relation_to_patient = ask_option(
"Relation to patient",
["Immediate Family", "Maternal Family", "Paternal Family"])
relation_degree_list.append(relation_to_patient)
type_relation = input("Specific Relationship:")
type_relation_list.append(type_relation)
age_at_detection_yrs = input('Age at detection (yrs) :')
age_detect_list.append(age_at_detection_yrs)
family_history = file_number, type_of_cancer, relation_to_patient, type_relation, age_at_detection_yrs
family_history_list = "; ".join([
type_of_cancer, relation_to_patient, type_relation,
age_at_detection_yrs
])
all_data.append(family_history_list)
columns = 'File_number, Type_Cancer, Relation_to_Patient, Type_Relation, Age_at_detection_yrs'
table = "Family_Cancer_History"
insert(conn, cursor, table, columns, family_history)
add_family = ask_y_n("Add more family cancer history? ")
all_data_flat = "|".join(all_data)
return (all_data_flat)
def clinical_tests(test):
import modules.ask_y_n_statement as ask_y_n_statement
test_name = test[0]
data_list = []
test_done = ask_y_n_statement.ask_y_n("Has " + test_name + " been done?")
if test_done:
test_done = test_name + " done"
data_list.append(test_done)
for index in range(1, len(test)):
abnormal = test[index]
test_diag = ask_y_n_statement.ask_option("Diagnosis",
["Normal", abnormal])
data_list.append(test_diag)
if test_diag == abnormal:
test_details = input("Please provide details of " + abnormal +
" diagnosis: ")
else:
test_details = "NA"
data_list.append(test_details)
else:
test_done = test_name + " not done"
data_list.append(test_done)
for index in range(1, len(test)):
not_done = ("NA", ) * 2
data_list.append(not_done)
return data_list
def birads():
import modules.ask_y_n_statement as ask_y_n_statement
mammo_birads = ask_y_n_statement.ask_option(
"BI-RADS",
["0", "I", "II", "III", "IV", "IVA", "IVB", "IVC", "V", "Other"])
check = False
while not check:
if mammo_birads == "0":
mammo_birads_det = "Incomplete – Need Additional Imaging Evaluation"
elif mammo_birads == "I":
mammo_birads_det = "Negative"
elif mammo_birads == "II":
mammo_birads_det = "Benign"
elif mammo_birads == "III":
mammo_birads_det = "Probably Benign"
elif mammo_birads == "IV":
mammo_birads_det = "Suspicious"
elif mammo_birads == "IVA":
mammo_birads_det = "Low suspicion for malignancy"
elif mammo_birads == "IVB":
mammo_birads_det = "Moderate suspicion for malignancy"
elif mammo_birads == "IVC":
mammo_birads_det = "High suspicion for malignancy"
elif mammo_birads == "V":
mammo_birads_det = "Highly Suggestive of Malignancy"
else:
mammo_birads_det = input("Details of BI-RADS category: ")
print("BI-RAD " + mammo_birads + ": " + mammo_birads_det)
check = ask_y_n_statement.ask_y_n("Is this correct?")
data_list = [mammo_birads, mammo_birads_det]
return tuple(data_list)
def tox_table(file_number, cyc_name, week, drug_cyc):
import modules.ask_y_n_statement as ask_y_n_statement
import additional_tables.chemo as chemo
import pandas as pd
import modules.pccm_names as names
from sql.add_update_sql import review_df as review
tox_all = pd.DataFrame(columns=names.names_nact("Tox_table"))
tox_index = 0
drugs = "/".join(drug_cyc)
check_tox = False
while not check_tox:
tox = ask_y_n_statement.ask_y_n("Were there any toxic effects in " +
week + " of " + cyc_name)
tox_grade_list, tox_list, tox_treatment, resp_treatment_list = [
list([]) for _ in range(4)
]
if tox:
for index in chemo.toxicity():
tox_grade = ask_y_n_statement.ask_option(
("the grade of " + index + " in " + cyc_name + "? "),
["Mild", "Moderate", "Severe", "Not Present", "Other"])
if tox_grade not in {"Not Present"}:
tox = index
check = False
while not check:
treatment = input("Treatment given for " + tox_grade +
" " + index +
" (include all details): ")
resp_treatment = ask_y_n_statement.ask_option(
("Response to treatment given for " + tox_grade +
" " + index),
["Partial", "Complete", "No Effect", "Other"])
data = [
file_number, week, cyc_name, drugs, tox, tox_grade,
treatment, resp_treatment
]
tox_all.loc[tox_index] = data
check = review(tox_all.loc[tox_index])
tox_grade_list.append(tox_grade)
tox_list.append(index)
tox_treatment.append(treatment)
resp_treatment_list.append(resp_treatment)
tox_index = tox_index + 1
else:
tox = "No Toxicity"
tox_grade, treatment, resp_treatment = ("NA", ) * 3
tox_list = ["No Toxicity"]
tox_grade_list, tox_treatment, resp_treatment_list = [["NA"]] * 3
data = [
file_number, week, cyc_name, drugs, tox, tox_grade, treatment,
resp_treatment
]
tox_all.loc[tox_index] = data
all_data = [
tox_grade_list, tox_list, tox_treatment, resp_treatment_list
]
response = ask_y_n_statement.join_lists(all_data, "; ")
check_tox = review(tox_all)
return response
def drug_add(file_number, cyc_name, cycle_number, week, patient_wt,
drug_per_week, drug_index):
import modules.ask_y_n_statement as ask
from sql.add_update_sql import review_df as review
import additional_tables.chemo as chemo
drug_add = True
drug_cyc = []
while drug_add:
check_drug = False
while not check_drug:
drug = ask.ask_option("Drug used for therapy " + cyc_name,
chemo.drug_list())
dose = input("Dose of " + drug + " in " + week + " of " +
cyc_name + ": ")
dose_unit = input("Dose unit: ")
cyc_freq = input("Cycle Frequency: ")
data_week = [
file_number, cycle_number, week, patient_wt, drug,
float(dose), dose_unit, cyc_freq
]
drug_per_week.loc[drug_index] = data_week
check_drug = review(drug_per_week.loc[drug_index])
drug_cyc.append(drug)
drug_index = drug_index + 1
drug_add = ask.ask_y_n("Add another drug")
return drug_per_week, drug_cyc, drug_index
def birads():
import modules.ask_y_n_statement as ask_y_n_statement
check = False
while not check:
mammo_birads = ask_y_n_statement.ask_option("BI-RADS Category", [
"Category 0", "Category 1", "Category 2", "Category 3",
"Category 4", "Category 4A", "Category 4B", "Category 4C",
"Category 5", "Other"
])
if mammo_birads == "Category 0":
mammo_birads_det = "Incomplete – Need Additional Imaging Evaluation"
elif mammo_birads == "Category 1":
mammo_birads_det = "Negative"
elif mammo_birads == "Category 2":
mammo_birads_det = "Benign"
elif mammo_birads == "Category 3":
mammo_birads_det = "Probably Benign"
elif mammo_birads == "Category 4":
mammo_birads_det = "Suspicious"
elif mammo_birads == "Category 4A":
mammo_birads_det = "Low suspicion for malignancy"
elif mammo_birads == "Category 4B":
mammo_birads_det = "Moderate suspicion for malignancy"
elif mammo_birads == "Category 4C":
mammo_birads_det = "High suspicion for malignancy"
elif mammo_birads == "Category 5":
mammo_birads_det = "Highly Suggestive of Malignancy"
else:
mammo_birads_det = input("Details of BI-RADS category: ")
birad = mammo_birads + ": " + mammo_birads_det
print(birad)
check = ask_y_n_statement.ask_y_n("Is this correct?")
data_list = birad
return data_list
def abvs(file_number):
module_name = "abvs"
check = False
while not check:
abvs = ask_y_n_statement.ask_y_n("Automated Breast Volume Scanner (ABVS) done?")
if abvs:
abvs = "Automated Breast Volume Scanner done"
abvs_date = input("Date of examination of ABVS: ")
abvs_acc = input("Accession number of ABVS: ")
abvs_lesion = ask_y_n_statement.ask_option("Location of lesion",
["Right Breast", "Left Breast", "Both", "Not present"])
if abvs_lesion in {"Right Breast", "Left Breast", "Both"}:
abvs_lesion_data = radio_tables_old.lesion_location(abvs_lesion)
else:
abvs_lesion_data = "NA"
abvs_size = ask_y_n_statement.ask_option("Size of lesion", ["<2 cm", "2-5 cm", ">5 cm", "Other"])
abvs_dist = ask_y_n_statement.ask_option("Distance from Skin (cm)", ["<0.5 cm", ">0.5 cm", "Other"])
abvs_pect = input("Distance from Pectoralis Major (cm): ")
abvs_diagnosis = ask_y_n_statement.ask_option("ABVS Diagnosis",
["Normal", "Benign", "Suspicious", "Diagnostic for Cancer"])
else:
abvs = "Automated Breast Volume Scanner done"
abvs_date, abvs_acc, abvs_lesion, abvs_lesion_data, abvs_size, abvs_dist, abvs_pect, \
abvs_diagnosis = ("NA",) * 8
data_list = [abvs, abvs_date, abvs_acc, abvs_lesion, abvs_lesion_data, abvs_size, abvs_dist, abvs_pect,
abvs_diagnosis]
columns_list = names(module_name)
check = add_update_sql.review_input(file_number, columns_list, data_list)
return (tuple(data_list))
def print_table(self, writer, table):
modules = table_dicts.table_module_dict(table)
if table == 'Patient_Information_History':
output_type = ask_y_n('Do you want a research print out for ' +
table + '?')
if output_type:
modules = table_dicts.table_module_research(table)
columns = []
if not modules:
modules = 'no_modules'
columns = table_dicts.db_dict(table, modules)
else:
for module in modules:
cols = table_dicts.db_dict(table, module)
columns = columns + cols
if table != 'Block_list':
col_list = table_dicts.create_col_list(columns)
else:
col_list = columns
sql = ('SELECT ' + ", ".join(col_list) + " FROM '" + table + "'")
df = pd.read_sql(sql, self.conn)
number = df.shape[0]
df.to_excel(writer,
sheet_name=table,
startrow=0,
index=False,
header=True)
return number
def drug_table_enter(file_number, drug_table):
drug_add = True
drug_index = 0
while drug_add:
check_drug= False
while not check_drug:
drug = ask_y_n_statement.ask_option("Drug used for therapy", chemo.drug_list())
try:
dose = input("Dose of " + drug +" (actual dose ammount without unit, numbers only): ")
dose_x = float(dose)
except:
print ('ERROR: enter numbers only')
dose = input("Dose of " + drug +" (actual dose ammount without unit, numbers only): ")
dose_unit = input("Dose unit: ")
cyc_freq_week = input("Cycle Frequency (frequency per week, so three weekly is 3 and weekly is 1): ")
try:
number_cycle = input("Number of cycles actually given: ")
dose_x = int(number_cycle)
except:
print('ERROR: enter numbers only')
number_cycle = input("Number of cycles actually given: ")
try:
drug_dose = float(dose) * int(number_cycle)
except:
drug_dose = 'PLEASE RE-ENTER DATA, DOSE AND NUMBER OF CYCLES MUST BE DIGITS ONLY'
data_drug = [file_number, number_cycle, drug, str(drug_dose), dose_unit, cyc_freq_week]
drug_table.loc[drug_index] = data_drug
check_drug, drug_table = review_df_row(drug_table)
drug_index = drug_index + 1
drug_add = ask_y_n_statement.ask_y_n("Add another drug")
return drug_table
def review_input(self):
col_number = len(self.data)
print("Entries for database are as follows : ")
for index in range(0, col_number):
print(self.columns[index] + ": " + self.data[index])
ans = ask.ask_y_n("Are entries for file " + self.file_number + " correct ?", True, False)
return ans
def check_file(conn, cursor, table, file_number, user_name, folders):
import modules.ask_y_n_statement as ask_y_n_statement
import add_edit.add_new as add_new
import add_edit.edit_record as edit_record
sql = "SELECT rowid FROM " + table + " WHERE File_number = ?"
cursor.execute(sql, (file_number, ))
data = cursor.fetchall()
if len(data) == 0:
if table != "Follow_up_Data":
cursor.execute("INSERT INTO " + table + "(File_number) VALUES ('" +
file_number + "')")
print(file_number + " does not exist in table " + table +
". Enter new record")
add_new.add_new(conn, cursor, file_number, table, user_name, folders)
else:
todo = ask_y_n_statement.ask_option(
file_number + " already exists in table " + table + ".", [
"Edit record", "Add new record for same file number",
"Edit None"
])
if todo == "Edit record":
edit_record.edit_record(conn, cursor, file_number, table,
user_name, folders)
elif todo == "Add new record for same file number":
print("Add additional record module TBD")
ask = ask_y_n_statement.ask_y_n("Add another table?")
return ask
def metastasis(file_number, user_name):
check = False
while not check:
met_has = ask_y_n_statement.ask_y_n(
"Has the patient been examined for metastatic disease?")
if not met_has:
met_has = "Not examined for metastatic disease"
else:
met_has = "Examined for metastatic disease"
date_last = input("Date of last follow-up: ")
recur = ask_y_n_statement.ask_y_n(
"Has the patient experienced a recurrence?")
if recur:
time_recur = input("Time to disease recurrence: ")
nature_recur = ask_y_n_statement.ask_option(
"Nature of recurrence", ["Distant", "Local", "Other"])
if nature_recur == "Distant":
distant_site = input("Site of distant recurrence: ")
else:
distant_site = "NA"
else:
time_recur, nature_recur, distant_site = ("NA", ) * 3
status = ask_y_n_statement.ask_option(
"Status at last follow up",
["Survivor", "Deceased", "Lost to follow-up", "Other"])
if status == "Survivor":
type_survivor = ask_y_n_statement.ask_option(
"the Survivor is ", [
"disease Free", "with recurrence",
"disease free with no known recurrence", "with disease"
])
status = status + ": " + type_survivor
if status == "Deceased":
type_death = ask_y_n_statement.ask_option(
"Cause of death",
["due to disease", "due to unrelated causes", "not known"])
status = status + ": " + type_death
last_update = datetime.now().strftime("%Y-%b-%d %H:%M")
data_list = [
met_has, date_last, time_recur, nature_recur, distant_site, status,
user_name, last_update
]
col_list = names.names_longterm("metastasis")
check = review_input(file_number, col_list, data_list)
return data_list
def review_df_row(df):
check_row = len(df) - 1
print(df.iloc[check_row].to_string())
check = ask.ask_y_n("Is data entered correct?")
if check:
return check, df
else:
df = df.drop(df.index[check_row])
return check, df
def add_data(conn, cursor, file_number, user_name):
table = "Clinical_Exam"
#file_row(cursor, file_number)
enter =ask_y_n_statement.ask_y_n("Enter Clinical Examination information")
if enter:
data = clinical_exam_initial(file_number, user_name)
add_update_sql.update_multiple(conn, cursor, table, pccm_names.name_clinical("clinical_exam_initial"),
file_number, data)
enter = ask_y_n_statement.ask_y_n("Enter Nipple Cytology report?")
if enter:
data = nipple_cytology(file_number)
add_update_sql.update_multiple(conn, cursor, table, pccm_names.name_clinical("nipple_cytology"), file_number,
data)
enter = ask_y_n_statement.ask_y_n("Enter results of other clinical tests?")
if enter:
data = other_test(file_number)
add_update_sql.update_multiple(conn, cursor, table, pccm_names.name_clinical("other_test"), file_number,
data)
def review_input(file_number, columns, data):
import modules.ask_y_n_statement as ask_y_n_statement
col_number = len(data)
print("Entries for database are as follows : ")
for index in range(0, col_number):
print(columns[index] + ": " + data[index])
ans = ask_y_n_statement.ask_y_n(
"Are entries for file " + file_number + " correct ?", True, False)
return ans
def review_data(conn, cursor, table, file_number, col_list):
import modules.ask_y_n_statement as ask
sql = ('SELECT ' + ", ".join(col_list) + ' FROM ' + table +
" WHERE File_number = '" + file_number + "'")
data = cursor.execute(sql)
data_list = data.fetchall()
data_list = list(data_list[0])
col_number = len(col_list)
if data_list == [None] * len(data_list):
print("This section of the database has not been entered")
enter = ask.ask_y_n("Do you want to enter now")
return enter
if None in set(data_list):
print("Some entries are missing from the database: ")
for index in range(0, col_number):
print(col_list[index] + " : " + str(data_list[index]))
enter = ask.ask_option("Do you want to proceed?",
["Edit all", "Add new data only"])
if enter == "Edit all":
return True
else:
edit_few(conn, cursor, table, col_list, file_number, data_list)
else:
print("Entries present in database are as follows : ")
for index in range(0, col_number):
print(col_list[index] + " : " + str(data_list[index]))
enter = ask.ask_option("Do you want to",
["Edit all", "Edit some entries", "Edit None"])
if enter == "Edit some entries":
for index in range(0, col_number):
print(col_list[index] + " : " + str(data_list[index]))
edit = ask.ask_y_n("Edit")
if edit:
data = input("Data for " + col_list[index] + ": ")
update_single(conn, cursor, table, col_list[index],
file_number, data)
return False
elif enter == "Edit all":
return True
else:
return False
