def create_batch_users(context,galaxy,template,start,end,
password,only_check):
"""
Create multiple Galaxy users from a template.
Creates a batch of users in GALAXY using TEMPLATE; this
should be a template email address which includes a
'#' symbol as a placeholder for an integer index.
The range of integers is defined by START and END; if
only one of these is supplied then START is assumed to be
1 and the supplied value is END.
For example: using the template 'user#@example.org'
with the range 1 to 5 will create new accounts:
[email protected]
...
[email protected]
"""
# Get a Galaxy instance
gi = context.galaxy_instance(galaxy)
if gi is None:
logger.critical("Failed to connect to Galaxy instance")
return 1
# Sort out start and end indices
if end is None:
end = start
start = 1
# Create users
return users.create_users_from_template(gi,template,
start,end,password,
only_check=only_check)
def manage_users(args=None):
"""
Implements the 'manage_users' utility
"""
deprecation_warning()
if args is None:
args = sys.argv[1:]
p = base_parser(usage=\
"\n\t%prog list GALAXY_URL [options]"
"\n\t%prog create GALAXY_URL EMAIL [PUBLIC_NAME]"
"\n\t%prog create GALAXY_URL -t TEMPLATE START [END]"
"\n\t%prog create GALAXY_URL -b FILE [options]",
description="Manage and create users in a Galaxy "
"instance")
commands = ['list','create']
# Get compulsory arguments
if len(args) == 1:
if args[0] == '-h' or args[0] == '--help':
p.print_usage()
elif args[0] == '--version':
p.print_version()
sys.exit(0)
if len(args) < 2:
p.error("need to supply a command and a Galaxy URL/alias")
command = args[0]
galaxy_url = args[1]
# Setup additional command line options
if command not in commands:
p.error("unrecognised command: '%s'" % command)
elif command == 'list':
p.set_usage("%prog list GALAXY_URL [options]")
p.add_option('--name',action='store',dest='name',default=None,
help="specific emails/user name(s) to list")
p.add_option('-l',action='store_true',
dest='long_listing_format',default=False,
help="use a long listing format (include ids, "
"disk usage and admin status)")
elif command == 'create':
p.set_usage("\n\t%prog create GALAXY_URL EMAIL [PUBLIC_NAME]"
"\n\t%prog create GALAXY_URL -t TEMPLATE START [END]"
"\n\t%prog create GALAXY_URL -b FILE [options]")
p.add_option('-p','--password',action='store',dest='passwd',
default=None,
help="specify password for new user account "
"(otherwise program will prompt for password)")
p.add_option('-c','--check',action='store_true',dest='check',
default=False,
help="check user details but don't try to create "
"the new account")
p.add_option('-t','--template',action='store_true',
dest='template',default=False,
help="indicates that EMAIL is actually a "
"'template' email address which includes a '#' "
"symbol as a placeholder where an integer index "
"should be substituted to make multiple accounts "
"(e.g. 'student#@galaxy.ac.uk').")
p.add_option('-b','--batch',action='store_true',dest='batch',
default=False,
help="create multiple users reading details from "
"TSV file (columns should be: "
"email,password[,public_name])")
p.add_option('-m','--message',action='store',
dest='message_template',default=None,
help="populate and output Mako template "
"MESSAGE_TEMPLATE")
# Process remaining arguments on command line
if args[1] in ('-h','--help','--version'):
args = args[1:]
else:
args = args[2:]
options,args = p.parse_args(args)
handle_debug(debug=options.debug)
handle_suppress_warnings(suppress_warnings=options.suppress_warnings)
handle_ssl_warnings(verify=(not options.no_verify))
# Handle password if required
email,password = handle_credentials(options.username,
options.galaxy_password,
prompt="Password for %s: " % galaxy_url)
# Get a Galaxy instance
gi = get_galaxy_instance(galaxy_url,api_key=options.api_key,
email=email,password=password,
verify_ssl=(not options.no_verify))
if gi is None:
logger.critical("Failed to connect to Galaxy instance")
sys.exit(1)
# Execute command
if command == 'list':
users.list_users(gi,name=options.name,long_listing_format=
options.long_listing_format)
elif command == 'create':
# Check message template is .mako file
if options.message_template:
if not os.path.isfile(options.message_template):
logger.critical("Message template '%s' not found"
% options.message_template)
sys.exit(1)
elif not options.message_template.endswith(".mako"):
logger.critical("Message template '%s' is not a .mako file"
% options.message_template)
sys.exit(1)
if options.template:
# Get the template and range of indices
template = args[0]
start = int(args[1])
try:
end = int(args[2])
except IndexError:
end = start
# Create users
retval = users.create_users_from_template(gi,template,
start,end,options.passwd,
only_check=options.check)
elif options.batch:
# Get the file with the user data
tsvfile = args[0]
# Create users
retval = users.create_batch_of_users(gi,tsvfile,
only_check=options.check,
mako_template=options.message_template)
else:
# Collect email and (optionally) public name
email = args[0]
try:
name = args[1]
if not users.check_username_format(name):
logger.critical("Invalid name: must contain only "
"lower-case letters, numbers and "
"'-'")
sys.exit(1)
except IndexError:
# No public name supplied, make from email address
name = users.get_username_from_login(email)
# Create user
print "Email : %s" % email
print "Name : %s" % name
retval = users.create_user(gi,email,name,options.passwd,
only_check=options.check,
mako_template=options.message_template)
