from omero.gateway import BlitzGateway
from Parse_OMERO_Properties import USERNAME, PASSWORD, HOST, PORT
print(HOST)
conn = BlitzGateway(USERNAME, PASSWORD, host=HOST, port=PORT)
conn.connect()
user = conn.getUser()
print "Current user:"******" ID:", user.getId()
print " Username:"******" Full Name:", user.getFullName()
if( args.group is not None ):
print("change group")
new_group = args.group
groups = [ g.getName() for g in conn.listGroups() ]
print(groups)
if( new_group not in groups ):
print("{} not found in groups:".format(new_group))
for gn in groups:
print(" {}".format(gn))
sys.exit(1)
else:
conn.setGroupNameForSession(group)
print conn.getGroupFromContext().getName()
path = os.getcwd()
mdict= setup_dict()
def package_file( mdict,conn, group, Id, path, name ):
print "processing {} {} as : {}/{}".format(group,Id,path,name)
password = getpass.getpass()
# Connect to the Python Blitz Gateway.
conn = BlitzGateway(username, password, host=HOST, port=PORT)
connected = conn.connect()
if not connected:
print >> sys.stderr, ("Error: Connection not available, please check your " "username and password.")
sys.exit(1)
else:
print "Login successful.\n"
# Set our default group so we can see the data.
# (I thought I had to do this, but now I am not sure it's needed.
# -JLM 2013/12/04)
try:
group = next(g for g in conn.listGroups() if g.getName() == GROUP)
except StopIteration:
print >> sys.stderr, "Error: could not find group '%s'" % GROUP
conn.setGroupForSession(group.getId())
# Get plate of interest.
# (ID 1552 is "RTK ligands induce differing FOXO3a translocation dynamics")
plate = conn.getObject("Plate", 1552)
# Get list of lists of well objects from the plate.
well_grid = plate.getWellGrid()
# Loop over all wells in the plate.
for (raw_row_num, row) in enumerate(well_grid):
for (raw_col_num, well) in enumerate(row):
# Fix up row and column numbers to match Pat's nomenclature.
row_num = raw_row_num + 1
# Connect to the Python Blitz Gateway.
conn = BlitzGateway(username, password, host=HOST, port=PORT)
connected = conn.connect()
if not connected:
print >> sys.stderr, ("Error: Connection not available, please check your "
"username and password.")
sys.exit(1)
else:
print "Login successful.\n"
# Set our default group so we can see the data.
# (I thought I had to do this, but now I am not sure it's needed.
# -JLM 2013/12/04)
try:
group = next(g for g in conn.listGroups() if g.getName() == GROUP)
except StopIteration:
print >> sys.stderr, "Error: could not find group '%s'" % GROUP
conn.setGroupForSession(group.getId())
# Get plate of interest.
# (ID 1552 is "RTK ligands induce differing FOXO3a translocation dynamics")
plate = conn.getObject('Plate', 1552)
# Get list of lists of well objects from the plate.
well_grid = plate.getWellGrid()
# Loop over all wells in the plate.
for (raw_row_num, row) in enumerate(well_grid):
for (raw_col_num, well) in enumerate(row):
# Fix up row and column numbers to match Pat's nomenclature.
row_num = raw_row_num + 1
