from biothings.web.index_base import main
from biothings.web.settings import BiothingESWebSettings
WEB_SETTINGS = BiothingESWebSettings(config=config)
def schedule_daily_job():
tomorrow = datetime.datetime.today() + datetime.timedelta(days=1)
midnight = datetime.datetime.combine(tomorrow, datetime.time.min)
IOLoop.current().add_timeout(midnight.timestamp(), daily_job)
def daily_job():
def sync_job():
backup_and_refresh()
update_uptime_status()
IOLoop.current().run_in_executor(None, sync_job)
schedule_daily_job()
if __name__ == '__main__':
(SRC_PATH, _) = os.path.split(os.path.abspath(__file__))
STATIC_PATH = os.path.join(SRC_PATH, 'static')
# IOLoop.current().add_callback(daily_job) # run upon start
schedule_daily_job()
main(WEB_SETTINGS.generate_app_list(),
app_settings={"cookie_secret": config.COOKIE_SECRET},
debug_settings={"static_path": STATIC_PATH},
use_curl=True)
def get_server(self, config_mod, **app_settings):
settings = BiothingESWebSettings(config=config_mod)
app = tornado.web.Application(settings.generate_app_list(),
**app_settings)
server = tornado.httpserver.HTTPServer(app)
return server
from biothings.web.index_base import main, options
from biothings.web.settings import BiothingESWebSettings
import os.path
import config
web_settings = BiothingESWebSettings(config=config)
if __name__ == '__main__':
(src_path, _) = os.path.split(os.path.abspath(__file__))
static_path = os.path.join(src_path, 'static')
main(web_settings.generate_app_list(),
app_settings={"cookie_secret": config.COOKIE_SECRET},
debug_settings={"static_path": static_path},
use_curl=True)
class BiothingsAPIApp(object):
def __init__(self, *args, **kwargs):
if kwargs.get('object_name',
False) or (len(args) >= 1 and not _is_module(args[0])
and not _is_file(args[0])):
_arg = args[0] if args else ''
self._configure_by_object_name(
object_name=kwargs.get('object_name', _arg))
elif ((kwargs.get('config_file', False)
and _file_exists(kwargs['config_file']))
or (len(args) >= 1 and _is_file(args[0]))):
_arg = args[0] if args else ''
self._configure_by_file(
config_file=os.path.abspath(kwargs.get('config_file', _arg)))
elif ((kwargs.get('config_module', False)
and _is_module(kwargs['config_module']))
or (len(args) >= 1 and _is_module(args[0]))):
_arg = args[0] if args else ''
self._configure_by_module(
config_module=kwargs.get('config_module', _arg))
else:
self._configure_by_kwargs(**kwargs)
def get_server(self, config_mod, **app_settings):
settings = BiothingESWebSettings(config=config_mod)
app = tornado.web.Application(settings.generate_app_list(),
**app_settings)
server = tornado.httpserver.HTTPServer(app)
return server
def start(self,
debug=True,
port=8000,
address='127.0.0.1',
app_settings={}):
if debug:
#import tornado.autoreload
import logging
logging.getLogger().setLevel(logging.DEBUG)
address = '0.0.0.0'
with NamedTemporaryFile(mode='w',
suffix='.py',
dir=os.path.abspath('.')) as _tempfile:
if not getattr(self, 'settings_mod', False):
if not getattr(self, 'settings_str', False):
raise ("Could not configure biothings app")
_tempfile.file.write(self.settings_str)
_tempfile.file.flush()
self.settings_mod = os.path.split(
_tempfile.name)[1].split('.')[0]
self.settings = BiothingESWebSettings(config=self.settings_mod)
application = tornado.web.Application(
self.settings.generate_app_list(), **app_settings)
http_server = tornado.httpserver.HTTPServer(application)
http_server.listen(port, address)
loop = tornado.ioloop.IOLoop.instance()
if debug:
#tornado.autoreload.start(loop)
logging.info('Server is running on "%s:%s"...' %
(address, port))
loop.start()
def _configure_by_object_name(self, object_name):
# get the config file template
config_string = """from biothings.web.settings.default import *\n""" + \
"""from biothings.web.api.es.handlers import *\n""" + \
"""ES_INDEX = '${src_package}_current'\n""" + \
"""ES_DOC_TYPE = '${es_doctype}'\n""" + \
"""API_VERSION = 'v1'\n""" + \
"""APP_LIST = [(r'/status', StatusHandler), (r'/metadata/?', MetadataHandler), (r'/metadata/fields/?', MetadataHandler), (r'/{}/${annotation_endpoint}/(.+)/?'.format(API_VERSION), BiothingHandler), (r'/{}/${annotation_endpoint}/?$$'.format(API_VERSION), BiothingHandler), (r'/{}/query/?'.format(API_VERSION), QueryHandler), (r'/{}/metadata/?'.format(API_VERSION), MetadataHandler), (r'/{}/metadata/fields/?'.format(API_VERSION), MetadataHandler),]\n""" + \
"""GA_RUN_IN_PROD = False"""
settings_dict = {
'src_package': 'my' + object_name.lower(),
'es_doctype': object_name.lower(),
'annotation_endpoint': object_name.lower()
}
self.settings_str = Template(config_string).substitute(settings_dict)
def _configure_by_module(self, config_module):
self.settings_mod = config_module
def _configure_by_kwargs(self, **kwargs):
self.settings_str = """from biothings.web.settings.default import *\nfrom biothings.web.api.es.handlers import *\n"""
for (k, v) in kwargs.items():
if k == 'APP_LIST':
self.settings_str += '{k}=['.format(k=k)
for (reg, handler_str) in v:
self.settings_str += "(r'{reg}', {handler}),".format(
reg=reg, handler=handler_str)
self.settings_str += ']\n'
elif k in [
'ES_QUERY_BUILDER', 'ES_QUERY', 'ES_RESULT_TRANSFORMER'
]:
self.settings_str += '{k}={v}\n'
elif is_str(v):
self.settings_str += '{k}="{v}"\n'.format(k=k, v=v)
else:
self.settings_str += '{k}={v}\n'
def _configure_by_file(self, config_file):
with open(config_file, 'r') as config_handle:
self.settings_str = config_handle.read()