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 edit_data(conn, cursor, file_number, user_name):
table = "clinical_exam"
print("Initial Clinical Examination")
col_list = pccm_names.name_clinical("clinical_exam_initial")
enter = add_update_sql.review_data(conn, cursor, table, file_number,
col_list)
if enter:
data = clinical_exam_initial(file_number, user_name)
add_update_sql.update_multiple(conn, cursor, table, col_list,
file_number, data)
print("Nipple Cytology")
col_list = pccm_names.name_clinical("nipple_cytology")
enter = add_update_sql.review_data(conn, cursor, table, file_number,
col_list)
if enter:
data = nipple_cytology(file_number)
add_update_sql.update_multiple(conn, cursor, table, col_list,
file_number, data)
def other_test(file_number):
module_name = "other_test"
other_tests = [["USG Abdomen", "Abnormal"],
["CECT Abdomen and Thorax", "Visceral Metastasis"],
["PET Scan", "Visceral Metastasis", "Skeletal Metastasis"],
["Bone Scan", "Skeletal Metastasis"]]
check = False
while not check:
data_all = []
for index in other_tests:
data = clinical_tests(index)
data_all.append(data)
data_all_flat = [item for sublist in data_all for item in sublist]
col_list = pccm_names.name_clinical(module_name)
check = add_update_sql.review_input(file_number, col_list,
data_all_flat)
return data_all_flat
def nipple_cytology(file_number):
module_name = "nipple_cytology"
check = False
while not check:
cyto = ask.ask_option("Nipple Cytology", ["Done", "Not Done"])
if cyto == "Not Done":
cyto_date, cyto_number, cyto_report = ("NA", ) * 3
else:
cyto_date = input("Date of nipple cytology: ")
cyto_number = input("Nipple Cytology number: ")
cyto_report = ask.ask_option(
"Nipple Cytology report and interpretation",
["Normal", "Suspicious", "Diagnostic for "
"Cancer", "Other"])
data_list = [cyto, cyto_date, cyto_number, cyto_report]
columns_list = pccm_names.name_clinical(module_name)
check = add_update_sql.review_input(file_number, columns_list,
data_list)
return (tuple(data_list))
def clinical_exam_initial(file_number, user_name):
module_name = "clinical_exam_initial"
check = False
while not check:
# con_stat = ask.ask_y_n("Has consent been taken from patient?", "Consent Taken", "No Consent")
# if con_stat == "Consent Taken":
# con_form = ask.ask_y_n("Is consent form with signature present in file ?",
# "Consent form with signature present in folder",
# "Completed consent form not present in folder")
# else:
# con_form = "NA"
prov_diag = input("Provisional Diagnosis: ")
options = ["Definite", "Vague", "Diffuse", "Nil", "Other"]
lump_palp = ask.ask_option("Palpable lump in the breast?", options)
lump_location = ask.ask_option(
"Location of lump",
["Right Breast", "Left Breast", "Both", "Not present"])
lump_location_data = []
if lump_location == "Right Breast" or lump_location == "Both":
category = "Lump location on Right Breast"
options = ["UOQ", "UIQ", "C", "UCQ", "LCQ", "LOQ", "LIQ"]
lump_location_rb = ask.ask_option(category, options)
lump_location_rb_data = "RB-" + lump_location_rb
lump_location_data.append(lump_location_rb_data)
if lump_location == "Left Breast" or lump_location == "Both":
category = "Lump location on Left Breast"
options = ["UOQ", "UIQ", "C", "UCQ", "LCQ", "LOQ", "LIQ"]
lump_location_lb = ask.ask_option(category, options)
lump_location_lb_data = "LB-" + lump_location_lb
lump_location_data.append(lump_location_lb_data)
lump_location_data = "; ".join(lump_location_data)
if lump_location == "Not present":
lump_location_data = "Lump " + lump_location
lump_size, lump_number, lump_consistency, lump_fixity = (
"NA", ) * 4
else:
lump_size = ask.ask_option("Lump size",
["< 2cm", "2-5 cm", ">5 cm"])
lump_number = ask.ask_option("Number of lumps",
["Single", "Multiple", "Other"])
lump_consistency = ask.ask_option(
"Consistency of lumps",
["Soft", "Firm", "Hard", "Cystic", "Mobile", "Other"])
lump_fixity = ask.ask_option("Lump fixity to ", [
"Skin", "Chest wall", "Pectoral major muscle", "No Fixation",
"Other"
])
mastitis_location = ask.ask_option(
"Location of mastitis",
["Right Breast", "Left Breast", "Both", "Not present"])
mastitis_location_data = []
if mastitis_location == "Right Breast" or mastitis_location == "Both":
category = "Mastitis location on Right Breast"
options = ["UOQ", "UIQ", "C", "UCQ", "LCQ", "LOQ", "LIQ"]
mastitis_location_rb = ask.ask_option(category, options)
mastitis_location_rb_data = "RB-" + mastitis_location_rb
mastitis_location_data.append(mastitis_location_rb_data)
if mastitis_location == "Left Breast" or mastitis_location == "Both":
category = "Mastitis location on Left Breast"
options = ["UOQ", "UIQ", "C", "UCQ", "LCQ", "LOQ", "LIQ"]
mastitis_location_lb = ask.ask_option(category, options)
mastitis_location_lb_data = "LB-" + mastitis_location_lb
mastitis_location_data.append(mastitis_location_lb_data)
mastitis_location_data = "; ".join(mastitis_location_data)
if mastitis_location == "Not present":
mastitis_location_data = "mastitis " + mastitis_location
mastitis_type = "NA"
else:
mastitis_type = ask.ask_option("Mastitis type",
["Diffuse", "Sectoral", "Other"])
tender = ask.ask_option(
"Tenderness in breast ?",
["Right Breast", "Left Breast", "Both", "Not Present", "Other"])
retract = ask.ask_option(
"Nipple Retraction ?",
["Right Breast", "Left Breast", "Both", "Not Present", "Other"])
discharge = ask.ask_option(
"Nipple Discharge ?",
["Right Breast", "Left Breast", "Both", "Not Present", "Other"])
if discharge == "Not Present":
discharge_type = "NA"
else:
discharge_type = ask.ask_option(
"Discharge Type?",
["Serous", "Milky", "Brown", "Bloody", "Other"])
skin_change_location = ask.ask_option(
"Skin Changes?",
["Right Breast", "Left Breast", "Both", "Not Present", "Other"])
if skin_change_location == "Not Present":
skin_change_type = "NA"
else:
skin_change = []
change_add = True
while change_add:
skin_change_type = ask.ask_option("Type of skin change?", [
"Dimpling", "Ulceration", "Discolouration", "Eczema",
"Edema", "Redness", "Peau d'orange", "Other"
])
skin_change.append(skin_change_type)
change_add = ask.ask_y_n("Enter another type of skin change?")
skin_change_type = "; ".join(skin_change)
ax_nodes = ask.ask_option(
"Palpable axillary nodes",
["Right Breast", "Left Breast", "Both", "Not palpable", "Other"])
if ax_nodes == "Not palpable":
ax_nodes_number, ax_nodes_size, ax_nodes_fixity = ("NA", ) * 3
else:
ax_nodes_number = input("Number of nodes: ")
ax_nodes_size = input("Size of nodes: ")
ax_nodes_fixity = ask.ask_y_n("Fixity of axillary nodes", "Yes",
"No")
supra_nodes = ask.ask_option(
"Palpable supraclavicular nodes",
["Right Breast", "Left Breast", "Both", "Not palpable", "Other"])
if supra_nodes == "Not palpable":
supra_nodes_number, supra_nodes_size, supra_nodes_fixity = (
"NA", ) * 3
else:
supra_nodes_number = input("Number of nodes: ")
supra_nodes_size = input("Size of nodes: ")
supra_nodes_fixity = ask.ask_y_n("Fixity of supraclavicular nodes",
"Yes", "No")
contra_breast = ask.ask_option(
"Contralateral Breast",
["Normal", "Diffuse Mastitis", "Localised Mastitis", "Other"])
arm_edema = ask.ask_option(
"Edema of arm", ["Right", "Left", "Both", "Not Present", "Other"])
arm_circ_right = input("Circumference of right arm (cm): ")
arm_volume_right = input("Upper limb volume - right arm (cc): ")
arm_elbow_right = input("Distance from the elbow - right arm (cm): ")
arm_circ_left = input("Circumference of left arm (cm): ")
arm_volume_left = input("Upper limb volume - left arm (cc): ")
arm_elbow_left = input("Distance from the elbow - left arm (cml): ")
follow_up_advised = input("Follow up tests advised for patient: ")
data_list = [
prov_diag, lump_palp, lump_location_data, lump_size, lump_number,
lump_consistency, lump_fixity, mastitis_location_data,
mastitis_type, tender, retract, discharge, discharge_type,
skin_change_location, skin_change_type, ax_nodes, ax_nodes_number,
ax_nodes_size, ax_nodes_fixity, supra_nodes, supra_nodes_number,
supra_nodes_size, supra_nodes_fixity, contra_breast, arm_edema,
arm_circ_right, arm_volume_right, arm_elbow_right, arm_circ_left,
arm_volume_left, arm_elbow_left, follow_up_advised, user_name,
add_update_sql.last_update()
]
columns_list = pccm_names.name_clinical(module_name)
check = add_update_sql.review_input(file_number, columns_list,
data_list)
return (tuple(data_list))
def makedb(self):
db_create = CreateTable(self.cursor)
file_number = "file_number"
table = "patient_information_history"
module_list = [
"bio_info", "phys_act", "habits", "nut_supplements",
"family_details", "med_history", "cancer_history", 'family_cancer',
'det_by', "breast_symptoms", 'other_test'
]
col_names = [pccm_names.names_info(module) for module in module_list]
col_list = ask.flatten_nested_list(col_names)
db_create.create_table(table,
file_number=file_number,
col_names=col_list)
table = "biopsy_path_report"
module_list = [
"biopsy_report_info", "biopsy_details", 'ihc_biopsy_data',
'review_biopsy'
]
col_names = [pccm_names.names_biopsy(module) for module in module_list]
col_list = ask.flatten_nested_list(col_names)
db_create.create_table_pk(table, col_list)
table = 'surgery_path_report_data'
module_list = [
"surgery_block_information_0", "surgery_block_information_1",
"surgery_block_information_2", "surgery_block_information_3"
]
col_names = [
pccm_names.names_surgery(module) for module in module_list
]
col_list = ask.flatten_nested_list(col_names)
db_create.create_table_pk(table, col_list, pk='fk')
table = "block_data"
col_names = pccm_names.names_surgery('block_data')[1:]
db_create.create_table_pk(table, col_names, pk='fk')
table = "mammography"
col_names = pccm_names.names_radio(table)
db_create.create_table_pk(table, col_names)
table = 'abvs'
col_names = pccm_names.names_radio(table)
db_create.create_table_pk(table, col_names)
table = 'ultrasound'
col_names = pccm_names.names_radio(table)
db_create.create_table_pk(table, col_names)
table = 'mri'
col_names = pccm_names.names_radio(table)
db_create.create_table_pk(table, col_names)
table = 'pet_reports'
module_list = [
'pet_report_identifier', 'pet_report_findings', 'pet_breast_cancer'
]
col_names = [pccm_names.names_pet(module) for module in module_list]
col_list = ask.flatten_nested_list(col_names)
db_create.create_table_pk(table, col_list)
table = "surgery_report"
module_list = ["surgery_information", "node_excision", "post_surgery"]
col_names = [
pccm_names.names_surgery_information(module)
for module in module_list
]
col_list = ask.flatten_nested_list(col_names)
db_create.create_table(table,
file_number='file_number',
col_names=col_list)
table = "general_medical_history"
col_names = ['condition', 'diagnosis_date', 'treatment']
# col_list = ask.flatten_nested_list(col_names)
db_create.create_table(table,
file_number='file_number',
col_names=col_names)
table = "family_cancer_history"
col_names = [
'type_cancer', 'relation_to_patient', 'type_relation',
'age_at_detection_yrs'
]
# col_list = ask.flatten_nested_list(col_names)
db_create.create_table(table,
file_number='file_number',
col_names=col_names)
table = "previous_cancer_history"
col_names = [
'type_cancer', 'year_diagnosis', 'surgery', 'type_surgery',
'duration_surgery', 'radiation', 'type_radiation',
'duration_radiation', 'chemotherapy', 'type_chemotherapy',
'duration_chemotherapy', 'hormone', 'type_hormone',
'duration_hormone', 'alternative', 'type_alternative',
'duration_alternative', 'homeremedy', 'type_homeremedy',
'duration_homeremedy'
]
col_list = ask.flatten_nested_list(col_names)
db_create.create_table(table,
file_number='file_number',
col_names=col_list)
table = "nutritional_supplements"
col_names = [
'type_nutritional_supplements',
'quantity_nutritional_supplements_per_day',
'duration_nutritional_supplements'
]
col_list = ask.flatten_nested_list(col_names)
db_create.create_table(table,
file_number='file_number',
col_names=col_list)
table = "physical_activity"
col_names = ['type_activity', 'frequency_activity']
col_list = ask.flatten_nested_list(col_names)
db_create.create_table(table,
file_number='file_number',
col_names=col_list)
table = "breast_feeding"
col_names = [
'child_number', 'feeding_duration', 'breast_usage_feeding'
]
col_list = ask.flatten_nested_list(col_names)
db_create.create_table(table,
file_number='file_number',
col_names=col_list)
table = "nact_tox_table"
col_names = pccm_names.names_nact(table)
db_create.create_table(table,
file_number='file_number',
col_names=col_names)
table = "nact_drug_table"
col_names = pccm_names.names_nact(table)
db_create.create_table(table,
file_number='file_number',
col_names=col_names)
table = "neo_adjuvant_therapy"
module_list = ["neo_adjuvant_therapy", "clip_information"]
col_names = [pccm_names.names_nact(module) for module in module_list]
col_list = ask.flatten_nested_list(col_names)
db_create.create_table(table,
file_number='file_number',
col_names=col_list)
table = "adjuvant_chemotherapy"
col_names = pccm_names.names_chemotherapy(table)
db_create.create_table(table,
file_number='file_number',
col_names=col_names)
table = "chemo_tox_table"
col_names = pccm_names.names_chemotherapy(table)
db_create.create_table(table,
file_number='file_number',
col_names=col_names)
table = "chemo_drug_table"
col_names = pccm_names.names_chemotherapy(table)
db_create.create_table(table,
file_number='file_number',
col_names=col_names)
table = "radiotherapy"
col_names = pccm_names.names_radiation()
db_create.create_table(table,
file_number='file_number',
col_names=col_names)
table = "follow_up_data"
col_names = pccm_names.name_follow_up()
db_create.create_table(table,
file_number='file_number',
col_names=col_names)
table = "hormonetherapy_survival"
module_list = ["hormone", "metastasis"]
col_names = [
pccm_names.names_longterm(module) for module in module_list
]
col_list = ask.flatten_nested_list(col_names)
db_create.create_table(table,
file_number='file_number',
col_names=col_list)
table = 'block_list'
col_names = pccm_names.block_list('all')
db_create.create_table_pk(table, col_names=col_names, pk='pk')
table = "clinical_exam"
module_list = ['clinical_exam_initial', 'nipple_cytology']
col_names = [
pccm_names.name_clinical(module) for module in module_list
]
col_list = ask.flatten_nested_list(col_names)
db_create.create_table(table,
file_number=file_number,
col_names=col_list)
self.conn.commit()
print(self.path + " file created")
self.conn.close()