def echo():
global config
update_sql_settings()
initial_button_type = echo_button.button_type
initial_label = echo_button.label
if validate_sql_connection(config):
echo_button.button_type = 'success'
echo_button.label = 'Success'
else:
echo_button.button_type = 'warning'
echo_button.label = 'Fail'
time.sleep(1.5)
echo_button.button_type = initial_button_type
echo_button.label = initial_label
def test_dvh_code():
if test_import_sql_cnx_definitions():
is_import_valid = validate_import_settings()
is_sql_connection_valid = validate_sql_connection()
if not is_import_valid and not is_sql_connection_valid:
print(
"ERROR: Create the directories listed above or input valid directories.\n",
"ERROR: Cannot connect to SQL.\n",
"Please run:\n $ python start.py settings",
sep='')
elif not is_import_valid:
print(
"ERROR: Create the directories listed above or input valid directories by running:\n",
" $ python start.py settings --dir",
sep='')
elif not is_sql_connection_valid:
print(
"ERROR: Cannot connect to SQL.\n",
"Verify database is active and/or update SQL connection information with:\n",
" $ python start.py settings --sql",
sep='')
else:
print("Importing test files")
dicom_to_sql(start_path="test_files/",
organize_files=False,
move_files=False,
force_update=False)
print("Reading data from SQL DB with analysis_tools.py")
test = DVH()
print(
"Reading dicom information from test files with utilities.py (for plan review module)"
)
test_files = Temp_DICOM_FileSet(start_path="test_files/")
print("Deleting test data from SQL database")
for i in range(0, test_files.count):
cond_str = "mrn = '" + test_files.mrn[i]
cond_str += "' and study_instance_uid = '" + test_files.study_instance_uid[
i] + "'"
DVH_SQL().delete_rows(cond_str)
print("Tests successful!")
def main():
parser = argparse.ArgumentParser(
description='Command line interface for DVH Analytics')
parser.add_argument('--sql',
help='Modify SQL connection settings',
default=False,
action='store_true')
parser.add_argument('--dir',
help='Modify import directory settings',
default=False,
action='store_true')
parser.add_argument('--start-path',
dest='start_path',
help='modify the start path for dicom import',
default=None)
parser.add_argument(
'--force-update',
help=
'Import will add to SQL DB even if DB already contains data from dicom files',
default=False,
action='store_true')
parser.add_argument(
'--allow-websocket-origin',
dest='allow_websocket_origin',
help='Allows Bokeh server to accept a non-default origin',
default=None)
parser.add_argument('--port',
dest='port',
help='Initializes Bokeh server on a non-default port',
default=None)
parser.add_argument('command', nargs='+', help='bar help')
args = parser.parse_args()
if args.command:
if args.command[0] == 'settings_simple':
if not args.sql and not args.dir:
settings()
else:
if args.sql:
settings(sql=True)
if args.dir:
settings(dir=True)
elif args.command[0] == 'test':
test_dvh_code()
elif args.command[0] == 'echo':
validate_sql_connection()
elif args.command[0] == 'print_mrns':
print_mrns()
elif args.command[0] == 'import':
# Set defaults
start_path = False
force_update = False
if args.start_path:
if os.path.isdir(args.start_path):
start_path = str(args.start_path)
else:
print(args.start_path, 'is not a valid path', sep=' ')
if args.force_update:
force_update = True
dicom_to_sql(start_path=start_path, force_update=force_update)
elif args.command[0] == 'run':
if test_import_sql_cnx_definitions():
if DVH_SQL().is_sql_table_empty('DVHs'):
print("There is no data in your SQL table.")
print(
"You may import data from the admin view (use the 'admin' command instead of 'run'"
)
else:
command = ["bokeh", "serve"]
if args.allow_websocket_origin:
command.append("--allow-websocket-origin")
command.append(args.allow_websocket_origin)
if args.port:
command.append("--port") # Defaults to 5006
command.append(args.port)
if not args.allow_websocket_origin and not args.port:
command.append("--show")
command.append(script_dir)
call(command)
else:
print(
"Could not connect to SQL. You may need to update/initiate settings."
)
print("Try running with 'settings' command instead of 'run'")
elif args.command[0] == 'admin':
if test_import_sql_cnx_definitions():
command = ["bokeh", "serve", "--show", "--port"]
if args.port:
command.append(args.port)
else:
command.append("5007")
if args.allow_websocket_origin:
command.append("--allow-websocket-origin")
command.append(args.allow_websocket_origin)
file_name = 'admin.py'
abs_file_path = os.path.join(script_dir, file_name)
command.append(abs_file_path)
call(command)
else:
print(
"Could not connect to SQL. You may need to update/initiate settings."
)
print("Try running with 'settings' command instead of 'admin'")
elif args.command[0] == 'settings':
initialize_default_import_settings_file()
initialize_default_sql_connection_config_file()
command = ["bokeh", "serve", "--show", "--port"]
if args.port:
command.append(args.port)
else:
command.append("5008")
if args.allow_websocket_origin:
command.append("--allow-websocket-origin")
command.append(args.allow_websocket_origin)
file_name = 'settings.py'
abs_file_path = os.path.join(script_dir, file_name)
command.append(abs_file_path)
call(command)
elif args.command[0] == 'create_tables':
DVH_SQL().initialize_database()