diff --git a/api/api.py b/api/api.py
index d6a8f21843d2e42a41701ecf3340b43924aca372..c14227dbf1ee133e67b02f23a092fbe65225983f 100644
--- a/api/api.py
+++ b/api/api.py
@@ -1,8 +1,10 @@
import os
import copy
import json
+import pytz
import webapp2
-import bson.json_util
+import datetime
+import bson.objectid
import webapp2_extras.routes
from . import core
@@ -98,16 +100,25 @@ for cls in [
]:
cls.post_schema = copy.deepcopy(schema_dict[cls.__name__.lower()])
cls.put_schema = copy.deepcopy(cls.post_schema)
- cls.put_schema['properties'].pop('_id')
+ cls.put_schema['properties'].pop('_id', None)
cls.put_schema.pop('required')
+def custom_json_serializer(obj):
+ if isinstance(obj, bson.objectid.ObjectId):
+ return str(obj)
+ elif isinstance(obj, datetime.datetime):
+ return pytz.timezone('UTC').localize(obj).isoformat()
+ raise TypeError(repr(obj) + " is not JSON serializable")
+
+
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.write(json.dumps(rv, default=custom_json_serializer))
response.headers['Content-Type'] = 'application/json; charset=utf-8'
+
try:
import newrelic.agent
app = newrelic.agent.WSGIApplicationWrapper(webapp2.WSGIApplication(routes))
diff --git a/api/base.py b/api/base.py
index f2bc2c8fb89be77dbf67768ff1ebb157549f2244..51251595b80012c3ac151b50b024099480ffc2f1 100644
--- a/api/base.py
+++ b/api/base.py
@@ -32,11 +32,11 @@ class RequestHandler(webapp2.RequestHandler):
# User (oAuth) authentication
if access_token and self.app.config['oauth2_id_endpoint']:
- token_request_time = datetime.datetime.now()
+ token_request_time = datetime.datetime.utcnow()
cached_token = self.app.db.authtokens.find_one({'_id': access_token})
if cached_token:
self.uid = cached_token['uid']
- log.debug('looked up cached token in %dms' % ((datetime.datetime.now() - token_request_time).total_seconds() * 1000.))
+ log.debug('looked up cached token in %dms' % ((datetime.datetime.utcnow() - token_request_time).total_seconds() * 1000.))
else:
r = requests.get(self.app.config['oauth2_id_endpoint'], headers={'Authorization': 'Bearer ' + access_token})
if r.status_code == 200:
@@ -45,7 +45,7 @@ class RequestHandler(webapp2.RequestHandler):
if not self.uid:
self.abort(400, 'OAuth2 token resolution did not return email address')
self.app.db.authtokens.replace_one({'_id': access_token}, {'uid': self.uid, 'timestamp': datetime.datetime.utcnow()}, upsert=True)
- log.debug('looked up remote token in %dms' % ((datetime.datetime.now() - token_request_time).total_seconds() * 1000.))
+ log.debug('looked up remote token in %dms' % ((datetime.datetime.utcnow() - token_request_time).total_seconds() * 1000.))
else:
headers = {'WWW-Authenticate': 'Bearer realm="%s", error="invalid_token", error_description="Invalid OAuth2 token."' % self.app.config['site_id']}
self.abort(401, 'invalid oauth2 token', headers=headers)
diff --git a/api/collections.py b/api/collections.py
index ab7acb2e98220667019f7d8d87f59ab5ec53d160..9eacbc4dba87278fe9e450ebd1b2d7058b9d2c3d 100644
--- a/api/collections.py
+++ b/api/collections.py
@@ -303,10 +303,7 @@ class CollectionSessions(sessions.Sessions):
projection['permissions'] = {'$elemMatch': {'_id': self.uid, 'site': self.source_site}}
sessions = list(self.dbc.find(query, projection)) # avoid permissions checking by not using ContainerList._get()
for sess in sessions:
- sess['_id'] = str(sess['_id']) # do this manually, since not going through ContainerList._get()
sess['subject_code'] = sess.pop('subject', {}).get('code', '') # FIXME when subject is pulled out of session
- sess.setdefault('timestamp', datetime.datetime.utcnow())
- sess['timestamp'], sess['timezone'] = util.format_timestamp(sess['timestamp'], sess.get('timezone'))
if self.debug:
for sess in sessions:
sid = str(sess['_id'])
@@ -342,9 +339,7 @@ class CollectionAcquisitions(acquisitions.Acquisitions):
projection['permissions'] = {'$elemMatch': {'_id': self.uid, 'site': self.source_site}}
acquisitions = list(self.dbc.find(query, projection))
for acq in acquisitions:
- acq['_id'] = str(acq['_id']) # do this manually, since not going through ContainerList._get()
acq.setdefault('timestamp', datetime.datetime.utcnow())
- acq['timestamp'], acq['timezone'] = util.format_timestamp(acq['timestamp'], acq.get('timezone'))
if self.debug:
for acq in acquisitions:
aid = str(acq['_id'])
diff --git a/api/containers.py b/api/containers.py
index 7d3847d4283ecf1df7bbc6123a2b08cbada418f8..090243dc89c5de3c0914a6e5cbac9be8b9bbd604 100644
--- a/api/containers.py
+++ b/api/containers.py
@@ -137,9 +137,7 @@ class ContainerList(base.RequestHandler):
projection['permissions'] = {'$elemMatch': {'_id': uid or self.uid, 'site': self.source_site}}
containers = list(self.dbc.find(query, projection))
for container in containers:
- container['_id'] = str(container['_id'])
container.setdefault('timestamp', datetime.datetime.utcnow())
- container['timestamp'], container['timezone'] = util.format_timestamp(container['timestamp'], container.get('timezone')) # TODO json serializer should do this
container['attachment_count'] = len([f for f in container.get('files', []) if f.get('flavor') == 'attachment'])
return containers
@@ -174,11 +172,7 @@ class Container(base.RequestHandler):
if self.request.GET.get('paths', '').lower() in ('1', 'true'):
for fileinfo in container['files']:
fileinfo['path'] = str(_id)[-3:] + '/' + str(_id) + '/' + fileinfo['filename']
- container['_id'] = str(container['_id'])
container.setdefault('timestamp', datetime.datetime.utcnow())
- container['timestamp'], container['timezone'] = util.format_timestamp(container['timestamp'], container.get('timezone')) # TODO json serializer should do this
- for note in container.get('notes', []):
- note['timestamp'], _ = util.format_timestamp(note['timestamp']) # TODO json serializer should do this
return container, user_perm
def _put(self, _id):
@@ -250,7 +244,7 @@ class Container(base.RequestHandler):
if self.request.GET.get('info', '').lower() in ('1', 'true'):
try:
with zipfile.ZipFile(filepath) as zf:
- return [(zi.filename, zi.file_size, util.format_timestamp(datetime.datetime(*zi.date_time))[0]) for zi in zf.infolist()]
+ return [(zi.filename, zi.file_size, datetime.datetime(*zi.date_time)) for zi in zf.infolist()]
except zipfile.BadZipfile:
self.abort(400, 'not a zip file')
elif self.request.GET.get('comment', '').lower() in ('1', 'true'):
diff --git a/api/jobs.py b/api/jobs.py
index e88d730476dd357f0133244f8116b89ebf8b1f94..721e10598c33d0381acfc530ea4f975ce900a269 100644
--- a/api/jobs.py
+++ b/api/jobs.py
@@ -164,14 +164,6 @@ def queue_job(db, algorithm_id, container_type, container_id, filename, filehash
log.info('Running %s as job %s to process %s %s' % (algorithm_id, str(_id), container_type, container_id))
return _id
-def serialize_job(job):
- if job:
- job['_id'] = str(job['_id'])
- job['created'] = util.format_timestamp(job['created'])
- job['modified'] = util.format_timestamp(job['modified'])
-
- return job
-
class Jobs(base.RequestHandler):
"""Provide /jobs API routes."""
@@ -184,8 +176,6 @@ class Jobs(base.RequestHandler):
self.abort(401, 'Request requires superuser')
results = list(self.app.db.jobs.find())
- for result in results:
- result = serialize_job(result)
return results
@@ -229,7 +219,7 @@ class Jobs(base.RequestHandler):
if result == None:
self.abort(400, 'No jobs to process')
- return serialize_job(result)
+ return result
class Job(base.RequestHandler):
@@ -240,7 +230,7 @@ class Job(base.RequestHandler):
self.abort(401, 'Request requires superuser')
result = self.app.db.jobs.find_one({'_id': bson.ObjectId(_id)})
- return serialize_job(result)
+ return result
def put(self, _id):
"""
diff --git a/api/users.py b/api/users.py
index 06fe0f673978c6139ed3ff04573557f3aba81e33..15477a96f78aec16a852bb1930446b1c19d660ae 100644
--- a/api/users.py
+++ b/api/users.py
@@ -61,9 +61,6 @@ class Users(base.RequestHandler):
if self.public_request:
self.abort(403, 'must be logged in to retrieve User list')
users = list(self.dbc.find({}, {'preferences': False}))
- for user in users:
- user['created'], _ = util.format_timestamp(user['created']) # TODO json serializer should do this
- user['modified'], _ = util.format_timestamp(user['modified']) # TODO json serializer should do this
if self.debug:
for user in users:
user['debug'] = {}
@@ -108,8 +105,6 @@ class User(base.RequestHandler):
user = self.dbc.find_one({'_id': _id}, projection or None)
if not user:
self.abort(404, 'no such User')
- user['created'], _ = util.format_timestamp(user['created']) # TODO json serializer should do this
- user['modified'], _ = util.format_timestamp(user['modified']) # TODO json serializer should do this
if self.debug and (self.superuser_request or _id == self.uid):
user['debug'] = {}
user['debug']['groups'] = self.uri_for('groups', _id, _full=True) + '?' + self.request.query_string
@@ -184,9 +179,6 @@ class Groups(base.RequestHandler):
query = {'roles._id': self.uid}
projection += ['roles.$']
groups = list(self.app.db.groups.find(query, projection))
- for group in groups:
- group['created'], _ = util.format_timestamp(group['created']) # TODO json serializer should do this
- group['modified'], _ = util.format_timestamp(group['modified']) # TODO json serializer should do this
if self.debug:
for group in groups:
group['debug'] = {}
@@ -219,8 +211,6 @@ class Group(base.RequestHandler):
group = self.app.db.groups.find_one({'_id': _id, 'roles': {'$elemMatch': {'_id': self.uid, 'access': 'admin'}}})
if not group:
self.abort(403, 'User ' + self.uid + ' is not an admin of Group ' + _id)
- group['created'], _ = util.format_timestamp(group['created']) # TODO json serializer should do this
- group['modified'], _ = util.format_timestamp(group['modified']) # TODO json serializer should do this
if self.debug:
group['debug'] = {}
group['debug']['projects'] = self.uri_for('g_projects', gid=group['_id'], _full=True) + '?' + self.request.query_string
diff --git a/api/util.py b/api/util.py
index 81683b8140d4b32f746d9ce2854b90b1284889c3..dc9fb2b29003dde7c71f29de5f99f3428b2f78ad 100644
--- a/api/util.py
+++ b/api/util.py
@@ -299,10 +299,5 @@ def guess_filetype(filepath, mimetype):
return subtype
-def format_timestamp(timestamp, tzname=None):
- timezone = pytz.timezone(tzname or 'UTC')
- return timezone.localize(timestamp).isoformat(), timezone.zone
-
-
def parse_timestamp(iso_timestamp):
return dateutil.parser.parse(iso_timestamp)