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Commit acd5ba3b authored by Kevin S. Hahn's avatar Kevin S. Hahn
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Merge branch 'no_config_file'

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api.py
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− 26
View file @ acd5ba3b
...@@ -106,41 +106,42 @@ app.config = { ...@@ -106,41 +106,42 @@ app.config = {
if __name__ == '__main__': if __name__ == '__main__':
import pymongo import pymongo
import argparse import argparse
import ConfigParser
import paste.httpserver import paste.httpserver
arg_parser = argparse.ArgumentParser() arg_parser = argparse.ArgumentParser()
arg_parser.add_argument('config_file', help='path to config file')
arg_parser.add_argument('--host', default='127.0.0.1', help='IP address to bind to') arg_parser.add_argument('--host', default='127.0.0.1', help='IP address to bind to')
arg_parser.add_argument('--port', default='8080', help='TCP port to listen on') arg_parser.add_argument('--port', default='8080', help='TCP port to listen on')
arg_parser.add_argument('--db_uri', help='NIMS DB URI') arg_parser.add_argument('--db_uri', help='NIMS DB URI', required=True)
arg_parser.add_argument('--data_path', help='path to storage area') arg_parser.add_argument('--data_path', help='path to storage area', required=True)
arg_parser.add_argument('--log_path', help='path to API log file') arg_parser.add_argument('--log_path', help='path to API log file', required=True)
arg_parser.add_argument('--ssl_cert', help='path to SSL certificate file, containing private key and certificate chain') arg_parser.add_argument('--ssl_cert', help='path to SSL certificate file, containing private key and certificate chain', required=True)
arg_parser.add_argument('--site_id', help='InterNIMS site ID') arg_parser.add_argument('--site_id', help='site ID for Scitran Central')
arg_parser.add_argument('--site_name', help='InterNIMS site name') arg_parser.add_argument('--site_name', help='site name for Scitran Central', nargs='+')
arg_parser.add_argument('--oauth2_id_endpoint', help='OAuth2 provider ID endpoint') arg_parser.add_argument('--oauth2_id_endpoint', help='OAuth2 provider ID endpoint', default='https://www.googleapis.com/plus/v1/people/me/openIdConnect')
arg_parser.add_argument('--demo', help='demo mode, enables auto user creation') arg_parser.add_argument('--demo', help='demo mode, enables auto user creation', action='store_true', default=False)
arg_parser.add_argument('--insecure', help='insecure mode, allow user info as urlencoded param', action='store_true', default=False)
arg_parser.add_argument('--log_level', help='log level [info]', default='info')
args = arg_parser.parse_args() args = arg_parser.parse_args()
args.site_name = ' '.join(args.site_name) if args.site_name else None # site_name as string
app.config['here'] = os.path.dirname(os.path.abspath(args.config_file)) logging.basicConfig()
config = ConfigParser.ConfigParser(app.config)
config.read(args.config_file)
logging.config.fileConfig(args.config_file, disable_existing_loggers=False)
logging.getLogger('paste.httpserver').setLevel(logging.INFO) # silence paste logging logging.getLogger('paste.httpserver').setLevel(logging.INFO) # silence paste logging
log.setLevel(getattr(logging, args.log_level.upper()))
app.config['site_id'] = args.site_id or app.config['site_id']
app.config['site_name'] = args.site_name or app.config['site_name'] app.config['site_id'] = args.site_id
app.config['data_path'] = os.path.join(args.data_path or config.get('nims', 'data_path'), 'nims') app.config['site_name'] = args.site_name
app.config['quarantine_path'] = os.path.join(args.data_path or config.get('nims', 'data_path'), 'quarantine') app.config['data_path'] = os.path.join(args.data_path, 'nims')
app.config['log_path'] = args.log_path or app.config['log_path'] app.config['quarantine_path'] = os.path.join(args.data_path, 'quarantine')
app.config['oauth2_id_endpoint'] = args.oauth2_id_endpoint or config.get('oauth2', 'id_endpoint') app.config['log_path'] = args.log_path
app.config['insecure'] = config.getboolean('nims', 'insecure') app.config['oauth2_id_endpoint'] = args.oauth2_id_endpoint
app.config['ssl_cert'] = args.ssl_cert or config.get('nims', 'ssl_cert') # to give to requests app.config['insecure'] = args.insecure
app.config['demo'] = arg.demo or config.getboolean('nims', 'demo') app.config['ssl_cert'] = args.ssl_cert
app.config['demo'] = args.demo
if not app.config['ssl_cert']: if not app.config['ssl_cert']:
log.warning('SSL certificate not specified, interNIMS functionality disabled') log.warning('SSL certificate not specified, interNIMS functionality disabled')
elif not app.config['site_id']:
log.warning('site_id not configured, interNIMS functionality disabled')
if not os.path.exists(app.config['data_path']): if not os.path.exists(app.config['data_path']):
os.makedirs(app.config['data_path']) os.makedirs(app.config['data_path'])
...@@ -148,8 +149,7 @@ if __name__ == '__main__': ...@@ -148,8 +149,7 @@ if __name__ == '__main__':
os.makedirs(app.config['quarantine_path']) os.makedirs(app.config['quarantine_path'])
kwargs = dict(tz_aware=True) kwargs = dict(tz_aware=True)
db_uri = args.db_uri or config.get('nims', 'db_uri') db_client = pymongo.MongoReplicaSetClient(args.db_uri, **kwargs) if 'replicaSet' in args.db_uri else pymongo.MongoClient(args.db_uri, **kwargs)
db_client = pymongo.MongoReplicaSetClient(db_uri, **kwargs) if 'replicaSet' in db_uri else pymongo.MongoClient(db_uri, **kwargs)
app.db = db_client.get_default_database() app.db = db_client.get_default_database()
app.debug = True # send stack trace for uncaught exceptions to client app.debug = True # send stack trace for uncaught exceptions to client
......
api.wsgi
+ 47
− 47
View file @ acd5ba3b
# @author: Gunnar Schaefer, Kevin S. Hahn # @author: Gunnar Schaefer, Kevin S. Hahn
import os import os
import sys
import site
import time import time
import logging
import pymongo
import argparse
import uwsgidecorators
import ConfigParser import api
import internimsclient
configfile = '/service/config/production.ini'
config = ConfigParser.ConfigParser(allow_no_value=True)
config.read(configfile)
site.addsitedir(os.path.join(config.get('nims', 'virtualenv'), 'lib/python2.7/site-packages')) os.environ['PYTHON_EGG_CACHE'] = '/tmp/python_egg_cache'
sys.path.append(config.get('nims', 'here'))
os.environ['PYTHON_EGG_CACHE'] = config.get('nims', 'python_egg_cache')
os.umask(0o022) os.umask(0o022)
import pymongo ap = argparse.ArgumentParser()
import uwsgidecorators ap.add_argument('--db_uri', help='mongodb uri', required=True)
ap.add_argument('--data_path', help='path to data', required=True)
ap.add_argument('--log_path', help='path to log', required=True) # for SHOWING the log, not where to write
ap.add_argument('--ssl_cert', help='path to ssl cert in pem format, key+cert', required=True)
ap.add_argument('--api_uri', help='api uri')
ap.add_argument('--site_id', help='site id')
ap.add_argument('--site_name', help='site name', nargs='+')
ap.add_argument('--oauth2_id_endpoint', help='oauth2 id endpoint url', default='https://www.googleapis.com/plus/v1/people/me/openIdConnect')
ap.add_argument('--demo', help='demo mode, enables auto user creation', action='store_true', default=False)
ap.add_argument('--insecure', help='insecure mode', action='store_true', default=False)
ap.add_argument('--central_uri', help='scitran central api', default='https://sdmc.scitran.io/api')
ap.add_argument('--log_level', help='log level [info]', default='info')
args = ap.parse_args()
args.site_name = ' '.join(args.site_name) if args.site_name else None # site_name as string
import logging logging.basicConfig(level=getattr(logging, args.log_level.upper()))
import logging.config
logging.config.fileConfig(configfile, disable_existing_loggers=False)
log = logging.getLogger('nimsapi') log = logging.getLogger('nimsapi')
import api
import internimsclient
# configure uwsgi application # configure uwsgi application
application = api.app application = api.app
application.config['data_path'] = os.path.join(config.get('nims', 'data_path'), 'nims') application.config['site_id'] = args.site_id
application.config['quarantine_path'] = os.path.join(config.get('nims', 'data_path'), 'quarantine') application.config['site_name'] = args.site_name
application.config['log_path'] = config.get('nims', 'log_path') application.config['data_path'] = os.path.join(args.data_path, 'nims')
application.config['site_name'] = config.get('nims', 'site_name') application.config['quarantine_path'] = os.path.join(args.data_path, 'quarantine')
application.config['site_id'] = config.get('nims', 'site_id') application.config['log_path'] = args.log_path
application.config['ssl_cert'] = config.get('nims', 'ssl_cert') application.config['ssl_cert'] = args.ssl_cert
application.config['oauth2_id_endpoint'] = config.get('oauth2', 'id_endpoint') application.config['oauth2_id_endpoint'] = args.oauth2_id_endpoint
application.config['insecure'] = config.getboolean('nims', 'insecure') application.config['insecure'] = args.insecure
application.config['demo'] = config.getboolean('nims', 'demo') application.config['demo'] = args.demo
if not os.path.exists(application.config['data_path']): if not os.path.exists(application.config['data_path']):
os.makedirs(application.config['data_path']) os.makedirs(application.config['data_path'])
...@@ -46,13 +51,10 @@ if not os.path.exists(application.config['quarantine_path']): ...@@ -46,13 +51,10 @@ if not os.path.exists(application.config['quarantine_path']):
# connect to db # connect to db
kwargs = dict(tz_aware=True) kwargs = dict(tz_aware=True)
db_uri = config.get('nims', 'db_uri')
db_client = None
application.db = None application.db = None
for x in range(0, 30): for x in range(0, 30):
try: try:
db_client = pymongo.MongoReplicaSetClient(db_uri, **kwargs) if 'replicaSet' in db_uri else pymongo.MongoClient(db_uri, **kwargs) db_client = pymongo.MongoReplicaSetClient(args.db_uri, **kwargs) if 'replicaSet' in args.db_uri else pymongo.MongoClient(args.db_uri, **kwargs)
application.db = db_client.get_default_database() application.db = db_client.get_default_database()
except: except:
time.sleep(1) time.sleep(1)
...@@ -60,27 +62,25 @@ for x in range(0, 30): ...@@ -60,27 +62,25 @@ for x in range(0, 30):
else: else:
break break
else: else:
raise Exception("Could not connect to MongoDB") raise Exception('Could not connect to MongoDB')
# internims, send is-alive signals if not args.ssl_cert:
site_id = config.get('nims', 'site_id') log.warning('SSL certificate not specified, Scitran Central functionality disabled')
site_name = config.get('nims', 'site_name') elif not args.api_uri:
ssl_cert = config.get('nims', 'ssl_cert') log.warning('api_uri not configured. scitran central functionality disabled.')
api_uri = config.get('nims', 'api_uri') elif not args.site_name:
try: log.warning('site_name not configured. scitran central functionality disabled.')
internims_url = config.get('nims', 'internims_url') elif not args.site_id:
except ConfigParser.NoOptionError: log.warning('site_id not configured. scitran central functionality disabled.')
internims_url = None elif not args.central_uri:
fail_count = 0 log.warning('central_uri not configured. scitran central functionality disabled.')
if not internims_url or internims_url == u'':
log.debug('internims url not configured. internims disabled.')
else: else:
fail_count = 0
@uwsgidecorators.timer(60) @uwsgidecorators.timer(60)
def internimsclient_timer(signum): def internimsclient_timer(signum):
global fail_count global fail_count
if not internimsclient.update(application.db, api_uri, site_name, site_id, ssl_cert, internims_url): if not internimsclient.update(application.db, args.api_uri, args.site_name, args.site_id, args.ssl_cert, args.central_uri):
fail_count += 1 fail_count += 1
else: else:
fail_count = 0 fail_count = 0
......
internimsclient.py
+ 13
− 23
View file @ acd5ba3b
...@@ -11,6 +11,7 @@ local users are permitted to access data in other instances. ...@@ -11,6 +11,7 @@ local users are permitted to access data in other instances.
import logging import logging
import logging.config import logging.config
logging.basicConfig()
log = logging.getLogger('internims') log = logging.getLogger('internims')
logging.getLogger('requests').setLevel(logging.WARNING) # silence Requests library logging logging.getLogger('requests').setLevel(logging.WARNING) # silence Requests library logging
...@@ -81,42 +82,31 @@ def clean_remotes(db): ...@@ -81,42 +82,31 @@ def clean_remotes(db):
if __name__ == '__main__': if __name__ == '__main__':
import os
import time import time
import pymongo import pymongo
import argparse import argparse
import ConfigParser
arg_parser = argparse.ArgumentParser() arg_parser = argparse.ArgumentParser()
arg_parser.add_argument('configfile', help='path to configuration file') arg_parser.add_argument('--internims_url', help='Scitran Central API URL', default='https://sdmc.scitran.io')
arg_parser.add_argument('--internims_url', help='https://internims.appspot.com') arg_parser.add_argument('--db_uri', help='DB URI', required=True)
arg_parser.add_argument('--db_uri', help='DB URI') arg_parser.add_argument('--api_uri', help='API URL, without http:// or https://', required=True)
arg_parser.add_argument('--api_uri', help='API URL, without http:// or https://') arg_parser.add_argument('--site_id', help='instance hostname (used as unique ID)', required=True)
arg_parser.add_argument('--site_id', help='instance hostname (used as unique ID)') arg_parser.add_argument('--site_name', help='instance name', nargs='+', required=True)
arg_parser.add_argument('--site_name', help='instance name') arg_parser.add_argument('--ssl_cert', help='path to server ssl certificate file', required=True)
arg_parser.add_argument('--sleeptime', default=60, type=int, help='time to sleep between is alive signals') arg_parser.add_argument('--sleeptime', default=60, type=int, help='time to sleep between is alive signals')
arg_parser.add_argument('--ssl_cert', help='path to server ssl certificate file')
arg_parser.add_argument('--debug', help='enable default mode', action='store_true', default=False) arg_parser.add_argument('--debug', help='enable default mode', action='store_true', default=False)
arg_parser.add_argument('--log_level', help='log level [info]', default='info')
args = arg_parser.parse_args() args = arg_parser.parse_args()
args.site_name = ' '.join(args.site_name) if args.site_name else None # site_name as string
config = ConfigParser.ConfigParser({'here': os.path.dirname(os.path.abspath(args.configfile))}) logging.basicConfig()
config.read(args.configfile) log.setLevel(getattr(logging, args.log_level.upper()))
logging.config.fileConfig(args.configfile, disable_existing_loggers=False)
ssl_cert = args.ssl_cert or config.get('nims', 'ssl_cert') db = (pymongo.MongoReplicaSetClient(args.db_uri) if 'replicaSet' in args.db_uri else pymongo.MongoClient(args.db_uri)).get_default_database()
db_uri = args.db_uri or config.get('nims', 'db_uri')
db = (pymongo.MongoReplicaSetClient(db_uri) if 'replicaSet' in db_uri else pymongo.MongoClient(db_uri)).get_default_database()
site_name = args.site_name or config.get('nims', 'site_name')
site_id = args.site_id or config.get('nims', 'site_id')
api_uri = args.api_uri or config.get('nims', 'api_uri')
internims_url = args.internims_url or config.get('nims', 'internims_url')
debug = args.debug or config.get('nims', 'insecure')
fail_count = 0 fail_count = 0
while True: while True:
if not update(db, api_uri, site_name, site_id, ssl_cert, internims_url): if not update(db, args.api_uri, args.site_name, args.site_id, args.ssl_cert, args.internims_url):
fail_count += 1 fail_count += 1
else: else:
fail_count = 0 fail_count = 0
......
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