def add_library_datasets(context,galaxy,dest,file,file_type,
dbkey,from_server,link):
"""
Add datasets to a data library.
Uploads one or more FILEs as new datasets in the
data library folder DEST in GALAXY.
DEST should be a path to a data library or library
folder of the form
'data_library[/folder[/subfolder[...]]]'. The library
and folder must already exist.
"""
# Get a Galaxy instance
gi = context.galaxy_instance(galaxy)
if gi is None:
logger.critical("Failed to connect to Galaxy instance")
return 1
# Add the datasets
libraries.add_library_datasets(gi,dest,file,
from_server=from_server,
link_only=link,
file_type=file_type,
dbkey=dbkey)
def manage_libraries(args=None):
"""
Implements the 'manage_libraries' 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_library GALAXY_URL [options] NAME"
"\n\t%prog create_folder GALAXY_URL [options] PATH"
"\n\t%prog add_datasets GALAXY_URL [options] DEST FILE...",
description="Manage and populate data libraries in a "
"Galaxy instance")
commands = ['list','create_library','create_folder','add_datasets']
# 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('-l',action='store_true',
dest='long_listing_format',default=False,
help="use a long listing format (include ids, "
"descriptions and file sizes and paths)")
elif command == 'create_library':
p.set_usage("%prog create_library GALAXY_URL [options] NAME")
p.add_option('-d','--description',action='store',
dest='description',default=None,
help="optional description")
p.add_option('-s','--synopsis',action='store',dest='synopsis',
default=None,help="optional synopsis")
elif command == 'create_folder':
p.set_usage("%prog create_folder GALAXY_URL [options] PATH")
p.add_option('-d','--description',action='store',
dest='description',default=None,
help="optional description")
elif command == 'add_datasets':
p.set_usage("%prog add_datasets GALAXY_URL [options] DEST FILE...")
p.add_option('--server',action='store_true',dest='from_server',
default=False,
help="upload files from Galaxy server file system "
"paths (default is to upload files from local "
"system)")
p.add_option('--link',action='store_true',dest='link',
default=False,
help="create symlinks to files on server (only "
"valid if used with --server; default is to copy "
"files into Galaxy)")
p.add_option('--dbkey',action='store',dest='dbkey',default='?',
help="dbkey to assign to files (default is '?')")
p.add_option('--file_type',action='store',dest='file_type',
default='auto',
help="file type to assign to files (default is "
"'auto')")
# 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':
if len(args) == 1:
# List folders in data library
libraries.list_library_contents(gi,args[0],long_listing_format=
options.long_listing_format)
else:
# List data libraries
libraries.list_data_libraries(gi)
elif command == 'create_library':
# Create a new data library
if len(args) == 1:
libraries.create_library(gi,args[0],
description=options.description,
synopsis=options.synopsis)
else:
p.error("Usage: create_library NAME")
elif command == 'create_folder':
# Create a new folder data library
if len(args) == 1:
libraries.create_folder(gi,args[0],
description=options.description)
else:
p.error("Usage: create_folder PATH")
elif command == 'add_datasets':
# Add a dataset to a library
if len(args) < 2:
p.error("Usage: add_datasets DEST FILE [FILE...]")
libraries.add_library_datasets(gi,args[0],args[1:],
from_server=options.from_server,
link_only=options.link,
file_type=options.file_type,
dbkey=options.dbkey)