def run(self, args):
if not os.path.exists(args.file):
self.ctx.die(670, "No such file: %s" % args.file)
else:
client = self.ctx.conn(args)
store = SessionsStore()
srv, usr, uuid, port = store.get_current()
props = store.get(srv, usr, uuid)
from omero.scripts import parse_file
from omero.util.temp_files import create_path
path = create_path()
text = """
omero.host=%(omero.host)s
omero.user=%(omero.sess)s
omero.pass=%(omero.sess)s
"""
path.write_text(text % props)
params = parse_file(args.file)
m = self._parse_inputs(args, params)
for k, v in list(m.items()):
if v is not None:
client.setInput(k, v)
p = self.ctx.popen([sys.executable, args.file],
stdout=sys.stdout,
stderr=sys.stderr,
ICE_CONFIG=str(path))
p.wait()
if p.poll() != 0:
self.ctx.die(p.poll(), "Execution failed.")
def __init__(self, parent=None):
super().__init__(parent)
self.store = SessionsStore()
self.destroyed.connect(self.close)
atexit.register(self.close)
self.worker: Optional[WorkerBase] = None
self._next_worker: Optional[WorkerBase] = None
def get_params_from_session():
store = SessionsStore()
session_props = store.get_current()
host, username, suuid, port = session_props
# If there is no suuid, there is no session
if suuid is None:
return None
return {'host': host, 'username': username, 'suuid': suuid, 'port': port}
def __init__(self, config_file=None):
# Set the connection as not established
self.conn = None
self.SUUID = None
self.HOST = None
self.PORT = None
self.USERNAME = None
self.PASSWORD = None
# If config_file not specified, first see if there's an active OMERO
# CLI session.
if config_file is None:
store = SessionsStore()
session_props = store.get_current()
self.HOST, self.USERNAME, self.SUUID, self.PORT = session_props
# config_file specified, or no active session. Continue with reading
# connection params from the config file.
if config_file is not None or self.SUUID is None:
# Normalize file path.
if config_file is None:
config_file = '~/.omero/config'
config_file = os.path.expanduser(config_file)
# Check config file exists.
if not (os.path.exists(config_file)
and os.path.isfile(config_file)):
sys.stderr.write('No active OMERO CLI session and '
'configuration file {} does not '
'exist\n'.format(config_file))
sys.exit(1)
# Check permisisons on config file.
if os.stat(config_file).st_mode & 0077:
sys.stderr.write('Configuration file contains private '
'credentials and must not be accessible by '
'other users. Please run:\n\n'
' chmod 600 {}\n\n'.format(config_file))
sys.exit(1)
# Read the credentials file.
config = ConfigParser.RawConfigParser()
config.read(config_file)
self.HOST = config.get('OMEROCredentials', 'host')
self.PORT = config.getint('OMEROCredentials', 'port')
self.USERNAME = config.get('OMEROCredentials', 'username')
self.PASSWORD = config.get('OMEROCredentials', 'password')
def timer(func):
"""Print the runtime of the decorated function"""
@functools.wraps(func)
def wrapper_timer(*args, **kwargs):
start_time = time.perf_counter() # 1
value = func(*args, **kwargs)
end_time = time.perf_counter() # 2
run_time = end_time - start_time # 3
logger.debug(f"Finished {func.__name__!r} in {run_time:.4f} secs")
return value
return wrapper_timer
STORE = SessionsStore()
def parse_omero_url(url):
m = re.search(
r"https?://(?P<host>[^/]+).*/webclient/\?show=(?P<type>[a-z]+)-(?P<id>[0-9]+)",
url,
)
if m:
return m.groupdict()
@timer
def get_gateway(path, host=None):
gateway = QGateWay()
if host:
