diff --git a/__init__.py b/__init__.py
index 28865f4b02b3b614d830ddfbb2e1132c9a4b06f0..e1e8b10697488c379dc643d1be9e177b23337379 100644
--- a/__init__.py
+++ b/__init__.py
@@ -1,3 +1,5 @@
# @author: Gunnar Schaefer
import nimsapi
+
+app = nimsapi.app
diff --git a/epochs.py b/epochs.py
index 945e06fc794b973a92ec24f83e17a16e7dc01aaa..34629c898fd07d2b40238a8ac9a998953dd7241e 100644
--- a/epochs.py
+++ b/epochs.py
@@ -9,9 +9,43 @@ import nimsapiutil
class Epochs(nimsapiutil.NIMSRequestHandler):
+ json_schema = {
+ '$schema': 'http://json-schema.org/draft-04/schema#',
+ 'title': 'Epoch List',
+ 'type': 'array',
+ 'items': {
+ 'title': 'Epoch',
+ 'type': 'object',
+ 'properties': {
+ '_id': {
+ 'title': 'Database ID',
+ },
+ 'timestamp': {
+ 'title': 'Timestamp',
+ },
+ 'datatype': {
+ 'title': 'Datatype',
+ 'type': 'string',
+ },
+ 'series': {
+ 'title': 'Series',
+ 'type': 'integer',
+ },
+ 'acquisition': {
+ 'title': 'Acquisition',
+ 'type': 'integer',
+ },
+ 'description': {
+ 'title': 'Description',
+ 'type': 'string',
+ },
+ }
+ }
+ }
+
def count(self, iid):
"""Return the number of Epochs."""
- self.response.write('epochs count\n')
+ self.response.write(json.dumps(self.app.db.epochs.count()))
def post(self, iid):
"""Create a new Epoch."""
@@ -39,6 +73,142 @@ class Epochs(nimsapiutil.NIMSRequestHandler):
class Epoch(nimsapiutil.NIMSRequestHandler):
+ json_schema = {
+ '$schema': 'http://json-schema.org/draft-04/schema#',
+ 'title': 'Epoch',
+ 'type': 'object',
+ 'properties': {
+ '_id': {
+ 'title': 'Database ID',
+ },
+ 'session': {
+ 'title': 'Session ID',
+ },
+ 'timestamp': {
+ 'title': 'Timestamp',
+ },
+ 'session_uid': {
+ 'title': 'DICOM UID',
+ 'type': 'string',
+ },
+ 'datatype': {
+ 'title': 'Datatype',
+ 'type': 'string',
+ },
+ 'series': {
+ 'title': 'Series',
+ 'type': 'integer',
+ },
+ 'acquisition': {
+ 'title': 'Acquisition',
+ 'type': 'integer',
+ },
+ 'description': {
+ 'title': 'Description',
+ 'type': 'string',
+ 'maxLength': 64,
+ },
+ 'protocol': {
+ 'title': 'Protocol',
+ 'type': 'string',
+ 'maxLength': 64,
+ },
+ 'rx_coil': {
+ 'title': 'Coil',
+ 'type': 'string',
+ 'maxLength': 64,
+ },
+ 'device': {
+ 'title': 'Device',
+ 'type': 'string',
+ 'maxLength': 64,
+ },
+ 'size': {
+ 'title': 'Size',
+ 'type': 'array',
+ 'items': {
+ 'type': 'integer',
+ }
+ },
+ 'acquisition_matrix': {
+ 'title': 'Acquisition Matrix',
+ 'type': 'array',
+ 'items': {
+ 'type': 'number',
+ }
+ },
+ 'fov': {
+ 'title': 'Field of View',
+ 'type': 'array',
+ 'items': {
+ 'type': 'number',
+ }
+ },
+ 'mm_per_voxel': {
+ 'title': 'mm per Voxel',
+ 'type': 'array',
+ 'items': {
+ 'type': 'number',
+ }
+ },
+ 'flip_angle': {
+ 'title': 'Flip Angle',
+ 'type': 'integer',
+ },
+ 'num_averages': {
+ 'title': 'Averages',
+ 'type': 'integer',
+ },
+ 'num_bands': {
+ 'title': 'Bands',
+ 'type': 'integer',
+ },
+ 'num_echos': {
+ 'title': 'Echos',
+ 'type': 'integer',
+ },
+ 'num_slices': {
+ 'title': 'Slices',
+ 'type': 'integer',
+ },
+ 'num_timepoints': {
+ 'title': 'Time Points',
+ 'type': 'integer',
+ },
+ 'pixel_bandwidth': {
+ 'title': 'Pixel Bandwidth',
+ 'type': 'number',
+ },
+ 'prescribed_duration': {
+ 'title': 'Prescribed Duration',
+ 'type': 'number',
+ },
+ 'duration': {
+ 'title': 'Duration',
+ 'type': 'number',
+ },
+ 'slice_encode_undersample': {
+ 'title': 'Slice Encode Undersample',
+ 'type': 'integer',
+ },
+ 'te': {
+ 'title': 'Te',
+ 'type': 'number',
+ },
+ 'tr': {
+ 'title': 'Tr',
+ 'type': 'number',
+ },
+ 'files': {
+ 'title': 'Files',
+ 'type': 'array',
+ 'items': nimsapiutil.NIMSRequestHandler.file_schema,
+ 'uniqueItems': True,
+ },
+ },
+ 'required': ['_id'],
+ }
+
def get(self, iid, eid):
"""Return one Epoch, conditionally with details."""
epoch = self.app.db.epochs.find_one({'_id': bson.objectid.ObjectId(eid)})
diff --git a/experiments.py b/experiments.py
index 8c0acfd767577866b7a4fd4a06bf678738a198dd..e617c338c2ad24416204a91c4dcdbad53b9db279 100644
--- a/experiments.py
+++ b/experiments.py
@@ -9,9 +9,35 @@ import nimsapiutil
class Experiments(nimsapiutil.NIMSRequestHandler):
+ json_schema = {
+ '$schema': 'http://json-schema.org/draft-04/schema#',
+ 'title': 'Experiment List',
+ 'type': 'array',
+ 'items': {
+ 'title': 'Experiment',
+ 'type': 'object',
+ 'properties': {
+ '_id': {
+ 'title': 'Database ID',
+ },
+ 'firstname': {
+ 'title': 'First Name',
+ 'type': 'string',
+ },
+ 'lastname': {
+ 'title': 'Last Name',
+ 'type': 'string',
+ },
+ 'email_hash': {
+ 'type': 'string',
+ },
+ }
+ }
+ }
+
def count(self, iid):
"""Return the number of Experiments."""
- self.response.write('%d experiments\n' % self.app.db.experiments.count())
+ self.response.write(json.dumps(self.app.db.experiments.count()))
def post(self, iid):
"""Create a new Experiment."""
@@ -38,6 +64,41 @@ class Experiments(nimsapiutil.NIMSRequestHandler):
class Experiment(nimsapiutil.NIMSRequestHandler):
+ json_schema = {
+ '$schema': 'http://json-schema.org/draft-04/schema#',
+ 'title': 'Experiment',
+ 'type': 'object',
+ 'properties': {
+ '_id': {
+ 'title': 'Database ID',
+ },
+ 'timestamp': {
+ 'title': 'Timestamp',
+ },
+ 'group': {
+ 'title': 'Group',
+ 'type': 'string',
+ },
+ 'name': {
+ 'title': 'Name',
+ 'type': 'string',
+ 'maxLength': 32,
+ },
+ 'permissions': {
+ 'title': 'Permissions',
+ 'type': 'object',
+ 'minProperties': 1,
+ },
+ 'files': {
+ 'title': 'Files',
+ 'type': 'array',
+ 'items': nimsapiutil.NIMSRequestHandler.file_schema,
+ 'uniqueItems': True,
+ },
+ },
+ 'required': ['_id', 'group', 'name'],
+ }
+
def get(self, iid, xid):
"""Return one Experiment, conditionally with details."""
experiment = self.app.db.experiments.find_one({'_id': bson.objectid.ObjectId(xid)})
diff --git a/nimsapi.py b/nimsapi.py
index 717f5f081a8cdc637c66de78b83dfdfebf0a9139..030afccd00346ddfeb7cb28512ef3888155a05a3 100755
--- a/nimsapi.py
+++ b/nimsapi.py
@@ -34,8 +34,44 @@ class NIMSAPI(nimsapiutil.NIMSRequestHandler):
def get(self):
"""Return API documentation"""
+ resources = [
+ ('/experiments', 'list of experiments'),
+ ('/collections', 'list of collections'),
+ ('/experiments/<xid>/sessions', 'list of sessions for one experiment'),
+ ('/collections/<xid>/sessions', 'list of sessions for one collection'),
+ ('/sessions/<sid>/epochs', 'list of epochs for one session'),
+ ('', ''),
+ ('/experiments/<xid>', 'details for one experiment'),
+ ('/collections/<xid>', 'details for one collection'),
+ ('/sessions/<sid>', 'details for one session'),
+ ('/epochs/<eid>', 'details for one epoch'),
+ ('', ''),
+ ('/users', 'list of users'),
+ ('/groups', 'list of groups'),
+ ('/users/<uid>', 'details for one user'),
+ ('/groups/<gid>', 'details for one group'),
+ ]
self.response.headers['Content-Type'] = 'text/html; charset=utf-8'
- self.response.write('nimsapi - {0}\n'.format(self.app.config['site_id']))
+ self.response.write('<html>\n')
+ self.response.write('<head>\n')
+ self.response.write('<title>NIMSAPI</title>\n')
+ self.response.write('<style type="text/css">\n')
+ self.response.write('.tftable {font-size:12px;color:#333333;width:100%;border-width: 1px;border-color: #a9a9a9;border-collapse: collapse;}\n')
+ self.response.write('.tftable th {font-size:12px;background-color:#b8b8b8;border-width: 1px;padding: 8px;border-style: solid;border-color: #a9a9a9;text-align:left;}\n')
+ self.response.write('.tftable tr {background-color:#cdcdcd;}\n')
+ self.response.write('.tftable td {font-size:12px;border-width: 1px;padding: 8px;border-style: solid;border-color: #a9a9a9;}\n')
+ self.response.write('</style>\n')
+ self.response.write('</head>\n')
+ self.response.write('<body>\n')
+ self.response.write('<p>nimsapi - ' + self.app.config['site_id'] + '</p>\n')
+ self.response.write('<table class="tftable" border="1">\n')
+ self.response.write('<tr><th>Resource</th><th>Description</th></tr>\n')
+ for r, d in resources:
+ r = r.replace('<', '<').replace('>', '>')
+ self.response.write('<tr><td>%s</td><td>%s</td></tr>\n' % (r, d))
+ self.response.write('</table>\n')
+ self.response.write('</body>\n')
+ self.response.write('</html>\n')
def upload(self):
# TODO add security: either authenticated user or machine-to-machine CRAM
@@ -46,7 +82,7 @@ class NIMSAPI(nimsapiutil.NIMSRequestHandler):
with nimsutil.TempDir(prefix='.tmp', dir=stage_path) as tempdir_path:
hash_ = hashlib.md5()
upload_filepath = os.path.join(tempdir_path, filename)
- log.info(os.path.basename(upload_filepath))
+ log.info('receiving upload ' + os.path.basename(upload_filepath))
with open(upload_filepath, 'wb') as upload_file:
for chunk in iter(lambda: self.request.body_file.read(2**20), ''):
hash_.update(chunk)
@@ -55,7 +91,7 @@ class NIMSAPI(nimsapiutil.NIMSRequestHandler):
self.abort(400, 'Content-MD5 mismatch.')
if not tarfile.is_tarfile(upload_filepath) and not zipfile.is_zipfile(upload_filepath):
self.abort(415)
- os.rename(upload_filepath, os.path.join(stage_path, str(uuid.uuid1()) + '_' + fid)) # add UUID to prevent clobbering files
+ os.rename(upload_filepath, os.path.join(stage_path, str(uuid.uuid1()) + '_' + filename)) # add UUID to prevent clobbering files
def download(self):
paths = []
@@ -72,6 +108,42 @@ class NIMSAPI(nimsapiutil.NIMSRequestHandler):
class Users(nimsapiutil.NIMSRequestHandler):
+ json_schema = {
+ '$schema': 'http://json-schema.org/draft-04/schema#',
+ 'title': 'User List',
+ 'type': 'array',
+ 'items': {
+ 'title': 'User',
+ 'type': 'object',
+ 'properties': {
+ '_id': {
+ 'title': 'Database ID',
+ 'type': 'string',
+ },
+ 'firstname': {
+ 'title': 'First Name',
+ 'type': 'string',
+ 'default': '',
+ },
+ 'lastname': {
+ 'title': 'Last Name',
+ 'type': 'string',
+ 'default': '',
+ },
+ 'email': {
+ 'title': 'Email',
+ 'type': 'string',
+ 'format': 'email',
+ 'default': '',
+ },
+ 'email_hash': {
+ 'type': 'string',
+ 'default': '',
+ },
+ }
+ }
+ }
+
def count(self, iid):
"""Return the number of Users."""
self.response.write('%d users\n' % self.app.db.users.count())
@@ -93,6 +165,43 @@ class Users(nimsapiutil.NIMSRequestHandler):
class User(nimsapiutil.NIMSRequestHandler):
+ json_schema = {
+ '$schema': 'http://json-schema.org/draft-04/schema#',
+ 'title': 'User',
+ 'type': 'object',
+ 'properties': {
+ '_id': {
+ 'title': 'Database ID',
+ 'type': 'string',
+ },
+ 'firstname': {
+ 'title': 'First Name',
+ 'type': 'string',
+ 'default': '',
+ },
+ 'lastname': {
+ 'title': 'Last Name',
+ 'type': 'string',
+ 'default': '',
+ },
+ 'email': {
+ 'title': 'Email',
+ 'type': 'string',
+ 'format': 'email',
+ 'default': '',
+ },
+ 'email_hash': {
+ 'type': 'string',
+ 'default': '',
+ },
+ 'superuser': {
+ 'title': 'Superuser',
+ 'type': 'boolean',
+ },
+ },
+ 'required': ['_id'],
+ }
+
def get(self, iid, uid):
"""Return User details."""
user = self.app.db.users.find_one({'_id': uid})
@@ -127,6 +236,22 @@ class User(nimsapiutil.NIMSRequestHandler):
class Groups(nimsapiutil.NIMSRequestHandler):
+ json_schema = {
+ '$schema': 'http://json-schema.org/draft-04/schema#',
+ 'title': 'Group List',
+ 'type': 'array',
+ 'items': {
+ 'title': 'Group',
+ 'type': 'object',
+ 'properties': {
+ '_id': {
+ 'title': 'Database ID',
+ 'type': 'string',
+ },
+ }
+ }
+ }
+
def count(self, iid):
"""Return the number of Groups."""
self.response.write('%d groups\n' % self.app.db.groups.count())
@@ -148,6 +273,46 @@ class Groups(nimsapiutil.NIMSRequestHandler):
class Group(nimsapiutil.NIMSRequestHandler):
+ json_schema = {
+ '$schema': 'http://json-schema.org/draft-04/schema#',
+ 'title': 'Group',
+ 'type': 'object',
+ 'properties': {
+ '_id': {
+ 'title': 'Database ID',
+ 'type': 'string',
+ },
+ 'pis': {
+ 'title': 'PIs',
+ 'type': 'array',
+ 'default': [],
+ 'items': {
+ 'type': 'string',
+ },
+ 'uniqueItems': True,
+ },
+ 'admins': {
+ 'title': 'Admins',
+ 'type': 'array',
+ 'default': [],
+ 'items': {
+ 'type': 'string',
+ },
+ 'uniqueItems': True,
+ },
+ 'memebers': {
+ 'title': 'Members',
+ 'type': 'array',
+ 'default': [],
+ 'items': {
+ 'type': 'string',
+ },
+ 'uniqueItems': True,
+ },
+ },
+ 'required': ['_id'],
+ }
+
def get(self, iid, gid):
"""Return Group details."""
group = self.app.db.groups.find_one({'_id': gid})
@@ -207,8 +372,8 @@ class ArgumentParser(argparse.ArgumentParser):
super(ArgumentParser, self).__init__()
self.add_argument('uri', help='NIMS DB URI')
self.add_argument('stage_path', help='path to staging area')
- self.add_argument('--pubkey', default='internims/NIMSpubkey.pub', help='path to ssl pubkey')
- self.add_argument('-u', '--uid', default='local', help='site uid')
+ self.add_argument('-k', '--pubkey', help='path to public SSL key')
+ self.add_argument('-u', '--uid', default='local', help='site UID')
self.add_argument('-f', '--logfile', help='path to log file')
self.add_argument('-l', '--loglevel', default='info', help='path to log file')
self.add_argument('-q', '--quiet', action='store_true', default=False, help='disable console logging')
@@ -218,36 +383,53 @@ routes = [
webapp2_extras.routes.PathPrefixRoute(r'/nimsapi', [
webapp2.Route(r'/download', NIMSAPI, handler_method='download', methods=['GET']),
webapp2.Route(r'/dump', NIMSAPI, handler_method='dump', methods=['GET']),
- webapp2.Route(r'/upload/<fid>', NIMSAPI, handler_method='upload', methods=['PUT']),
+ webapp2.Route(r'/upload', NIMSAPI, handler_method='upload', methods=['PUT']),
webapp2.Route(r'/remotes', Remotes),
- ]),
- # webapp2_extras.routes.PathPrefixRoute has bug, variable MUST have regex
+ ]),
webapp2_extras.routes.PathPrefixRoute(r'/nimsapi/<iid:[^/]+>', [
webapp2.Route(r'/users', Users),
webapp2.Route(r'/users/count', Users, handler_method='count', methods=['GET']),
+ webapp2.Route(r'/users/listschema', Users, handler_method='schema', methods=['GET']),
+ webapp2.Route(r'/users/schema', User, handler_method='schema', methods=['GET']),
webapp2.Route(r'/users/<uid>', User),
webapp2.Route(r'/groups', Groups),
webapp2.Route(r'/groups/count', Groups, handler_method='count', methods=['GET']),
+ webapp2.Route(r'/groups/listschema', Groups, handler_method='schema', methods=['GET']),
+ webapp2.Route(r'/groups/schema', Group, handler_method='schema', methods=['GET']),
webapp2.Route(r'/groups/<gid>', Group),
webapp2.Route(r'/experiments', experiments.Experiments),
webapp2.Route(r'/experiments/count', experiments.Experiments, handler_method='count', methods=['GET']),
+ webapp2.Route(r'/experiments/listschema', experiments.Experiments, handler_method='schema', methods=['GET']),
+ webapp2.Route(r'/experiments/schema', experiments.Experiment, handler_method='schema', methods=['GET']),
webapp2.Route(r'/experiments/<xid:[0-9a-f]{24}>', experiments.Experiment),
webapp2.Route(r'/experiments/<xid:[0-9a-f]{24}>/sessions', sessions.Sessions),
webapp2.Route(r'/sessions/count', sessions.Sessions, handler_method='count', methods=['GET']),
+ webapp2.Route(r'/sessions/listschema', sessions.Sessions, handler_method='schema', methods=['GET']),
+ webapp2.Route(r'/sessions/schema', sessions.Session, handler_method='schema', methods=['GET']),
webapp2.Route(r'/sessions/<sid:[0-9a-f]{24}>', sessions.Session),
webapp2.Route(r'/sessions/<sid:[0-9a-f]{24}>/move', sessions.Session, handler_method='move'),
webapp2.Route(r'/sessions/<sid:[0-9a-f]{24}>/epochs', epochs.Epochs),
webapp2.Route(r'/epochs/count', epochs.Epochs, handler_method='count', methods=['GET']),
+ webapp2.Route(r'/epochs/listschema', epochs.Epochs, handler_method='schema', methods=['GET']),
+ webapp2.Route(r'/epochs/schema', epochs.Epoch, handler_method='schema', methods=['GET']),
webapp2.Route(r'/epochs/<eid:[0-9a-f]{24}>', epochs.Epoch),
]),
]
+app = webapp2.WSGIApplication(routes, debug=True)
+
if __name__ == '__main__':
args = ArgumentParser().parse_args()
nimsutil.configure_log(args.logfile, not args.quiet, args.loglevel)
from paste import httpserver
- app = webapp2.WSGIApplication(routes, debug=True, config=dict(stage_path=args.stage_path, site_id=args.uid, pubkey=args.pubkey))
+ app.config = dict(stage_path=args.stage_path, site_id=args.uid, pubkey=args.pubkey)
app.db = (pymongo.MongoReplicaSetClient(args.uri) if 'replicaSet' in args.uri else pymongo.MongoClient(args.uri)).get_default_database()
httpserver.serve(app, host=httpserver.socket.gethostname(), port='8080')
+
+# import nimsapi, webapp2, pymongo, bson.json_util
+# nimsapi.app.db = pymongo.MongoClient('mongodb://nims:cnimr750@slice.stanford.edu/nims').get_default_database()
+# response = webapp2.Request.blank('/nimsapi/local/users').get_response(nimsapi.app)
+# response.status
+# response.body
diff --git a/nimsapi.wsgi b/nimsapi.wsgi
index 7a83f7e4bf06cdde4962f753038394d9519ea68b..da8167645281ee17df0ec622978a3c87142a90da 100644
--- a/nimsapi.wsgi
+++ b/nimsapi.wsgi
@@ -17,11 +17,12 @@ import nimsapi
import nimsutil
logfile = '/var/local/log/nimsapi.log'
-db_uri = 'mongodb://nimsfs.stanford.edu,nimsbk.stanford.edu/nims?replicaSet=cni'
+db_uri = 'mongodb://nims:cnimr750@cnifs.stanford.edu,cnibk.stanford.edu/nims?replicaSet=cni'
stage_path = '/scratch/upload'
nimsutil.configure_log(logfile, False)
db_client = pymongo.MongoReplicaSetClient(db_uri) if 'replicaSet' in db_uri else pymongo.MongoClient(db_uri)
-application = webapp2.WSGIApplication(nimsapi.nimsapi.routes, debug=False, config=dict(stage_path=stage_path))
+application = nimsapi.app
+application.config = dict(stage_path=stage_path))
application.db = db_client.get_default_database()
diff --git a/nimsapiutil.py b/nimsapiutil.py
index 08d817be4766edbd25a068f25b2cbdcc8b362ace..231134761e95fa325ed45785d96b6a7b45827a0e 100644
--- a/nimsapiutil.py
+++ b/nimsapiutil.py
@@ -1,25 +1,62 @@
-# @author: Gunnar Schaefer
-# @author: Kevin S. Hahn
+# @author: Gunnar Schaefer, Kevin S. Hahn
-import base64
-import datetime
import json
+import base64
+import socket # socket.gethostname()
import logging
-import requests
import webapp2
-import socket # socket.gethostname()
+import datetime
+import requests
+import bson.json_util
from Crypto.Hash import HMAC
from Crypto.Random import random
-logging.basicConfig(level=logging.INFO)
+
+log = logging.getLogger('nimsapi')
class NIMSRequestHandler(webapp2.RequestHandler):
"""fetches pubkey from own self.db.remotes. needs to be aware of OWN site uid"""
+ json_schema = None
+
+ file_schema = {
+ 'title': 'File',
+ 'type': 'object',
+ 'properties': {
+ 'datakind': {
+ 'title': 'Data Kind',
+ 'type': 'string',
+ },
+ 'datatype': {
+ 'title': 'Data Type',
+ 'type': 'string',
+ },
+ 'filetype': {
+ 'title': 'File Type',
+ 'type': 'string',
+ },
+ 'filename': {
+ 'title': 'File Name',
+ 'type': 'string',
+ },
+ 'ext': {
+ 'title': 'File Name Extension',
+ 'type': 'string',
+ },
+ 'md5': {
+ 'title': 'MD5',
+ 'type': 'string',
+ },
+ 'size': {
+ 'title': 'Size',
+ 'type': 'integer',
+ },
+ }
+ }
+
def __init__(self, request=None, response=None):
- webapp2.RequestHandler.__init__(self, request, response)
- # call initialize, isntead of __init__
+ self.initialize(request, response)
self.request.remote_user = self.request.get('user', None) # FIXME: auth system should set REMOTE_USER
self.userid = self.request.remote_user or '@public'
self.user = self.app.db.users.find_one({'_id': self.userid})
@@ -29,18 +66,17 @@ class NIMSRequestHandler(webapp2.RequestHandler):
self.target_id = request.route_kwargs['iid'] # for what site is the request meant
except KeyError:
self.target_id = 'local' # change to site_id?
- self.useragent = self.request.headers['user-agent'] # browser or internimsP2P request
self.site_id = self.app.config['site_id'] # what is THIS site
- self.pubkey = open(self.app.config['pubkey']).read()
+ self.pubkey = open(self.app.config['pubkey']).read() if self.app.config['pubkey'] is not None else None
# requests coming from another NIMS instance are dealt with differently
- if self.useragent.startswith('NIMS Instance'):
- logging.info("request from '{0}', interNIMS p2p initiated".format(self.useragent))
+ if self.request.user_agent.startswith('NIMS Instance'):
+ log.info("request from '{0}', interNIMS p2p initiated".format(self.request.user_agent))
try:
authinfo = self.request.headers['authorization']
challenge_id, digest = base64.b64decode(authinfo).split()
user, remote_site = challenge_id.split(':')
- # logging.info('{0} {1} {2}'.format(user, remote_site, digest))
+ # log.info('{0} {1} {2}'.format(user, remote_site, digest))
projection = {'_id': False, 'pubkey': True}
remote_pubkey = self.app.db.remotes.find_one({'_id': remote_site}, projection)['pubkey']
# get the challenge from db.challenges
@@ -52,7 +88,7 @@ class NIMSRequestHandler(webapp2.RequestHandler):
h = HMAC.new(remote_pubkey, challenge)
self.expected = base64.b64encode('%s %s' % (challenge_id, h.hexdigest()))
if self.expected == authinfo:
- logging.info('CRAM successful')
+ log.info('CRAM successful')
else:
self.abort(403, 'Not Authorized: cram failed')
except KeyError, e:
@@ -71,14 +107,14 @@ class NIMSRequestHandler(webapp2.RequestHandler):
def dispatch(self):
"""dispatching and request forwarding"""
if self.target_id in ['local', self.site_id]:
- logging.info('{0} delegating to local {1}'.format(socket.gethostname(), self.request.url))
+ log.info('{0} delegating to local {1}'.format(socket.gethostname(), self.request.url))
super(NIMSRequestHandler, self).dispatch()
else:
- logging.info('{0} delegating to remote {1}'.format(socket.gethostname(), self.target_id))
+ log.info('{0} delegating to remote {1}'.format(socket.gethostname(), self.target_id))
# is target registered?
target = self.app.db.remotes.find_one({'_id': self.target_id}, {'_id':False, 'hostname':True})
if not target:
- logging.info('remote host {0} not in auth list. DENIED'.format(self.target_id))
+ log.info('remote host {0} not in auth list. DENIED'.format(self.target_id))
self.abort(403, 'forbidden: site is not registered with interNIMS')
self.cid = self.userid + ':' + self.site_id
reqheaders = dict(self.request.headers)
@@ -94,12 +130,15 @@ class NIMSRequestHandler(webapp2.RequestHandler):
if r.status_code == 401:
challenge = base64.b64decode(r.headers['www-authenticate'])
- # logging.info('challenge {0} recieved'.format(challenge))
+ # log.info('challenge {0} recieved'.format(challenge))
h = HMAC.new(self.pubkey, challenge)
response = base64.b64encode('%s %s' % (self.cid, h.hexdigest()))
- # logging.info('sending: {0} {1}'.format(self.cid, h.hexdigest()))
+ # log.info('sending: {0} {1}'.format(self.cid, h.hexdigest()))
#adjust the request and try again
reqheaders['authorization'] = response
r = requests.request(method=self.request.method, url=target_api, params=reqparams, data=self.request.body, headers=reqheaders, cookies=self.request.cookies)
self.response.write(r.content)
+
+ def schema(self, *args, **kwargs):
+ self.response.write(json.dumps(self.json_schema, default=bson.json_util.default))
diff --git a/sessions.py b/sessions.py
index 3be07e3efc38f461c872931c080ca6b34a05a7d8..4b69170606bcffedb8f60fcd357bbc247ca5beda 100644
--- a/sessions.py
+++ b/sessions.py
@@ -9,9 +9,31 @@ import nimsapiutil
class Sessions(nimsapiutil.NIMSRequestHandler):
+ json_schema = {
+ '$schema': 'http://json-schema.org/draft-04/schema#',
+ 'title': 'Session List',
+ 'type': 'array',
+ 'items': {
+ 'title': 'Session',
+ 'type': 'object',
+ 'properties': {
+ '_id': {
+ 'title': 'Database ID',
+ },
+ 'timestamp': {
+ 'title': 'Timestamp',
+ },
+ 'subject': {
+ 'title': 'Subject Code',
+ 'type': 'string',
+ },
+ }
+ }
+ }
+
def count(self, iid):
"""Return the number of Sessions."""
- self.response.write('sessions count\n')
+ self.response.write(json.dumps(self.app.db.sessions.count()))
def post(self, iid):
"""Create a new Session"""
@@ -36,6 +58,54 @@ class Sessions(nimsapiutil.NIMSRequestHandler):
class Session(nimsapiutil.NIMSRequestHandler):
+ json_schema = {
+ '$schema': 'http://json-schema.org/draft-04/schema#',
+ 'title': 'Session',
+ 'type': 'object',
+ 'properties': {
+ '_id': {
+ 'title': 'Database ID',
+ },
+ 'experiment': {
+ 'title': 'Experiment ID',
+ },
+ 'timestamp': {
+ 'title': 'Timestamp',
+ },
+ 'uid': {
+ 'title': 'DICOM UID',
+ 'type': 'string',
+ },
+ 'firstname': {
+ 'title': 'First Name',
+ 'type': 'string',
+ },
+ 'lastname': {
+ 'title': 'Last Name',
+ 'type': 'string',
+ },
+ 'patient_id': {
+ 'title': 'Patient ID',
+ 'type': 'string',
+ },
+ 'subject': {
+ 'title': 'Subject Code',
+ 'type': 'string',
+ },
+ 'exam': {
+ 'title': 'Exam Number',
+ 'type': 'integer',
+ },
+ 'files': {
+ 'title': 'Files',
+ 'type': 'array',
+ 'items': nimsapiutil.NIMSRequestHandler.file_schema,
+ 'uniqueItems': True,
+ },
+ },
+ 'required': ['_id', 'experiment', 'uid', 'patient_id', 'subject'],
+ }
+
def get(self, iid, sid):
"""Return one Session, conditionally with details."""
session = self.app.db.sessions.find_one({'_id': bson.objectid.ObjectId(sid)})