def list_tool_panel(context,galaxy,name,list_tools):
"""
List tool panel contents.
Prints details of tool panel sections including the
displayed text and the internal section id, and any
tools available outside of any section.
"""
# Get a Galaxy instance
gi = context.galaxy_instance(galaxy)
if gi is None:
logger.critical("Failed to connect to Galaxy instance")
return 1
# List tool panel contents
tools.list_tool_panel(gi,name=name,
list_tools=list_tools)
def manage_tools(args=None):
"""
Implements the 'manage_tools' 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 installed GALAXY_URL [options]"
"\n\t%prog tool_panel GALAXY_URL [options]"
"\n\t%prog install GALAXY_URL [options] SHED OWNER TOOL [REVISION]"
"\n\t%prog update GALAXY_URL [options] SHED OWNER TOOL",
description="Manage and install tools in a Galaxy "
"instance")
commands = ['list','installed','tool_panel','install','update']
# 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 tool name(s) to list")
p.add_option('--installed',action='store_true',
dest='installed_only',default=False,
help="only list tools installed from a toolshed")
elif command == 'installed':
p.set_usage("%prog installed GALAXY_URL [options]")
p.add_option('--name',action='store',dest='name',default=None,
help="specific tool repository/ies to list")
p.add_option('--toolshed',action='store',dest='toolshed',default=None,
help="only list repositories from TOOLSHED")
p.add_option('--owner',action='store',dest='owner',default=None,
help="only list repositories owned by OWNER")
p.add_option('--list-tools',action='store_true',dest='list_tools',
default=None,
help="list the associated tools for each repository")
p.add_option('--updateable',action='store_true',dest='updateable',
default=None,
help="only show repositories with uninstalled updates "
"or upgrades")
elif command == 'tool_panel':
p.set_usage("%prog tool_panel GALAXY_URL [options]")
p.add_option('--name',action='store',dest='name',default=None,
help="specific tool panel section(s) to list")
p.add_option('--list-tools',action='store_true',dest='list_tools',
default=None,
help="list the associated tools for each section")
elif command == 'install':
p.set_usage("%prog install GALAXY_URL [options] SHED OWNER TOOL "
"[REVISION]")
p.add_option('--tool-panel-section',action='store',
dest='tool_panel_section',default=None,
help="tool panel section name or id to install the "
"tool under")
elif command == 'update':
p.set_usage("%prog update GALAXY_URL [options] SHED OWNER TOOL")
# 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':
tools.list_tools(gi,name=options.name,
installed_only=options.installed_only)
elif command == 'installed':
tools.list_installed_repositories(gi,name=options.name,
toolshed=options.toolshed,
owner=options.owner,
list_tools=options.list_tools,
only_updateable=options.updateable)
elif command == 'tool_panel':
tools.list_tool_panel(gi,name=options.name,
list_tools=options.list_tools)
elif command == 'install':
if len(args) < 3:
p.error("Need to supply toolshed, owner, repo and optional "
"revision")
toolshed,owner,repo = args[:3]
if len(args) == 4:
revision = args[3]
else:
revision = None
status = tools.install_tool(
gi,toolshed,repo,owner,revision=revision,
tool_panel_section=options.tool_panel_section)
sys.exit(status)
elif command == 'update':
if len(args) != 3:
p.error("Need to supply toolshed, owner and repo")
toolshed,owner,repo = args[:3]
status = tools.update_tool(gi,toolshed,repo,owner)
sys.exit(status)