#!/usr/bin/env python
#
# @author: Gunnar Schaefer, Kevin S. Hahn
import logging
import logging.config
log = logging.getLogger('scitran.api')
logging.getLogger('scitran.data').setLevel(logging.WARNING) # silence scitran.data logging
logging.getLogger('MARKDOWN').setLevel(logging.WARNING) # silence Markdown library logging
import os
import json
import webapp2
import bson.json_util
import webapp2_extras.routes
import core
import users
import projects
import sessions
import acquisitions
import collections_
routes = [
webapp2.Route(r'/api', core.Core),
webapp2_extras.routes.PathPrefixRoute(r'/api', [
webapp2.Route(r'/download', core.Core, handler_method='download', methods=['GET', 'POST'], name='download'),
webapp2.Route(r'/sites', core.Core, handler_method='sites', methods=['GET']),
webapp2.Route(r'/log', core.Core, handler_method='log', methods=['GET']),
webapp2.Route(r'/search', core.Core, handler_method='search', methods=['GET', 'POST']),
]),
webapp2.Route(r'/api/users', users.Users),
webapp2_extras.routes.PathPrefixRoute(r'/api/users', [
webapp2.Route(r'/count', users.Users, handler_method='count', methods=['GET']),
webapp2.Route(r'/self', users.User, handler_method='self', methods=['GET']),
webapp2.Route(r'/roles', users.User, handler_method='roles', methods=['GET']),
webapp2.Route(r'/schema', users.User, handler_method='schema', methods=['GET']),
webapp2.Route(r'/<_id>', users.User, name='user'),
webapp2.Route(r'/<_id>/groups', users.Groups, name='groups'),
]),
webapp2.Route(r'/api/groups', users.Groups),
webapp2_extras.routes.PathPrefixRoute(r'/api/groups', [
webapp2.Route(r'/count', users.Groups, handler_method='count', methods=['GET']),
webapp2.Route(r'/schema', users.Group, handler_method='schema', methods=['GET']),
webapp2.Route(r'/<_id>', users.Group, name='group'),
]),
webapp2.Route(r'/api/projects', projects.Projects),
webapp2_extras.routes.PathPrefixRoute(r'/api/projects', [
webapp2.Route(r'/count', projects.Projects, handler_method='count', methods=['GET']),
webapp2.Route(r'/groups', projects.Projects, handler_method='groups', methods=['GET']),
webapp2.Route(r'/schema', projects.Project, handler_method='schema', methods=['GET']),
webapp2.Route(r'/<:[0-9a-f]{24}>', projects.Project, name='project'),
webapp2.Route(r'/<:[0-9a-f]{24}>/file', projects.Project, handler_method='get_file', methods=['GET', 'POST']),
webapp2.Route(r'/<:[0-9a-f]{24}>/file', projects.Project, handler_method='put_file', methods=['PUT']),
webapp2.Route(r'/<:[0-9a-f]{24}>/sessions', sessions.Sessions, name='sessions'),
]),
webapp2.Route(r'/api/collections', collections_.Collections),
webapp2_extras.routes.PathPrefixRoute(r'/api/collections', [
webapp2.Route(r'/count', collections_.Collections, handler_method='count', methods=['GET']),
webapp2.Route(r'/curators', collections_.Collections, handler_method='curators', methods=['GET']),
webapp2.Route(r'/schema', collections_.Collection, handler_method='schema', methods=['GET']),
webapp2.Route(r'/<:[0-9a-f]{24}>', collections_.Collection, name='collection'),
webapp2.Route(r'/<:[0-9a-f]{24}>/file', collections_.Collection, handler_method='get_file', methods=['GET', 'POST']),
webapp2.Route(r'/<:[0-9a-f]{24}>/file', collections_.Collection, handler_method='put_file', methods=['PUT']),
webapp2.Route(r'/<:[0-9a-f]{24}>/sessions', collections_.CollectionSessions, name='coll_sessions'),
webapp2.Route(r'/<:[0-9a-f]{24}>/acquisitions', collections_.CollectionAcquisitions, name='coll_acquisitions'),
]),
webapp2_extras.routes.PathPrefixRoute(r'/api/sessions', [
webapp2.Route(r'/count', sessions.Sessions, handler_method='count', methods=['GET']),
webapp2.Route(r'/schema', sessions.Session, handler_method='schema', methods=['GET']),
webapp2.Route(r'/<:[0-9a-f]{24}>', sessions.Session, name='session'),
webapp2.Route(r'/<:[0-9a-f]{24}>/file', sessions.Session, handler_method='get_file', methods=['GET', 'POST']),
webapp2.Route(r'/<:[0-9a-f]{24}>/file', sessions.Session, handler_method='put_file', methods=['PUT']),
webapp2.Route(r'/<:[0-9a-f]{24}>/acquisitions', acquisitions.Acquisitions, name='acquisitions'),
]),
webapp2_extras.routes.PathPrefixRoute(r'/api/acquisitions', [
webapp2.Route(r'/count', acquisitions.Acquisitions, handler_method='count', methods=['GET']),
webapp2.Route(r'/schema', acquisitions.Acquisition, handler_method='schema', methods=['GET']),
webapp2.Route(r'/<:[0-9a-f]{24}>', acquisitions.Acquisition, name='acquisition'),
webapp2.Route(r'/<:[0-9a-f]{24}>/file', acquisitions.Acquisition, handler_method='get_file', methods=['GET', 'POST']),
webapp2.Route(r'/<:[0-9a-f]{24}>/file', acquisitions.Acquisition, handler_method='put_file', methods=['PUT']),
]),
]
def dispatcher(router, request, response):
rv = router.default_dispatcher(request, response)
if rv is not None:
response.write(json.dumps(rv, default=bson.json_util.default))
response.headers['Content-Type'] = 'application/json; charset=utf-8'
app = webapp2.WSGIApplication(routes)
app.router.set_dispatcher(dispatcher)
app.config = {
'data_path': 'nims',
'quarantine_path': 'quarantine',
'site_id': 'local',
'site_name': 'Local',
'ssl_cert': None,
'insecure': False,
'log_path': None,
'demo': False,
}
if __name__ == '__main__':
import pymongo
import argparse
import paste.httpserver
arg_parser = argparse.ArgumentParser()
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('--db_uri', help='NIMS DB URI', required=True)
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', required=True)
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='site ID for Scitran Central')
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', default='https://www.googleapis.com/plus/v1/people/me/openIdConnect')
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.site_name = ' '.join(args.site_name) if args.site_name else None # site_name as string
logging.basicConfig()
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
app.config['site_name'] = args.site_name
app.config['data_path'] = os.path.join(args.data_path, 'nims')
app.config['quarantine_path'] = os.path.join(args.data_path, 'quarantine')
app.config['log_path'] = args.log_path
app.config['oauth2_id_endpoint'] = args.oauth2_id_endpoint
app.config['insecure'] = args.insecure
app.config['ssl_cert'] = args.ssl_cert
app.config['demo'] = args.demo
if not app.config['ssl_cert']:
log.warning('SSL certificate not specified, scitran central functionality disabled')
elif not app.config['site_id']:
log.warning('site_id not configured, scitran central functionality disabled')
if not os.path.exists(app.config['data_path']):
os.makedirs(app.config['data_path'])
if not os.path.exists(app.config['quarantine_path']):
os.makedirs(app.config['quarantine_path'])
kwargs = dict(tz_aware=True)
db_client = pymongo.MongoReplicaSetClient(args.db_uri, **kwargs) if 'replicaSet' in args.db_uri else pymongo.MongoClient(args.db_uri, **kwargs)
app.db = db_client.get_default_database()
app.debug = True # send stack trace for uncaught exceptions to client
paste.httpserver.serve(app, host=args.host, port=args.port, ssl_pem=args.ssl_cert)