supporting patching simulator specs

biosimulators_utils/_version.py

@@ -1 +1 @@
-__version__ = '0.1.17'
+__version__ = '0.1.18'

biosimulators_utils/simulator/io.py

@@ -13,11 +13,12 @@
 import simplejson.errors
 
 
-def read_simulator_specs(path_or_url):
+def read_simulator_specs(path_or_url, patch=None):
     """ Read the specifications of a simulator
 
     Args:
         path_or_url (:obj:`str`): file path or URL for the specifications of a simulator
+        patch (:obj:`dict`, optional): values of properties to supersede those in :obj:`path_or_url`
 
     Returns:
         :obj:`dict`: specifications of a simulator
@@ -55,6 +56,11 @@ def read_simulator_specs(path_or_url):
                 'Specifications must be encoded into JSON.\n\n  {}'.format(str(error).replace('\n', '\n  ')),
             ]))
 
+    # apply patch
+    if patch:
+        for key, val in patch.items():
+            specs[key] = val
+
     # validate specifications
     api_endpoint = get_config().BIOSIMULATORS_API_ENDPOINT
     response = requests.post('{}simulators/validate'.format(api_endpoint), json=specs)

tests/simulator/test_simulator_io.py

@@ -25,7 +25,8 @@ def test_file   (self):
 
     def test_url(self):
         url = 'https://raw.githubusercontent.com/biosimulators/Biosimulators_tellurium/dev/biosimulators.json'
-        specs = read_simulator_specs(url)
+        specs = read_simulator_specs(url, patch={'version': '0.0.0'})
+        self.assertEqual(specs['version'], '0.0.0')
 
         with self.assertRaises(requests.RequestException):
             url = 'https://raw.githubusercontent.com/biosimulators/Biosimulators_tellurium/dev/__undefined__'