def main():
parser = argparse.ArgumentParser(description='blood_flow_rest: the rest service for blood_flow')
parser.add_argument('-c', '--config', default="api.json", help="config file, can be overridden by parameters")
parser.add_argument('-l', '--logfile', default=None, help="Logfile to write to, default is stdout")
parser.add_argument('-p', '--port', help="Port to bind to")
parser.add_argument('-v', '--verbose', default=4, action="count", help="Increase the verbosity of logging output")
args = parser.parse_args()
config = config_utils.readin_config_file( args.config )
if args.port:
config.server.port = args.port
if args.logfile:
config.logfile = args.logfile
logger.init(name=config.name, log_file=config.logfile )
logger.set_log_level( args.verbose )
if 'database' in config:
global db
db = <PROJECT>_db.DB()
db.connect( config.database )
urls = [('/', RootHandler),
] + oauth.init( **config.oauth )
tornado.run_app( urls, **config.server )
def init(args):
global config
if args.config:
config = config_utils.readin_config_file(args.config[0])
logger.init(name=program_name,
log_file=config.ecc.get('logfile', None))
logger.set_log_level(args.verbose)
logger.info(f'{program_name} (v:{version})')
config.ecc.name_regex = config.ecc.name_template.format("(\d+)")
ecc.set_config(config)
ecc.openstack_connect(config.openstack)
cloudflare_utils.init(config.ecc.cloudflare_apikey,
config.ecc.cloudflare_email)
else:
logger.init(name=program_name)
logger.set_log_level(args.verbose)
logger.info(f'{program_name} (v:{version})')
def main():
parser = argparse.ArgumentParser(description='consumes a mq ')
parser.add_argument('-c',
'--config',
required=True,
help="conductor config file ",
default="conductor.yml")
parser.add_argument('-l',
'--logfile',
default=None,
help="Logfile to write to, default is stdout")
parser.add_argument('-v',
'--verbose',
default=4,
action="count",
help="Increase the verbosity of logging output")
args = parser.parse_args()
config = init(args.config)
if args.logfile:
logger.init(name='nga_runner', log_file=args.logfile, rotate_logs=True)
else:
logger.init(name='nga_runner')
logger.set_log_level(args.verbose)
logger.info(f'startup (v:{version})')
api_requests.set_token(config['key'])
global mq
mq.connect(uri=config['mq_uri'], prefetch_count=1)
try:
mq.consume(route='default', callback=do_work)
except KeyboardInterrupt:
mq.channel.stop_consuming()
# Wait for all to complete
# logger.debug('waiting for threads')
mq.channel.close()
def main():
# Endpoints setup
parser = argparse.ArgumentParser(
description='nels-galaxy-api: extending the functionality of galaxy')
parser.add_argument('-c',
'--config-file',
required=True,
help="nels-galaxy-api config file")
parser.add_argument('-l',
'--logfile',
default=None,
help="Logfile to write to, default is stdout")
parser.add_argument('-v',
'--verbose',
default=4,
action="count",
help="Increase the verbosity of logging output")
parser.add_argument('-D',
'--development',
default=False,
action="store_true",
help="run in developemt mode")
args = parser.parse_args()
if args.development:
global DEV
DEV = True
if args.logfile:
logger.init(name='nels-galaxy-api', log_file=args.logfile)
else:
logger.init(name='nels-galaxy-api')
logger.set_log_level(args.verbose)
logger.info(f'startup nels_galaxy_api (v:{version})')
config = init(args.config_file)
# Base functionality
urls = [
('/', RootHandler), # Done
(r'/info/?$', Info), # Done
(r'/state/(\w+)/?$', State), # Done
# for the cli...
(r'/users/?$', Users), # Done
(r"/user/({email_match})/histories/?$".format(
email_match=string_utils.email_match), UserHistories), # Done
(r"/user/({email_match})/exports/?$".format(
email_match=string_utils.email_match), UserExports),
# all, brief is default #Done
(r"/user/({email_match})/imports/?$".format(
email_match=string_utils.email_match), UserImports),
# all, brief is default #Done
(r"/user/({email_match})/api-key/?$".format(
email_match=string_utils.email_match), UserApikey), # to test
# for proxying into the usegalaxy tracking api, will get user email and instance from the galaxy client.
(r"/user/exports/?$", ExportsListProxy), # done
(r"/user/export/(\w+)/?$", UserExport), # done
(r"/user/imports/?$", UserImportsList), #
(r"/user/import/(\w+)/?$", UserImport), # done
(r'/user/(\w+)/?$', User), # Done
(r'/history/export/request/?$',
HistoryExportRequest), # Register export request #Done
(r'/history/import/request/?$', HistoryImportRequest), #
(r'/history/export/(\w+)?$',
HistoryExport), # export_id, last one pr history is default # skip
(r'/history/export/?$', HistoryExport
), # possible to search by history_id # ship
(r'/history/import/(\w+)?$',
HistoryImport), # export_id, last one pr history is default # skip
(r'/history/import/?$', HistoryImport
), # possible to search by history_id # ship
(r'/history/exports/(all)/?$', HistoryExportsList
), # for the local instance, all, brief is default # done
(r'/history/exports/?$', HistoryExportsList
), # for the local instance, all, brief is default # done
(r'/history/imports/(all)/?$', HistoryImportsList
), # for the local instance, all, brief is default # done
(r'/history/imports/?$', HistoryImportsList
), # for the local instance, all, brief is default # done
(r'/history/download/(\w+)/?$', HistoryDownload
), # fetching exported histories # skip
]
# Terms of service server:
if 'tos_server' in config and config['tos_server']:
urls += [(r'/tos/?$', Tos)]
# for the orchestrator functionality:
if 'master' in config and config['master']:
logger.debug("setting the master endpoints")
urls += [
(r'/rabbitmq_status/?$',
RabbitMQStatus), # check rabbitmq connection status
(r'/export/(\w+)/requeue/?$',
RequeueExport), # requeue export request
(r'/import/(\w+)/requeue/?$',
RequeueImport), # requeue export request
(r"/export/(\w+)/(\w+)/?$",
Export), # instance-id, state-id (post) #done
(r'/export/(\w+)/?$',
Export), # get or patch an export request # skip
(r"/import/(\w+)/?$", Import), # state-id (post) #
(r"/exports/({email_match})/?$".format(
email_match=string_utils.email_match), ExportsList),
# user_email # done
(r"/exports/({email_match})/(\w+)/?$".format(
email_match=string_utils.email_match), ExportsList),
# user_email, instance. If user_email == all, export all entries for instance # done
(r"/exports/(all)/(\w+)/?$", ExportsList), # done
(r"/imports/({email_match})/?$".format(
email_match=string_utils.email_match), ImportsList),
# user_id #
# user_email, instance. If user_email == all, export all entries for instance
(r'/exports/?$', ExportsList
), # All entries in the table, for the cli (differnt key?) # done
(r'/imports/?$', ImportsList
), # All entries in the table, for the cli (differnt key?) # done
(r'/jobs/?$', JobsList
), # All entries in the table, for the cli (differnt key?) # done
# For testing the setup -> ONLY FOR THE MASTER
(r'/proxy/?$', ProxyTest
), # an endpoint for testing the proxy connection #done
# Might drop these two
(r'/decrypt/(\w+)/?$', Decrypt),
(r'/encrypt/(\w+)/?$', Encrypt)
]
if DEV:
sid = states.set({'id': 1234, 'name': 'tyt'})
logger.info(f"TEST STATE ID: {sid}")
logger.info(f"Running on port: {config.get('port', 8008)}")
try:
tornado.run_app(urls, port=config.get('port', 8008))
except KeyboardInterrupt:
logger.info(f'stopping nels_galaxy_api')
def main():
parser = argparse.ArgumentParser(
description='ehos_status: print ehos status in telegraf format')
# parser.add_argument('config_file', metavar='config-file', nargs="*", help="yaml formatted config file",
# default=ecc.utils.find_config_file('ecc.yaml'))
parser.add_argument('config_file',
metavar='config-file',
nargs="*",
help="yaml formatted config file",
default='ecc.yaml')
parser.add_argument('--list', action='store_true') # expected by ansible
parser.add_argument(
'-H',
'--host-group',
default='slurm',
help='host group to put the nodes in') # expected by ansible
parser.add_argument(
'-u',
'--ansible-user',
default='centos',
help='host group to put the nodes in') # expected by ansible
parser.add_argument(
'-t',
'--trusted-host',
default='yes',
help='host group to put the nodes in') # expected by ansible
args = parser.parse_args()
config = config_utils.readin_config_file(args.config_file)
logger.init(name='ecc_nodes', log_file=None)
logger.set_log_level(0)
hosts = readin_inventory(config.ecc.ansible_dir)
config.ecc.name_regex = config.ecc.name_template.format("([01-99])")
ecc.openstack_connect(config.openstack)
nodes = ecc.servers(config.ecc.name_regex)
# get the current nodes
#instances.update( condor.nodes() )
#nodes = instances.node_state_counts()
if args.host_group not in hosts:
hosts[args.host_group] = {"hosts": []}
for node in nodes:
# print( node )
if len(node['ip']) == 0:
continue
ip_addr = node['ip'][0]
node_name = node['name']
hosts[f"{args.host_group}"]['hosts'].append(node_name)
hosts["_meta"]['hostvars'][node_name] = {
'ansible_host': ip_addr,
'ansible_user': args.ansible_user,
'trusted_host': args.trusted_host
}
# pp.pprint( hosts )
print(json.dumps(hosts))