diff --git a/api/config.py b/api/config.py
index befc6a227745a5d567f2249661bb7bf58b710261..e12bb18591e9fb337e321427f8b83dd5c861ff98 100644
--- a/api/config.py
+++ b/api/config.py
@@ -5,6 +5,7 @@ import logging
import pymongo
import datetime
import elasticsearch
+from . import util
logging.basicConfig(
@@ -34,7 +35,7 @@ DEFAULT_CONFIG = {
'api_url': 'https://localhost/api',
'central_url': 'https://sdmc.scitran.io/api',
'registered': False,
- 'ssl_cert': None,
+ 'ssl_cert': None
},
'queue': {
'max_retries': 3,
@@ -221,7 +222,7 @@ def get_config():
db_config = db.singletons.find_one({'_id': 'config'})
if db_config is not None:
startup_config = copy.deepcopy(__config)
- startup_config.update(db_config)
+ startup_config = util.deep_update(startup_config, db_config)
# Precedence order for config is env vars -> db values -> default
__config = apply_env_variables(startup_config)
else:
diff --git a/api/download.py b/api/download.py
index c91cebdfc0faaf5b68957be9b9d9096bac59398e..50d3615c5a18e10a79eb37ce06eb9d9faff7ef0c 100644
--- a/api/download.py
+++ b/api/download.py
@@ -267,7 +267,7 @@ class Download(base.RequestHandler):
if self.is_true('bulk'):
return self._bulk_preflight_archivestream(req_spec.get('files', []))
else:
- payload_schema_uri = util.schema_uri('input', 'download.json')
+ payload_schema_uri = validators.schema_uri('input', 'download.json')
validator = validators.from_schema_path(payload_schema_uri)
validator(req_spec, 'POST')
log.debug(json.dumps(req_spec, sort_keys=True, indent=4, separators=(',', ': ')))
diff --git a/api/handlers/containerhandler.py b/api/handlers/containerhandler.py
index 4f35b01368d9461fcbff79136908edfd6c352642..cc385ba630af13f2facf6137aca5a72e97ade5e6 100644
--- a/api/handlers/containerhandler.py
+++ b/api/handlers/containerhandler.py
@@ -487,9 +487,9 @@ class ContainerHandler(base.RequestHandler):
return list(config.db.groups.find({'_id': {'$in': group_ids}}, ['name']))
def _get_validators(self):
- mongo_schema_uri = util.schema_uri('mongo', self.config.get('storage_schema_file'))
+ mongo_schema_uri = validators.schema_uri('mongo', self.config.get('storage_schema_file'))
mongo_validator = validators.decorator_from_schema_path(mongo_schema_uri)
- payload_schema_uri = util.schema_uri('input', self.config.get('payload_schema_file'))
+ payload_schema_uri = validators.schema_uri('input', self.config.get('payload_schema_file'))
payload_validator = validators.from_schema_path(payload_schema_uri)
return mongo_validator, payload_validator
diff --git a/api/handlers/grouphandler.py b/api/handlers/grouphandler.py
index f8034da62d1d4a42651c2806b62ecfe2af2ded81..6d1e07853c548eb6385893830e7ec25c82535674 100644
--- a/api/handlers/grouphandler.py
+++ b/api/handlers/grouphandler.py
@@ -63,9 +63,9 @@ class GroupHandler(base.RequestHandler):
self.abort(404, 'no such Group: ' + _id)
permchecker = groupauth.default(self, group)
payload = self.request.json_body
- mongo_schema_uri = util.schema_uri('mongo', 'group.json')
+ mongo_schema_uri = validators.schema_uri('mongo', 'group.json')
mongo_validator = validators.decorator_from_schema_path(mongo_schema_uri)
- payload_schema_uri = util.schema_uri('input', 'group.json')
+ payload_schema_uri = validators.schema_uri('input', 'group.json')
payload_validator = validators.from_schema_path(payload_schema_uri)
payload_validator(payload, 'PUT')
result = mongo_validator(permchecker(self.storage.exec_op))('PUT', _id=_id, payload=payload)
@@ -78,9 +78,9 @@ class GroupHandler(base.RequestHandler):
self._init_storage()
permchecker = groupauth.default(self, None)
payload = self.request.json_body
- mongo_schema_uri = util.schema_uri('mongo', 'group.json')
+ mongo_schema_uri = validators.schema_uri('mongo', 'group.json')
mongo_validator = validators.decorator_from_schema_path(mongo_schema_uri)
- payload_schema_uri = util.schema_uri('input', 'group.json')
+ payload_schema_uri = validators.schema_uri('input', 'group.json')
payload_validator = validators.from_schema_path(payload_schema_uri)
payload_validator(payload, 'POST')
payload['created'] = payload['modified'] = datetime.datetime.utcnow()
diff --git a/api/handlers/listhandler.py b/api/handlers/listhandler.py
index d95e68d00dd8969a74207d4a3d1023352499740b..51ac5770d3c1c566e3d11b50f14dd7b68cdb165f 100644
--- a/api/handlers/listhandler.py
+++ b/api/handlers/listhandler.py
@@ -206,9 +206,9 @@ class ListHandler(base.RequestHandler):
permchecker = permchecker(self, container)
else:
self.abort(404, 'Element {} not found in container {}'.format(_id, storage.cont_name))
- mongo_schema_uri = util.schema_uri('mongo', config.get('storage_schema_file'))
+ mongo_schema_uri = validators.schema_uri('mongo', config.get('storage_schema_file'))
mongo_validator = validators.decorator_from_schema_path(mongo_schema_uri)
- input_schema_uri = util.schema_uri('input', config.get('input_schema_file'))
+ input_schema_uri = validators.schema_uri('input', config.get('input_schema_file'))
input_validator = validators.from_schema_path(input_schema_uri)
keycheck = validators.key_check(mongo_schema_uri)
return container, permchecker, storage, mongo_validator, input_validator, keycheck
diff --git a/api/handlers/userhandler.py b/api/handlers/userhandler.py
index 1bc1dcde502919d72640a55ec751b0026841eaef..844d7d6d5b14514dd044daaf2d052f6151aafc09 100644
--- a/api/handlers/userhandler.py
+++ b/api/handlers/userhandler.py
@@ -102,9 +102,9 @@ class UserHandler(base.RequestHandler):
user = self._get_user(_id)
permchecker = userauth.default(self, user)
payload = self.request.json_body
- mongo_schema_uri = util.schema_uri('mongo', 'user.json')
+ mongo_schema_uri = validators.schema_uri('mongo', 'user.json')
mongo_validator = validators.decorator_from_schema_path(mongo_schema_uri)
- payload_schema_uri = util.schema_uri('input', 'user.json')
+ payload_schema_uri = validators.schema_uri('input', 'user.json')
payload_validator = validators.from_schema_path(payload_schema_uri)
payload_validator(payload, 'PUT')
payload['modified'] = datetime.datetime.utcnow()
@@ -147,9 +147,9 @@ class UserHandler(base.RequestHandler):
self._init_storage()
permchecker = userauth.default(self)
payload = self.request.json_body
- mongo_schema_uri = util.schema_uri('mongo', 'user.json')
+ mongo_schema_uri = validators.schema_uri('mongo', 'user.json')
mongo_validator = validators.decorator_from_schema_path(mongo_schema_uri)
- payload_schema_uri = util.schema_uri('input', 'user.json')
+ payload_schema_uri = validators.schema_uri('input', 'user.json')
payload_validator = validators.from_schema_path(payload_schema_uri)
payload_validator(payload, 'POST')
payload['created'] = payload['modified'] = datetime.datetime.utcnow()
diff --git a/api/placer.py b/api/placer.py
index 3aba5648b59b13213ca6966a1d50a09301f0ca2c..25b0a2d9a359e4568f577ca57d19f93373f2699d 100644
--- a/api/placer.py
+++ b/api/placer.py
@@ -128,7 +128,7 @@ class UIDPlacer(Placer):
def check(self):
self.requireMetadata()
- payload_schema_uri = util.schema_uri('input', self.metadata_schema)
+ payload_schema_uri = validators.schema_uri('input', self.metadata_schema)
metadata_validator = validators.from_schema_path(payload_schema_uri)
metadata_validator(self.metadata, 'POST')
diff --git a/api/util.py b/api/util.py
index 60e1cc1009811df92fbdf23ca0e888e50a75b85a..ee9b9a46e017f5b9843d7d26aa2680eec3e2c936 100644
--- a/api/util.py
+++ b/api/util.py
@@ -9,7 +9,6 @@ import uuid
import requests
import hashlib
-from . import config
MIMETYPES = [
('.bvec', 'text', 'bvec'),
('.bval', 'text', 'bval'),
@@ -65,6 +64,18 @@ def mongo_sanitize_fields(d):
else:
return d
+def deep_update(d, u):
+ """
+ Makes a deep update of dict d with dict u
+ Adapted from http://stackoverflow.com/a/3233356
+ """
+ for k, v in u.iteritems():
+ if isinstance(v, dict):
+ r = deep_update(d.get(k, {}), v)
+ d[k] = r
+ else:
+ d[k] = u[k]
+ return d
def user_perm(permissions, _id, site=None):
@@ -163,12 +174,6 @@ def send_json_http_exception(response, message, code):
response.headers['Content-Type'] = 'application/json; charset=utf-8'
response.write(content)
-def schema_uri(type_, schema_name):
- return '/'.join([
- config.get_item('site', 'api_url'),
- 'schemas',
- type_, schema_name
- ])
class Enum(baseEnum.Enum):
# Enum strings are prefixed by their class: "Category.classifier".
diff --git a/api/validators.py b/api/validators.py
index 2f3350e36b31c9709d3aaeaf6f539154253a5101..9ca334007f409d52efa0db03819776c008e57249 100644
--- a/api/validators.py
+++ b/api/validators.py
@@ -27,8 +27,8 @@ def validate_data(data, schema_json, schema_type, verb, optional=False):
if optional and data is None:
return
- schema_uri = util.schema_uri(schema_type, schema_json)
- validator = from_schema_path(schema_uri)
+ suri = schema_uri(schema_type, schema_json)
+ validator = from_schema_path(suri)
validator(data, verb)
def _validate_json(json_data, schema, resolver):
@@ -74,6 +74,13 @@ def _resolve_schema(schema_url):
def no_op(g, *args):
return g
+def schema_uri(type_, schema_name):
+ return '/'.join([
+ config.get_item('site', 'api_url'),
+ 'schemas',
+ type_, schema_name
+ ])
+
def decorator_from_schema_path(schema_url):
if schema_url is None:
return no_op