def connect(self):
try:
server = self.omero_server_ctrl.GetValue()
port = int(self.omero_port_ctrl.GetValue())
user = self.omero_user_ctrl.GetValue()
except:
self.message_ctrl.Label = (
"The port number must be an integer between 0 and 65535 (try 4064)"
)
self.message_ctrl.ForegroundColour = "red"
self.message_ctrl.Refresh()
return False
try:
self.session_id = bioformats.formatreader.set_omero_credentials(
server, port, user, self.omero_password_ctrl.GetValue())
self.message_ctrl.Label = "Connected"
self.message_ctrl.ForegroundColour = "green"
self.message_ctrl.Refresh()
self.server = server
self.port = port
self.user = user
set_omero_server(server)
set_omero_port(port)
set_omero_user(user)
self.ok_button.Enable(True)
return True
except:
self.message_ctrl.Label = "Failed to log onto server"
self.message_ctrl.ForegroundColour = "red"
self.message_ctrl.Refresh()
return False
def set_omero_credentials_from_string(credentials_string):
"""Set the OMERO server / port / session ID
credentials_string: a comma-separated key/value pair string (key=value)
that gives the credentials. Keys are
host - the DNS name or IP address of the OMERO server
port - the TCP port to use to connect
user - the user name
session-id - the session ID used for authentication
"""
if re.match("([^=^,]+=[^=^,]+,)*([^=^,]+=[^=^,]+)",
credentials_string) is None:
logging.root.error(
'The OMERO credentials string, "%s", is badly-formatted.' %
credentials_string)
logging.root.error(
'It should have the form: "host=hostname.org,port=####,user=<user>,session-id=<session-id>\n'
)
raise ValueError("Invalid format for --omero-credentials")
credentials = {}
for k, v in [kv.split("=", 1) for kv in credentials_string.split(",")]:
k = k.lower()
credentials = {
bioformats.formatreader.K_OMERO_SERVER: get_omero_server(),
bioformats.formatreader.K_OMERO_PORT: get_omero_port(),
bioformats.formatreader.K_OMERO_USER: get_omero_user(),
bioformats.formatreader.K_OMERO_SESSION_ID: get_omero_session_id(),
}
if k == OMERO_CK_HOST:
set_omero_server(v, globally=False)
credentials[bioformats.formatreader.K_OMERO_SERVER] = v
elif k == OMERO_CK_PORT:
set_omero_port(v, globally=False)
credentials[bioformats.formatreader.K_OMERO_PORT] = v
elif k == OMERO_CK_SESSION_ID:
credentials[bioformats.formatreader.K_OMERO_SESSION_ID] = v
elif k == OMERO_CK_USER:
set_omero_user(v, globally=False)
credentials[bioformats.formatreader.K_OMERO_USER] = v
elif k == OMERO_CK_PASSWORD:
credentials[bioformats.formatreader.K_OMERO_PASSWORD] = v
elif k == OMERO_CK_CONFIG_FILE:
credentials[bioformats.formatreader.K_OMERO_CONFIG_FILE] = v
if not os.path.isfile(v):
msg = "Cannot find OMERO config file, %s" % v
logging.root.error(msg)
raise ValueError(msg)
else:
logging.root.error('Unknown --omero-credentials keyword: "%s"' % k)
logging.root.error('Acceptable keywords are: "%s"' % '","'.join(
[OMERO_CK_HOST, OMERO_CK_PORT, OMERO_CK_SESSION_ID]))
raise ValueError("Invalid format for --omero-credentials")
bioformats.formatreader.use_omero_credentials(credentials)