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
'''
import cellprofiler.preferences as cpprefs
from bioformats.formatreader import use_omero_credentials
from bioformats.formatreader import \
K_OMERO_SERVER, K_OMERO_PORT, K_OMERO_USER, K_OMERO_SESSION_ID, \
K_OMERO_PASSWORD, K_OMERO_CONFIG_FILE
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")
for k, v in [kv.split("=", 1) for kv in credentials_string.split(",")]:
k = k.lower()
credentials = {
K_OMERO_SERVER: cpprefs.get_omero_server(),
K_OMERO_PORT: cpprefs.get_omero_port(),
K_OMERO_USER: cpprefs.get_omero_user(),
K_OMERO_SESSION_ID: cpprefs.get_omero_session_id()
}
if k == OMERO_CK_HOST:
cpprefs.set_omero_server(v, globally=False)
credentials[K_OMERO_SERVER] = v
elif k == OMERO_CK_PORT:
cpprefs.set_omero_port(v, globally=False)
credentials[K_OMERO_PORT] = v
elif k == OMERO_CK_SESSION_ID:
credentials[K_OMERO_SESSION_ID] = v
elif k == OMERO_CK_USER:
cpprefs.set_omero_user(v, globally=False)
credentials[K_OMERO_USER] = v
elif k == OMERO_CK_PASSWORD:
credentials[K_OMERO_PASSWORD] = v
elif k == OMERO_CK_CONFIG_FILE:
credentials[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")
use_omero_credentials(credentials)
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
'''
import cellprofiler.preferences as cpprefs
from bioformats.formatreader import use_omero_credentials
from bioformats.formatreader import \
K_OMERO_SERVER, K_OMERO_PORT, K_OMERO_USER, K_OMERO_SESSION_ID,\
K_OMERO_PASSWORD, K_OMERO_CONFIG_FILE
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")
for k, v in [kv.split("=", 1) for kv in credentials_string.split(",")]:
k = k.lower()
credentials = {
K_OMERO_SERVER: cpprefs.get_omero_server(),
K_OMERO_PORT: cpprefs.get_omero_port(),
K_OMERO_USER: cpprefs.get_omero_user(),
K_OMERO_SESSION_ID: cpprefs.get_omero_session_id()
}
if k == OMERO_CK_HOST:
cpprefs.set_omero_server(v)
credentials[K_OMERO_SERVER] = v
elif k == OMERO_CK_PORT:
cpprefs.set_omero_port(v)
credentials[K_OMERO_PORT] = v
elif k == OMERO_CK_SESSION_ID:
credentials[K_OMERO_SESSION_ID] = v
elif k == OMERO_CK_USER:
cpprefs.set_omero_user(v)
credentials[K_OMERO_USER] = v
elif k == OMERO_CK_PASSWORD:
credentials[K_OMERO_PASSWORD] = v
elif k == OMERO_CK_CONFIG_FILE:
credentials[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")
use_omero_credentials(credentials)