def surgery_block_information_3(self):
module_name = self.module_list[3]
review_surgery_date, review_surgery_source, review_surgery_diagnosis, review_surgery_diagnosis_comment, \
review_surgery_block_id, review_surgery_er, review_surgery_er_percent, review_surgery_pr, review_surgery_pr_percent, \
review_surgery_her2, review_surgery_her2_grade, review_surgery_fish, review_surgery_ki67 = ['NA', ] * 13
data_list = ['NA', ] * 13
check = False
while not check:
review = ask.ask_y_n('Has a review (of diagnosis or IHC details) been done of this surgery block?')
if review:
review_surgery_date = ask.check_date('Date of review (if multiple dates?): ')
review_surgery_source = input(
'Name of Review Laboratory (Enter multiple if required Lab_test): ')
review_surgery_diagnosis = input('Enter diagnosis of review: ')
review_surgery_diagnosis_comment = input('Additional comments for review diagnosis: ')
review_surgery_block_id = self.surgery_block_id
block_id = ask.ask_y_n('Has the block been relabelled in the review?')
if block_id:
old_block_id = input('Please enter old block id: ')
new_block_id = input('Please enter new block id: ')
review_surgery_block_id = old_block_id + ' relabelled to ' + new_block_id
review_ihc = ask.ask_y_n('Has the IHC result for any marker been reviewed by another lab?')
if review_ihc:
review_surgery_er, review_surgery_er_percent, review_surgery_pr, review_surgery_pr_percent, \
review_surgery_her2, review_surgery_her2_grade, review_surgery_fish, review_surgery_ki67 = \
BlockDescription.ihc_report('review_surgery')
data_list = [review_surgery_date, review_surgery_source, review_surgery_diagnosis,
review_surgery_diagnosis_comment, review_surgery_block_id, review_surgery_er,
review_surgery_er_percent, review_surgery_pr, review_surgery_pr_percent, review_surgery_her2,
review_surgery_her2_grade, review_surgery_fish, review_surgery_ki67]
col_list = names(module_name)
check = sql.review_input(self.file_number, col_list[:-2], data_list)
data = data_list + [self.user_name, sql.last_update()]
return data
def add_path_report(self, table):
file_number = 'test'
table_type = table.split("_")[0]
folder_next = True
while folder_next:
check = False
while not check:
file_number = input("File Number: ")
print("File Number: " + file_number)
check = ask.ask_y_n("Is this file number correct")
block_list_table = BlockInformation(self.conn, self.cursor,
file_number)
pk, block_id, number_of_blocks = block_list_table.get_block_pk(
self.user_name, col_filter_value=table_type)
#print(block_id, number_of_blocks)
check_path_report_entry(conn=self.conn,
cursor=self.cursor,
file_number=file_number,
table_to_check=table,
pk=pk,
block_id=block_id,
number_of_blocks=number_of_blocks,
user_name=self.user_name)
folder_next = ask.ask_y_n("Add/update another file for table " +
table + "?")
def add_data(self):
col_list = names(self.module_list[0])
enter = ask.ask_y_n("Enter " + self.print_statements[0])
if enter:
data = self.surgery_block_information_0()
sql.update_multiple_key(self.conn, self.cursor, self.table_name, col_list, key_name='fk', key_value=self.fk,
data=data)
col_list = names(self.module_list[1])
enter = ask.ask_y_n("Enter " + self.print_statements[1])
if enter:
data, block_desc_df = self.surgery_block_information_1
sql.update_multiple_key(self.conn, self.cursor, self.table_name, col_list, key_name='fk', key_value=self.fk,
data=data)
block_desc_df.to_sql("block_data", self.conn, index=False, if_exists="append")
col_list = names(self.module_list[2])
enter = ask.ask_y_n("Enter " + self.print_statements[2])
if enter:
data = self.surgery_block_information_2()
sql.update_multiple_key(self.conn, self.cursor, self.table_name, col_list, key_name='fk', key_value=self.fk,
data=data)
col_list = names(self.module_list[3])
enter = ask.ask_y_n("Enter " + self.print_statements[3])
if enter:
data = self.surgery_block_information_3()
sql.update_multiple_key(self.conn, self.cursor, self.table_name, col_list, key_name='fk', key_value=self.fk,
data=data)
def add_data(conn, cursor, file_number, user_name):
table = "radiology"
#file_row(cursor, file_number)
enter = ask_y_n("Enter Mammography Report?")
if enter:
data = mammography(conn, cursor, file_number)
add_update_sql.update_multiple(conn, cursor, table,
names("mammography"), file_number, data)
enter = ask_y_n("Enter 3D Tomosynthesis?")
if enter:
data = tomosynthesis(file_number)
add_update_sql.update_multiple(conn, cursor, table,
names("tomosynthesis"), file_number,
data)
enter = ask_y_n("Enter Automated Breast Volume Scanner")
if enter:
data = abvs(file_number)
add_update_sql.update_multiple(conn, cursor, table, names("abvs"),
file_number, data)
enter = ask_y_n("Enter Sono-Mammography")
if enter:
data = sonomammo(conn, cursor, file_number)
add_update_sql.update_multiple(conn, cursor, table, names("sonomammo"),
file_number, data)
enter = ask_y_n("Enter MRI-Breast")
if enter:
data = mri_breast(conn, cursor, file_number, user_name)
add_update_sql.update_multiple(conn, cursor, table,
names("mri_breast"), file_number, data)
def add_block_list(self):
block_list = NewBlock(self.conn, self.cursor, self.user_name)
add_data = True
while add_data:
categories = ['Add Block', 'Edit Block', 'Exit']
new_update = ask.ask_list('you want to do?', categories)
if new_update == 'Edit Block':
block_list.edit_data()
add_data = ask.ask_y_n(
'Do you want to add/edit another block?')
elif new_update == 'Add Block':
file_number = 'test'
check_file = False
while not check_file:
file_number = input("Enter File Number: ")
print("File Number: " + file_number)
check_file = ask.ask_y_n("Is this file number correct")
if not sql.check_file_number_exist(
self.cursor, file_number, table='block_list'):
block_list.add_data(file_number)
else:
print(
'This file_number already exists. Add a new block if for '
+ file_number)
block_type = ask.ask_list('Block type',
['biopsy', 'surgery'])
block_list.add_new_pk(file_number, block_type)
add_data = ask.ask_y_n(
'Do you want to add/edit another block?')
else:
add_data = False
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
sql.insert(conn, cursor, table_cancer, col, data)
print("Please enter the type of treatment used: ")
treat_list = []
type_list = []
duration_list = []
treated, type, duration = ("NA", ) * 3
for treatment in PatientInfo.previous_cancer_treatment:
treat = ask_y_n(treatment)
if treat:
treat_list.append(treatment)
type_treat = input("Type of " + treatment)
type_list.append(type_treat)
duration_treat = input("Duration of " + treatment)
duration_list.append(duration_treat)
data = treatment, type_treat, duration_treat
columns = [
treatment, ("type_" + treatment), ("duration_" + treatment)
]
treated = "; ".join(treat_list)
type = "; ".join(type_list)
duration = "; ".join(duration_list)
sql.update_multiple(conn, cursor, table_cancer, columns,
file_number, data)
elif not treat:
index_no = "No " + treatment
type_treat, duration_treat = ("NA", ) * 2
data = index_no, type_treat, duration_treat
columns = [
treatment, ("type_" + treatment), ("duration_" + treatment)
]
sql.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 metastasis(file_number, user_name):
check = False
while not check:
met_has = ask.ask_y_n(
"Has the patient been examined for metastatic disease?")
if not met_has:
met_has = "Not examined for metastatic disease"
else:
met_has = "Examined for metastatic disease"
date_last = ask.check_date("Date of last follow-up: ")
recur = ask.ask_y_n("Has the patient experienced a recurrence?")
if recur:
time_recur = input("Time to disease recurrence: ")
nature_recur = ask.ask_option("Nature of recurrence",
["Distant", "Local", "Other"])
if nature_recur == "Distant":
distant_site = input("Site of distant recurrence: ")
else:
distant_site = "NA"
else:
time_recur, nature_recur, distant_site = ("NA", ) * 3
status = patient_status()
data_list = [
met_has, date_last, time_recur, nature_recur, distant_site, status,
user_name,
last_update()
]
col_list = names.names_longterm("metastasis")
check = review_input(file_number, col_list, data_list)
return data_list
def clinical_tests():
other_tests = {'USG Abdomen': ['Abnormal'],
'CECT Abdomen and Thorax': ['Visceral Metastasis'],
'PET Scan': ['Visceral Metastasis', 'Skeletal Metastasis'],
'Bone Scan': ['Skeletal Metastasis']}
test_key = list(other_tests.keys())
data_list = []
for test in test_key:
test_name = test
test_done = ask.ask_y_n("Has "+test_name+" been done?")
if test_done:
test_done = test_name+" done"
data_list.append(test_done)
abnormal = other_tests[test]
for diagnosis in abnormal:
test_diag = ask.ask_y_n('Is the result ' + diagnosis + '?')
if test_diag:
test_details = input("Please provide details of "
+ diagnosis + " diagnosis: ")
else:
diagnosis = 'Normal'
test_details = "NA"
data_list.append(diagnosis)
data_list.append(test_details)
else:
test_done = test_name+"_not_done"
data_list.append(test_done)
abnormal = other_tests[test]
for i in range(2*len(abnormal)):
i = 'NA'
data_list.append(i)
return data_list
def edit_table(df, pk_col, df_col):
import helper_function.ask_y_n_statement as ask
rows = (df.shape)[0]
for row in range(0,rows):
print(df.iloc[row].to_string()+'\n')
to_correct = ask.ask_y_n("Are entries correct?")
if not to_correct:
to_correct = ask.ask_y_n("Re-enter entire table?")
if to_correct:
return to_correct, df
else:
change_row = True
while change_row:
pk_list = list(df[pk_col])
print(pk_list)
pk = input("Enter " + pk_col + " to change: ")
index = pk_list.index(id)
to_do = True
while to_do:
print(df.loc[index, :])
col_change = ask.ask_option("Name of column to change", df_col)
old_val = df.loc[index, col_change]
print(old_val + '\n')
new_val = input("Enter correct value for " + col_change + ' for ' + pk + ": ")
df.loc[index, col_change] = new_val
print(df.iloc[index].to_string() + '\n')
to_do = ask.ask_y_n("Make more changes to " + pk_col + ' ' + pk + '?')
print_df(df)
change_row = ask.ask_y_n("Change another row?")
to_correct = False
return to_correct, df
def add_data(self):
pk = uuid.uuid4().hex
sql.add_pk_fk_to_table(self.conn,
self.cursor,
self.table_name,
col_name='pk',
pk=pk)
pet_present = ask.ask_y_n(
"Does the patient file contain a PET/CT report to be entered?")
if not pet_present:
data_length = len(self.col_list_all) - 3
data = [self.file_number
] + ['pet_report_not_present'] * data_length + [
self.user_name, sql.last_update()
]
sql.update_multiple_key(self.conn,
self.cursor,
self.table_name,
self.col_list_all,
key_name='pk',
key_value=pk,
data=data)
else:
print(self.print_statements[0])
col_list = names(self.module_list[0])
enter = ask.ask_y_n("Enter " + self.print_statements[0])
if enter:
data = self.pet_report_identifier()
sql.update_multiple_key(self.conn,
self.cursor,
self.table_name,
col_list,
key_name='pk',
key_value=pk,
data=data)
col_list = names(self.module_list[1])
enter = ask.ask_y_n("Enter " + self.print_statements[1])
if enter:
data = self.pet_report_findings()
sql.update_multiple_key(self.conn,
self.cursor,
self.table_name,
col_list,
key_name='pk',
key_value=pk,
data=data)
enter = ask.ask_y_n("Enter " + self.print_statements[2])
col_list = names(self.module_list[2])
if enter:
data = self.pet_breast_cancer()
sql.update_multiple_key(self.conn,
self.cursor,
self.table_name,
col_list,
key_name='pk',
key_value=pk,
data=data)
def node_excision (file_number):
check = False
while not check:
surgery_guide, frozen, gross_tumour, skin, nodes, number_lymph, level_lymph, sentinel_method, sentinel_blue, \
sentinel_hot, sentinel_blue_hot, sentinel_non_blue_hot, sentinel_palpable = (" ",)*13
guide_add = True
guide = []
while guide_add:
surgery_guide = ask_option("Excision guided by",
["Palpation", "USG guided", "Wire placement guided", 'Gamma camera guided',
'Clipped node'])
guide.append(surgery_guide)
guide_add = ask_y_n("Add another method to guide?")
surgery_guide = "; ".join(guide)
frozen_samples = ask_option_y_n("Any samples sent for histopathology (frozen)?")
if frozen_samples == 'Yes':
frozen_samples = []
sn_frozen = ask_y_n("Sentinel Node sent for histopathology (frozen)?", yes_ans="Sentinel Node")
if sn_frozen == 'Sentinel Node':
frozen_samples.append(sn_frozen)
specimen_frozen = ask_y_n_na("Specimen sent for histopathology (frozen)?")
if specimen_frozen == 'Yes':
nipple_frozen = ask_y_n_na("Under Nipple Surface sent for histopathology (frozen)?",
yes_ans='Under Nipple Surface')
if nipple_frozen == 'Under Nipple Surface':
frozen_samples.append(nipple_frozen)
other_frozen = ask_y_n_na("Any other specimen sent for histopathology (frozen)?")
if other_frozen == 'Yes':
other_frozen = input("Type of tissue sent for histopathology (frozen): ")
frozen_samples.append(other_frozen)
frozen = "; ".join(frozen_samples)
else:
frozen = "NA"
gross_tumour = input ("Size of tumour on cross section (cm): ")
skin = ask_option_y_n("Skin involved", yes_ans="Skin involved", no_ans="Skin not involved")
nodes = ask_option("Nodes excised", ["Sentinel Node", "Sentinel and Axillary Nodes", "Axillary Nodes only",
"Other"])
number_lymph = input("Number of lymph nodes excised (if available): ")
level_lymph = ask_option("Level of lymph node excised", ["I", "II", "III", "Data not available", "Other"])
if nodes == 'Axillary Nodes only':
sentinel_method, sentinel_blue, sentinel_hot, sentinel_blue_hot, sentinel_non_blue_hot, sentinel_palpable = \
('No Sentinel Node excised', )*6
else:
sentinel_method = ask_option("Method of labelling Sentinel Node", ["Isotope", "Blue Dye", "Isotope + Blue Dye",
"Not done", "Other"])
sentinel_blue = ask_option_y_n("Blue Node", yes_ans="Blue Node", no_ans="No Blue Node")
sentinel_hot = ask_option_y_n("Hot Node", yes_ans="Hot Node", no_ans="No Hot Node")
sentinel_blue_hot = ask_option_y_n("Blue Hot Node", yes_ans="Blue Hot Node", no_ans="No Blue Hot Node")
sentinel_non_blue_hot = ask_option_y_n("Non Blue, Hot Node", yes_ans= "Non Blue, Hot Node",
no_ans="No Non Blue, Hot Node")
sentinel_palpable = ask_option_y_n("Palpable Node", yes_ans="Palpable Node", no_ans="No Palpable Node")
data_list = [surgery_guide, frozen, gross_tumour, skin, nodes, number_lymph, level_lymph, sentinel_method,
sentinel_blue, sentinel_hot, sentinel_blue_hot, sentinel_non_blue_hot, sentinel_palpable]
col_list = names("node_excision")
check = add_update_sql.review_input(file_number, col_list, data_list)
return data_list
def add_insert():
import sqlite3
import helper_function.ask_y_n_statement as ask
import sql.add_update_sql as add_update_sql
from datetime import datetime
import os
import textwrap
from helper_function.pccm_names import db_tables
folders = "d:/repos/pccm_db/main/DB"
file = 'PCCM_BreastCancerDB_check_new_all_2_2019-05-27.db'
#file = 'PCCM_BreastCancerDB_all_data_rituja_surgery_data.db'
check_path = False
while not check_path:
print('\nDatabase file ' + file + ' in folder ' + folders +
' is being used\n')
check_location = ask.ask_y_n('Is this correct?')
if not check_location:
print("\n File is currently set as " + file)
file = input(
'Please enter database file name (with .db extension): ')
print("\n Folder is currently set as " + folders)
folders = input(
'Please enter database folder name (full path as given above): '
)
else:
check_path = True
path = os.path.join(folders, file)
if os.path.isfile(path):
conn = sqlite3.connect(path)
cursor = conn.cursor()
user_name = input("Please input username/user_id: ")
folder_next = True
files_table_added = []
while folder_next:
check = False
while not check:
file_number = input("File Number: ")
print("File Number: " + file_number)
check = ask.ask_y_n("Is this file number correct")
check_table = True
while check_table:
table = ask.ask_list("Table", db_tables())
file_table = file_number + "-" + table
files_table_added.append(file_table)
check_table = add_update_sql.check_file(
conn, cursor, table, file_number, user_name, folders, file)
folder_next = ask.ask_y_n("Add/update another record?")
else:
note = "current path: '" + path + "' to database is not valid. Check path and database name and run " \
"start_pccm_db() again."
wrapper = textwrap.TextWrapper(width=100)
string = wrapper.fill(text=note)
print(string)
def pet_breast_cancer(self):
module_name = self.module_list[2]
breast_report = [
'NA',
] * 7
check = False
while not check:
pet_breast = ask.ask_y_n(
'Does this report describe a breast cancer?')
if pet_breast:
print('\nPlease describe primary breast lesion\n')
pet_breast_lesion_size = input(
'Dimensions of breast lesion/s: ')
pet_breast_lesion_size_unit = ask.ask_list(
'Unit of breast lesion size', ['mm', 'cm'])
pet_breast_lesion_suv = ask.check_number_input(
'Please enter SUV max of breast lesion: ',
'Please enter only SUV not description')
pet_breast_lesion_location = input(
'Please enter description of lesion location: ')
pet_breast_lesion_type = input(
'Please input description of lesion: ')
pet_breast_lesion_comments = input(
'Please input any additional notes for breast lesion: ')
pet_breast_nodes = ask.ask_y_n(
'Does the report describe breast related nodes?')
if pet_breast_nodes:
pet_breast_nodes_description = input(
'Please enter nodes description as given: ')
else:
pet_breast_nodes_description = 'nodes_not_described'
pet_breast_skin = ask.ask_y_n(
'Does the PET report describe any skin changes?')
if pet_breast_skin:
pet_breast_lesion_skin = input(
'Please enter description of skin changes: ')
else:
pet_breast_lesion_skin = 'skin_changes_not_described'
else:
pet_breast_lesion_size, pet_breast_lesion_size_unit, pet_breast_lesion_suv, pet_breast_lesion_location,\
pet_breast_lesion_type, pet_breast_lesion_comments, pet_breast_nodes_description, \
pet_breast_lesion_skin = ['no_breast_cancer', ] * 8
breast_report = [
pet_breast_lesion_size, pet_breast_lesion_size_unit,
pet_breast_lesion_suv, pet_breast_lesion_location,
pet_breast_lesion_type, pet_breast_lesion_comments,
pet_breast_nodes_description, pet_breast_lesion_skin
]
columns_list = names(module_name)
check = sql.review_input(self.file_number, columns_list[:-2],
breast_report)
data_list = breast_report + [self.user_name, sql.last_update()]
return data_list
def add_data(self):
block_list_table = BlockInformation(self.conn, self.cursor,
self.file_number)
enter = ask.ask_y_n("Enter Biopsy Report information?")
if enter:
data = self.biopsy_report_info()
sql.update_multiple_key(self.conn,
self.cursor,
self.table_name,
names.names_biopsy("biopsy_report_info"),
key_name='pk',
key_value=self.pk,
data=data)
enter = ask.ask_y_n("Enter Biopsy data?")
if enter:
data = self.biopsy_details()
sql.update_multiple_key(self.conn,
self.cursor,
self.table_name,
names.names_biopsy("biopsy_details"),
key_name='pk',
key_value=self.pk,
data=data)
data = self.ihc_biopsy_data()
sql.update_multiple_key(self.conn,
self.cursor,
self.table_name,
names.names_biopsy("ihc_biopsy_data"),
key_name='pk',
key_value=self.pk,
data=data)
data = self.review_biopsy()
sql.update_multiple_key(self.conn,
self.cursor,
self.table_name,
names.names_biopsy("review_biopsy"),
key_name='pk',
key_value=self.pk,
data=data)
is_surgery = ask.ask_y_n(
'Is a surgery associated with this biopsy?')
if is_surgery:
surgery_block_id, surgery_number_of_blocks = block_list_table.get_block_id(
'surgery')
else:
surgery_block_id = 'NA'
sql.update_single_key(self.conn,
self.cursor,
self.table_name,
'surgery_block_id',
key_name='pk',
key_value=self.pk,
var=surgery_block_id)
def tox_table(file_number, drug_cyc, tox_all):
tox_index = 0
check_tox = False
while not check_tox:
tox = ask.ask_y_n(
"Were there any toxic effects in administration of " + drug_cyc)
if tox:
add_tox = True
while add_tox:
check = False
while not check:
tox_present = ask.ask_option("Toxic effects of type",
chemo.toxicity())
tox_grade = ask.ask_option(
("the grade of " + tox_present + "? "),
["Mild", "Moderate", "Severe", "Other"])
treatment = input("Treatment given for " + tox_grade +
" " + tox_present +
" (include all details): ")
resp_treatment = ask.ask_option(
("Response to treatment given for " + tox_grade + " " +
tox_present),
["Partial", "Complete", "No Effect", "Other"])
cyc_tox = input("Cycle at which toxicity occurred: ")
change_tox = ask.ask_option("Changes to treatment", [
"No change", "Therapy changed due to toxicity",
"Therapy "
"stopped due to toxicity", "Therapy changed due "
"to other reasons",
"Therapy stopped due to other reasons"
])
if change_tox == "Therapy changed due to toxicity" or change_tox == "Therapy changed due to other reasons":
change = input("Please describe changes to Therapy: ")
change_tox = change_tox + ": " + change
data = [
file_number, drug_cyc, tox_present, tox_grade, treatment,
resp_treatment, cyc_tox, change_tox
]
tox_all.loc[tox_index] = data
check = review_df_row(tox_all)
tox_index = tox_index + 1
add_tox = ask.ask_y_n('Add another toxicity type?')
else:
tox_present, tox_grade, treatment, resp_treatment, cyc_tox,
change_tox = ("No Toxicity", ) * 6
data = [
file_number, drug_cyc, tox_present, tox_grade, treatment,
resp_treatment, cyc_tox, change_tox
]
tox_all.loc[tox_index] = data
check_tox = review_df(tox_all)
return tox_all
def add_data(conn, cursor, file_number, user_name):
#file_row(cursor, file_number)
table = "hormonetherapy_survival"
enter = ask.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.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 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 review_data_key(conn, cursor, table, key_name, key_value, columns, col_name, col_value):
if 'file_number' in columns:
# remove 1st position from column names (assumes it is file_number)
col_list = columns[1:]
else:
col_list = columns
sql_statement = 'SELECT ' + ", ".join(col_list) + ' FROM ' + table + " WHERE " + key_name + "= '" + key_value + "'"
data = cursor.execute(sql_statement)
data_list = data.fetchall()
if not data_list:
print("This " + col_name + ' ' + col_value + ' has not been entered in ' + table)
enter = ask.ask_y_n("Do you want to enter now")
if enter:
add_pk_fk_to_table(conn, cursor, table, col_name=key_name, pk=key_value)
print('added new row for this ' + key_name)
return enter
else:
data_list = list(data_list[0])
col_number = len(col_list)
if data_list == [None]*len(data_list):
print("This section of the database has not been entered")
enter = ask.ask_y_n("Do you want to enter now")
return enter
elif None in set(data_list):
print("Some entries are missing from the database: ")
for index in range(0, col_number):
print(col_list[index] + " : " + str(data_list[index]))
enter = ask.ask_option("Do you want to proceed?", ["Edit all", "Add new data only"])
if enter == "Edit all":
return True
else:
enter = edit_few(conn, cursor, table, col_list, key_value, data_list)
return enter
else:
print("Entries present in database are as follows : ")
for index in range(0, col_number):
print(col_list[index] + " : " + str(data_list[index]))
enter = ask.ask_option("Do you want to", ["Edit all", "Edit some entries", "Edit None"])
if enter == "Edit some entries":
for index in range(0, col_number):
print(col_list[index] + " : " + str(data_list[index]))
edit = ask.ask_y_n("Edit")
if edit:
data = input("Data for " + col_list[index] + ": ")
update_single_pk(conn, cursor, table, col_list[index], pk_value=key_name, pk=key_value, var=data)
return False
elif enter == "Edit all":
return True
else:
return False
def add_data(conn, cursor, file_number, user_name):
table = "surgery_seport"
#file_row(cursor, file_number)
enter = ask_y_n("Do you want to enter Surgery Information?")
if enter:
data = surgery_information(file_number)
add_update_sql.update_multiple(conn, cursor, table, names("surgery_information"), file_number, data)
enter = ask_y_n("Do you want to enter dnter Node Excision Information?")
if enter:
data = node_excision(file_number)
add_update_sql.update_multiple(conn, cursor, table, names("node_excision"), file_number, data)
enter = ask_y_n("Do you want to enter details of Post-Surgery management (plans and complications)?")
if enter:
data = post_surgery(file_number, user_name)
add_update_sql.update_multiple(conn, cursor, table, names("post_surgery"), file_number, data)
def drug_table_enter(file_number, drug_table):
drug_add = True
drug_index = 0
while drug_add:
check_drug = False
while not check_drug:
drugs_administered = ask.ask_option("Drug used for therapy",
chemo.drug_list())
dose_check = ask.ask_y_n('Is the drug dose available?')
if dose_check:
dose = ask.check_number_input(
"Dose of " + drugs_administered + ':',
'Please input dose amount'
'without unit')
if dose == 'NA':
dose_unit = 'NA'
else:
dose_unit = input("Dose unit: ")
else:
dose, dose_unit = [
'NA',
] * 2
cycle_check = ask.ask_y_n('Is the drug cycle available?')
if cycle_check:
cycle_frequency_per_week = ask.check_number_input(
"Cycle Frequency: ", 'Please enter frequency per '
'week, so three weekly is 3 and '
'weekly is 1')
number_cycle = ask.check_number_input(
"Number of cycles actually given: ",
'Please enter numbers only')
else:
cycle_frequency_per_week, number_cycle = [
'NA',
] * 2
drug_dose = 'NA'
if number_cycle != 'NA' and dose != 'NA':
drug_dose = float(dose) * int(number_cycle)
data_drug = [
file_number, drugs_administered, number_cycle,
cycle_frequency_per_week,
str(drug_dose), dose_unit
]
drug_table.loc[drug_index] = data_drug
check_drug, drug_table = review_df_row(drug_table)
drug_index = drug_index + 1
drug_add = ask.ask_y_n("Add another drug")
return drug_table
def create_block_id(blocks_total):
block_id_list = []
frozen = ask.ask_y_n('Are frozen sections (labelled FS) present?')
no_frozen = 0
if frozen:
no_frozen = int(input('Number of frozen sections: '))
frozen_list = [str(x) for x in range(no_frozen + 1)]
frozen_id = ['FS-' + s for s in frozen_list[1:]]
else:
frozen_id = []
blocks = blocks_total - no_frozen
block_id_chunks = list(divmod(blocks, 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)
block_id_list = block_id_list + frozen_id
print(", ".join(block_id_list))
check_list = ask.ask_y_n("Is block list correct?")
while not check_list:
block_id_list = []
check = ask.ask_y_n('Is Frozen series correct?')
if not check:
for i in range(blocks_total):
block_id = input('Block id of block number ' + str(i + 1) +
': ')
block_id_list.append(block_id)
else:
block_id_list = frozen_id
for i in range(blocks):
block_id = input('Block id of block number ' + str(i + 1) +
': ')
block_id_list.append(block_id)
print((", ").join(block_id_list))
check_list = ask.ask_y_n("Is block list correct?")
return block_id_list
def family_cancer_table(conn, cursor, file_number):
add_family = True
type_cancer_list, relation_degree_list, type_relation_list, age_detect_list = [], [], [], []
all_data = []
while add_family:
type_of_cancer = input("Type of Cancer: ")
type_cancer_list.append(type_of_cancer)
relation_to_patient = ask_option("Relation to patient",
PatientInfo.family)
relation_degree_list.append(relation_to_patient)
type_relation = input("Specific Relationship:")
type_relation_list.append(type_relation)
age_at_detection_yrs = input('Age at detection (yrs) :')
age_detect_list.append(age_at_detection_yrs)
family_history = file_number, type_of_cancer, relation_to_patient, type_relation, age_at_detection_yrs
family_history_list = "; ".join([
type_of_cancer, relation_to_patient, type_relation,
age_at_detection_yrs
])
all_data.append(family_history_list)
columns = 'file_number, type_cancer, relation_to_patient, type_relation, age_at_detection_yrs'
table = "family_cancer_history"
sql.insert(conn, cursor, table, columns, family_history)
add_family = ask_y_n("Add more family cancer history? ")
all_data_flat = "|".join(all_data)
return (all_data_flat)
def add_data(conn, cursor, file_number, user_name):
table = "clinical_exam"
#file_row(cursor, file_number)
enter = ask.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.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)
def review_input (file_number, columns, data):
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.ask_y_n("Are entries for file "+ file_number+ " correct ?", True, False)
return ans
def get_folder_name():
folders = "d:/repos/pccm_db/main/DB"
file = 'PCCM_BreastCancerDB_2019_07_03.db'
check_path = False
path = os.path.join(folders, file)
while not check_path:
print('\nDatabase file ' + file + ' in folder ' + folders +
' is being used\n')
check_location = ask.ask_y_n('Is this correct?')
if not check_location:
print("\n File is currently set as " + file)
file = input(
'Please enter database file name (with .db extension): ')
print("\n Folder is currently set as " + folders)
folders = input(
'Please enter database folder name (full path as given above): '
)
path = os.path.join(folders, file)
if os.path.isfile(path):
check_path = True
else:
note = "current path: '" + path + "' to database is not valid. Check path and database name and enter " \
"again"
wrapper = textwrap.TextWrapper(width=100)
string = wrapper.fill(text=note)
print(string)
user_name = input("Please input username/user_id: ")
return folders, file, user_name
def mri_mass(self, mass_id):
check = False
data_list = ask.default_data_list(self.col_list)
while not check:
if self.mammo_breast == "bilateral":
mass_location = ask.ask_option("Location of mass " + str(
mass_id), RadioTables.breast)
else:
mass_location = self.mammo_breast
check_t1_t2 = ask.ask_y_n('Are both T1 and T2 image analysis'
'available for this mass?')
type_of_imaging = ['T1', 'T2']
if not check_t1_t2:
type_of_imaging = ask.ask_list('Observation of this mass is a'
'result of which type of'
'imaging? ',
RadioTables.mri_image_type)
data_list = self.mri_mass_detail(type_of_imaging, mass_id)
if type_of_imaging in {'T1', 'T2'}:
data_list = [('{0}_{1}'.format(type_of_imaging, data)) for
data in data_list]
mass_name = "Lesion " + str(mass_id)
data_list = [self.file_number, mass_location, mass_name]+data_list
check = sql.review_input(self.file_number, columns=self.col_list,
data=data_list)
data_list = [data_list] + [self.user_name, sql.last_update()]
data_list = data_list + [self.user_name, sql.last_update()]
return data_list
def check_file(conn, cursor, table, file_number, user_name, folders, file):
from add_edit.edit_record import edit_record
from add_edit.add_new import add_new
from reports.radiology import Radiology
if table != 'radiology':
sql_statement = "SELECT rowid FROM " + table + " WHERE file_number = ?"
cursor.execute(sql_statement, (file_number, ))
data = cursor.fetchall()
if len(data) == 0:
if table not in {"follow_up_data", "pet_reports", 'radiology'}:
cursor.execute("INSERT INTO " + table + "(file_number) VALUES ('" + file_number + "')")
print(file_number + " does not exist in table " + table + ". Enter new record")
add_new(conn, cursor, file_number, table, user_name, folders, file)
else:
todo = ask.ask_list(file_number + " already exists in table " + table + ".", ["Edit record",
"Add new record for same file number",
"Edit None"])
if todo == "Edit record":
edit_record(conn, cursor, file_number, table, user_name, folders, file)
elif todo == "Add new record for same file number":
print("Add additional record module TBD")
ask_table = ask.ask_y_n("Add another table?")
else:
radio = Radiology(conn, cursor, file_number, user_name)
tables = radio.tables
for tab in tables:
ask_table = True
while ask_table:
sql_statement = "SELECT rowid FROM " + tab + " WHERE file_number = ?"
cursor.execute(sql_statement, (file_number, ))
dat = cursor.fetchall()
if len(dat) == 0:
print(file_number + " does not exist in table " + tab)
enter_tab = ask.ask_y_n('Enter data?')
if enter_tab:
cursor.execute("INSERT INTO " + tab + "(file_number) VALUES ('" + file_number + "')")
add_new(conn, cursor, file_number, tab, user_name, folders, file)
else:
todo = ask.ask_list(file_number + " already exists in table " + tab + ".", ["Edit record", "Edit None"])
if todo == "Edit record":
edit_record(conn, cursor, file_number, tab, user_name, folders, file)
# data.append(dat)
# print(data, 'length data is =', len(data))
# # remove later - test_function
ask_table = ask.ask_y_n("Add another data set for " + tab + "?")
return ask_table
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_ffpe(self):
table_next = True
while table_next:
table = AddBlockData.get_table()
if table == ffpe_db_tables()[0]:
self.add_block_list()
else:
self.add_path_report(table)
table_next = ask.ask_y_n("Add/update another table?")
def add_data(self):
add_block = True
while add_block:
data = self.add_update_patient()
data.to_sql("block_list",
self.conn,
index=False,
if_exists="append")
add_block = ask.ask_y_n('Add another block?')
