def main():
'''
Script to deprecate any repositories that are older than n days, and have been empty since creation.
'''
parser = OptionParser()
parser.add_option( "-d", "--days", dest="days", action="store", type="int", help="number of days (14)", default=14 )
parser.add_option( "-i", "--info_only", action="store_true", dest="info_only", help="info about the requested action", default=False )
parser.add_option( "-v", "--verbose", action="store_true", dest="verbose", help="verbose mode, print the name of each repository", default=False )
( options, args ) = parser.parse_args()
try:
ini_file = args[0]
except IndexError:
sys.exit( "Usage: python %s <tool shed .ini file> [options]" % sys.argv[ 0 ] )
config_parser = ConfigParser.ConfigParser( {'here': os.getcwd()} )
config_parser.read( ini_file )
config_dict = {}
for key, value in config_parser.items( "app:main" ):
config_dict[key] = value
config = tool_shed_config.Configuration( **config_dict )
app = DeprecateRepositoriesApplication( config )
cutoff_time = datetime.utcnow() - timedelta( days=options.days )
now = strftime( "%Y-%m-%d %H:%M:%S" )
print "\n####################################################################################"
print "# %s - Handling stuff older than %i days" % ( now, options.days )
if options.info_only:
print "# Displaying info only ( --info_only )"
deprecate_repositories( app, cutoff_time, days=options.days, info_only=options.info_only, verbose=options.verbose )
def main():
'''Script that checks repositories to see if the tools contained within them have functional tests defined.'''
parser = OptionParser()
parser.add_option("-i",
"--info_only",
action="store_true",
dest="info_only",
help="info about the requested action",
default=False)
parser.add_option(
"-s",
"--section",
action="store",
dest="section",
default='server:main',
help="which .ini file section to extract the host and port from")
parser.add_option("-v",
"--verbose",
action="count",
dest="verbosity",
default=1,
help="Control the amount of detail in the log output.")
parser.add_option(
"--verbosity",
action="store",
dest="verbosity",
metavar='VERBOSITY',
type="int",
help="Control the amount of detail in the log output. --verbosity=1 is "
"the same as -v")
(options, args) = parser.parse_args()
try:
ini_file = args[0]
except IndexError:
print "Usage: python %s <tool shed .ini file> [options]" % sys.argv[0]
exit(127)
config_parser = ConfigParser.ConfigParser({'here': os.getcwd()})
config_parser.read(ini_file)
config_dict = {}
for key, value in config_parser.items("app:main"):
config_dict[key] = value
config = tool_shed_config.Configuration(**config_dict)
config_section = options.section
now = strftime("%Y-%m-%d %H:%M:%S")
print "#############################################################################"
print "# %s - Checking repositories for tools with functional tests." % now
print "# This tool shed is configured to listen on %s:%s." % (
config_parser.get(config_section,
'host'), config_parser.get(config_section, 'port'))
app = FlagRepositoriesApplication(config)
if options.info_only:
print "# Displaying info only ( --info_only )"
if options.verbosity:
print "# Displaying extra information ( --verbosity = %d )" % options.verbosity
check_and_flag_repositories(app,
info_only=options.info_only,
verbosity=options.verbosity)
def get_sa_session_and_needed_config_settings( path_to_tool_shed_config ):
conf_parser = ConfigParser.ConfigParser( { 'here' : os.getcwd() } )
conf_parser.read( path_to_tool_shed_config )
kwds = dict()
for key, value in conf_parser.items( "app:main" ):
kwds[ key ] = value
config_settings = config.Configuration( **kwds )
db_con = config_settings.database_connection
if not db_con:
db_con = "sqlite:///%s?isolation_level=IMMEDIATE" % config_settings.database
model = galaxy.webapps.tool_shed.model.mapping.init( config_settings.file_path, db_con, engine_options={}, create_tables=False )
return model.context.current, config_settings
"""Validates the public username."""
if len(username) < 3:
return "Public name must be at least 3 characters in length"
if len(username) > 255:
return "Public name cannot be more than 255 characters in length"
if not(VALID_PUBLICNAME_RE.match(username)):
return "Public name must contain only lower-case letters, numbers and '-'"
return ''
if __name__ == "__main__":
parser = optparse.OptionParser(description='Create a user with API key.')
parser.add_option('-c', dest='config', action='store', help='.ini file to retried toolshed configuration from')
(args, options) = parser.parse_args()
ini_file = args.config
config_parser = ConfigParser.ConfigParser({'here': os.getcwd()})
print "Reading ini file: ", ini_file
config_parser.read(ini_file)
config_dict = {}
for key, value in config_parser.items("app:main"):
config_dict[key] = value
config = tool_shed_config.Configuration(**config_dict)
app = BootstrapApplication(config)
user = create_user(app)
if user is not None:
api_key = create_api_key(app, user)
print "Created new user with public username '", user.username, ". An API key was also created and associated with the user."
sys.exit(0)
else:
sys.exit("Problem creating a new user and an associated API key.")
def main():
'''Script that validates all repositories of type tool_dependency_definition.'''
parser = OptionParser()
parser.add_option("-i",
"--info_only",
action="store_true",
dest="info_only",
help="info about the requested action",
default=False)
parser.add_option(
"-s",
"--section",
action="store",
dest="section",
default='server:main',
help=".ini file section from which to extract the host and port")
parser.add_option("-v",
"--verbose",
action="count",
dest="verbosity",
default=1,
help="Control the amount of detail in the log output.")
parser.add_option(
"--verbosity",
action="store",
dest="verbosity",
metavar='VERBOSITY',
type="int",
help=
"Control the amount of detail in the log output, --verbosity=1 is the same as -v"
)
(options, args) = parser.parse_args()
try:
ini_file = args[0]
except IndexError:
print "Usage: python %s <tool shed .ini file> [options]" % sys.argv[0]
exit(127)
config_parser = ConfigParser.ConfigParser({'here': os.getcwd()})
config_parser.read(ini_file)
config_dict = {}
for key, value in config_parser.items("app:main"):
config_dict[key] = value
config = tool_shed_config.Configuration(**config_dict)
config_section = options.section
now = strftime("%Y-%m-%d %H:%M:%S")
print "#############################################################################"
print "# %s - Validating repositories of type %s" % (
now, TOOL_DEPENDENCY_DEFINITION)
print "# This tool shed is configured to listen on %s:%s" % (
config_parser.get(config_section,
'host'), config_parser.get(config_section, 'port'))
app = RepositoryMetadataApplication(config)
if options.info_only:
print "# Displaying info only ( --info_only )"
if options.verbosity:
print "# Displaying extra information ( --verbosity = %d )" % options.verbosity
validate_repositories(app,
info_only=options.info_only,
verbosity=options.verbosity)
