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