adding yaml loader to accommodate yaml 5.1 spec

CHANGELOG.rst

@@ -8,7 +8,8 @@ Changed
 ^^^^^^^
 - Setting ``verify`` default back to True
 - Changed JHU db check to look for SCISERVER environment variable
-
+- Added new get_yaml_loader function to get proper yaml Loader for 3.1/5.1 spec
+- Used new yaml Loader to accommodate 5.1 spec
 
 [0.1.1] - 2018/12/10
 --------------------

python/brain/__init__.py

@@ -13,7 +13,7 @@
 import warnings
 import yaml
 from brain.core.exceptions import BrainError, BrainUserWarning
-from brain.utils.general.general import merge
+from brain.utils.general.general import merge, get_yaml_loader
 
 # Set the Brain version
 __version__ = '0.1.2dev'
@@ -94,10 +94,10 @@ def has_netrc(self):
     def _load_defaults(self):
         ''' Load the Brain config yaml file '''
 
-        config = yaml.load(open(os.path.join(os.path.dirname(__file__), 'data/brain.yml')))
+        config = yaml.load(open(os.path.join(os.path.dirname(__file__), 'data/brain.yml')), Loader=get_yaml_loader())
         user_config_path = os.path.expanduser('~/.brain/brain.yml')
         if os.path.exists(user_config_path):
-            config = merge(yaml.load(open(user_config_path)), config)
+            config = merge(yaml.load(open(user_config_path), Loader=get_yaml_loader()), config)
 
         # update any matching Config values
         for key, value in config.items():

python/brain/utils/general/general.py

@@ -3,6 +3,8 @@
 import datetime
 import numpy as np
 import json
+import yaml
+from pkg_resources import parse_version
 from brain.core.exceptions import BrainError, BrainWarning
 from hashlib import md5
 from passlib.apache import HtpasswdFile
@@ -17,7 +19,8 @@
 
 __all__ = ['getDbMachine', 'merge', 'convertIvarToErr', 'compress_data',
            'uncompress_data', 'inspection_authenticate', 'validate_user',
-           'get_db_user', 'build_routemap', 'collaboration_authenticate']
+           'get_db_user', 'build_routemap', 'collaboration_authenticate',
+           'get_yaml_loader']
 
 
 def getDbMachine():
@@ -429,3 +432,12 @@ def build_routemap(app):
 
     return output
 
+
+def get_yaml_loader():
+    ''' Get a yaml loader based on the yaml package version '''
+
+    if parse_version(yaml.__version__) >= parse_version('5.1'):
+        loader = yaml.FullLoader
+    else:
+        loader = yaml.SafeLoader
+    return loader