diff --git a/api.py b/api.py
index e51679a68b2902f6a79e07737f096f850e30c5fe..ab2695647530bd37255b4e7d1f4231e5fece241a 100755
--- a/api.py
+++ b/api.py
@@ -3,7 +3,11 @@
# @author: Gunnar Schaefer, Kevin S. Hahn
import logging
-import logging.config
+logging.basicConfig(
+ format='%(asctime)s %(name)16.16s:%(levelname)4.4s %(message)s',
+ datefmt='%Y-%m-%d %H:%M:%S',
+ level=logging.DEBUG,
+ )
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
@@ -90,16 +94,6 @@ def dispatcher(router, request, response):
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__':
@@ -108,39 +102,29 @@ if __name__ == '__main__':
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('--host', default='127.0.0.1', help='IP address to bind to [127.0.0.1]')
+ arg_parser.add_argument('--port', default='8080', help='TCP port to listen on [8080]')
+ arg_parser.add_argument('--db_uri', help='SciTran DB URI', default='mongodb://localhost/scitran')
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('--log_level', help='log level [info]', default='info')
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('--site_id', help='site ID for Scitran Central [local]', default='local')
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')
+ arg_parser.add_argument('--demo', help='enable automatic user creation', action='store_true', default=False)
+ arg_parser.add_argument('--insecure', help='allow user info as urlencoded param', action='store_true', default=False)
args = arg_parser.parse_args()
- args.site_name = ' '.join(args.site_name) if args.site_name else None # site_name as string
- logging.basicConfig()
+ args.data_path = os.path.join(args.data_path, 'scitran')
+ args.quarantine_path = os.path.join(args.data_path, 'quarantine')
+ app.config = vars(args)
+
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')
+ log.warning('SSL certificate not specified, SciTran Central functionality disabled')
+ if app.config['site_id'] == 'local':
+ 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'])
diff --git a/api.wsgi b/api.wsgi
index 3743b69eac241bfe94dd21f2def5777f833341e7..08caff2aae9c63c74f75d926d2a41bae6733f5f6 100644
--- a/api.wsgi
+++ b/api.wsgi
@@ -14,35 +14,28 @@ os.environ['PYTHON_EGG_CACHE'] = '/tmp/python_egg_cache'
os.umask(0o022)
ap = argparse.ArgumentParser()
-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('--db_uri', help='SciTran DB URI', required=True)
+ap.add_argument('--data_path', help='path to storage area', required=True)
+ap.add_argument('--ssl_cert', help='path to SSL certificate file, containing private key and certificate chain', required=True)
ap.add_argument('--api_uri', help='api uri, with https:// prefix')
-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('--site_id', help='site ID for Scitran Central [local]', default='local')
+ap.add_argument('--site_name', help='site name')
+ap.add_argument('--oauth2_id_endpoint', help='OAuth2 provider ID endpoint', default='https://www.googleapis.com/plus/v1/people/me/openIdConnect')
+ap.add_argument('--demo', help='enable automatic user creation', action='store_true', default=False)
+ap.add_argument('--insecure', help='allow user info as urlencoded param', 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
-logging.basicConfig(level=getattr(logging, args.log_level.upper()))
+args.data_path = os.path.join(args.data_path, 'scitran')
+args.quarantine_path = os.path.join(args.data_path, 'quarantine')
+
+logging.basicConfig(level=getattr(logging, args.log_level.upper())) #FIXME probably not necessary, because done in api.py
log = logging.getLogger('nimsapi')
# configure uwsgi application
application = api.app
-application.config['site_id'] = args.site_id
-application.config['site_name'] = args.site_name
-application.config['data_path'] = os.path.join(args.data_path, 'nims')
-application.config['quarantine_path'] = os.path.join(args.data_path, 'quarantine')
-application.config['log_path'] = args.log_path
-application.config['ssl_cert'] = args.ssl_cert
-application.config['oauth2_id_endpoint'] = args.oauth2_id_endpoint
-application.config['insecure'] = args.insecure
-application.config['demo'] = args.demo
+application.config = vars(args)
if not os.path.exists(application.config['data_path']):
os.makedirs(application.config['data_path'])
diff --git a/base.py b/base.py
index d46a7a68913249b5c1c068660c8005a003d48a13..da3d5f06998ef947a4960b837ff40f13d14b7c52 100644
--- a/base.py
+++ b/base.py
@@ -14,8 +14,6 @@ import requests
class RequestHandler(webapp2.RequestHandler):
- """fetches pubkey from own self.db.remotes. needs to be aware of OWN site uid"""
-
json_schema = None
def __init__(self, request=None, response=None):
@@ -54,7 +52,7 @@ class RequestHandler(webapp2.RequestHandler):
if self.request.environ['SSL_CLIENT_VERIFY'] != 'SUCCESS':
self.abort(401, 'no valid SSL client certificate')
remote_instance = self.request.user_agent.replace('NIMS Instance', '').strip()
- if not self.app.db.remotes.find_one({'_id': remote_instance}):
+ if not self.app.db.sites.find_one({'_id': remote_instance}):
self.abort(402, remote_instance + ' is not authorized')
self.public_request = not bool(self.uid)
if self.public_request or self.source_site:
@@ -88,7 +86,7 @@ class RequestHandler(webapp2.RequestHandler):
self.abort(500, 'api site_id is not configured')
if not self.app.config['ssl_cert']:
self.abort(500, 'api ssl_cert is not configured')
- target = self.app.db.remotes.find_one({'_id': target_site}, ['api_uri'])
+ target = self.app.db.sites.find_one({'_id': target_site}, ['api_uri'])
if not target:
self.abort(402, 'remote host ' + target_site + ' is not an authorized remote')
# adjust headers
diff --git a/centralclient.py b/centralclient.py
index 54dea35b048d39c3b6fced9599a08855f3f72650..0168d4455d92c5322a4fded586a19bc9901fec26 100755
--- a/centralclient.py
+++ b/centralclient.py
@@ -51,8 +51,8 @@ def update(db, api_uri, site_name, site_id, ssl_cert, central_url):
for _id, remotes in response['users'].iteritems():
db.users.update({'_id': _id}, {'$set': {'remotes': remotes}})
if sites:
- db.remotes.remove({'_id': {'$nin': [site['_id'] for site in response['sites']]}})
- [db.remotes.update({'_id': site['_id']}, site, upsert=True) for site in sites]
+ db.sites.remove({'_id': {'$nin': [site['_id'] for site in response['sites']]}})
+ [db.sites.update({'_id': site['_id']}, site, upsert=True) for site in sites]
db.users.update( # clean users who no longer have remotes
{'remotes': {'$exists': True}, '_id': {'$nin': users.keys()}},
{'$unset': {'remotes': ''}},
@@ -60,7 +60,7 @@ def update(db, api_uri, site_name, site_id, ssl_cert, central_url):
)
log.info('%3d users with remote data, %3d remotes' % (
len([u['_id'] for u in db.users.find({'remotes': {'$exists': True}}, {'_id': True})]),
- len([s['_id'] for s in db.remotes.find({}, {'_id': True})])
+ len([s['_id'] for s in db.sites.find({}, {'_id': True})])
))
return True
else:
@@ -76,9 +76,9 @@ def update(db, api_uri, site_name, site_id, ssl_cert, central_url):
def clean_remotes(db):
- """Remove db.remotes, and removes remotes field from all db.users."""
+ """Remove db.sites, and removes remotes field from all db.users."""
log.debug('removing remotes from users, and remotes collection')
- db.remotes.remove({})
+ db.sites.remove({})
db.users.update({'remotes': {'$exists': True}}, {'$unset': {'remotes': ''}}, multi=True)
diff --git a/collections_.py b/collections_.py
index 6e75a922aa13da0c461f91b3d42dd0085b77a692..2d6955cae9eaebb457958c7d05f2dfabe3ba76bd 100644
--- a/collections_.py
+++ b/collections_.py
@@ -145,10 +145,6 @@ COLLECTION_SCHEMA = {
'site': {
'type': 'string',
},
- 'site_name': {
- 'title': 'Site',
- 'type': 'string',
- },
'permissions': {
'title': 'Permissions',
'type': 'array',
diff --git a/core.py b/core.py
index 14699dcd599c8e8e3e8bbf584d5d54b9bdaf9527..fded44f9e27ea55a480bf38a562ae0c856cd8280 100644
--- a/core.py
+++ b/core.py
@@ -186,28 +186,14 @@ class Core(base.RequestHandler):
def sites(self):
"""Return local and remote sites."""
+ if self.app.config['site_id'] == 'local':
+ return [{'_id': 'local', 'name': 'Local', 'onload': True}]
if self.public_request or self.request.get('all').lower() in ('1', 'true'):
- sites = list(self.app.db.remotes.find(None, ['name']))
+ sites = list(self.app.db.sites.find(None, ['name']))
else:
- sites = (self.app.db.users.find_one({'_id': self.uid}, ['remotes']) or {}).get('remotes', [])
- return sites + [{'_id': self.app.config['site_id'], 'name': self.app.config['site_name'], 'onload': True}]
-
- def log(self):
- """Return logs."""
- try:
- logs = open(self.app.config['log_path']).readlines()
- except IOError as e:
- if 'Permission denied' in e:
- body_template = '${explanation}<br /><br />${detail}<br /><br />${comment}'
- comment = 'To fix permissions, run the following command: chmod o+r ' + self.app.config['log_path']
- self.abort(500, detail=str(e), comment=comment, body_template=body_template)
- else: # file does not exist
- self.abort(500, 'log_path variable misconfigured or not set')
- try:
- n = int(self.request.get('n', 10000))
- except:
- self.abort(400, 'n must be an integer')
- return [line.strip() for line in reversed(logs) if re.match('[-:0-9 ]{18} +api:(?!.*[/a-z]*/log )', line)][:n]
+ remote_ids = (self.app.db.users.find_one({'_id': self.uid}, ['remotes']) or {}).get('remotes', []) + [self.app.config['site_id']]
+ sites = list(self.app.db.sites.find({'_id': {'$in': remote_ids}}, ['name']))
+ return sites
search_schema = {
'title': 'Search',
diff --git a/projects.py b/projects.py
index c8d2ebeb46df865794a71d73e11549d6e0c9b290..b1c0b21e3e251463a0a7105a73470802729ec2de 100644
--- a/projects.py
+++ b/projects.py
@@ -103,13 +103,6 @@ class Project(containers.Container):
'properties': {
'_id': {
},
- 'site': {
- 'type': 'string',
- },
- 'site_name': {
- 'title': 'Site',
- 'type': 'string',
- },
'permissions': {
'title': 'Permissions',
'type': 'object',
@@ -138,8 +131,6 @@ class Project(containers.Container):
"""Return one Project, conditionally with details."""
_id = bson.ObjectId(pid)
proj, _ = self._get(_id)
- proj['site'] = self.app.config['site_id']
- proj['site_name'] = self.app.config['site_name']
if self.debug:
proj['sessions'] = self.uri_for('sessions', pid, _full=True) + '?' + self.request.query_string
return proj