Support serialization of UUID objects to JSON

Support UUID objects in get_lab_from_endpoint_id
Fix syntax error in python publish workflow

Author: k1o0

.github/workflows/python-publish.yaml

@@ -54,6 +54,6 @@ jobs:
     - name: Publish distribution to PyPI
       # GitHub recommends pinning 3rd party actions to a commit SHA.
       uses: pypa/gh-action-pypi-publish@6f7e8d9c0b1a2c3d4e5f6a7b8c9d0e1f2a3b4c5d
-        with:
-          user: __token__
-          password: ${{ secrets.PYPI_API_TOKEN }}
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

one/__init__.py

@@ -1,2 +1,2 @@
 """The Open Neurophysiology Environment (ONE) API."""
-__version__ = '3.0b3'
+__version__ = '3.0b4'

one/remote/globus.py

@@ -358,7 +358,7 @@ def get_lab_from_endpoint_id(endpoint=None, alyx=None):
     alyx = alyx or AlyxClient(silent=True)
     if not endpoint:
         endpoint = get_local_endpoint_id()
-    lab = alyx.rest('labs', 'list', django=f'repositories__globus_endpoint_id,{endpoint}')
+    lab = alyx.rest('labs', 'list', django=f'repositories__globus_endpoint_id,{str(endpoint)}')
     if len(lab):
         lab_names = [la['name'] for la in lab]
         return lab_names

one/tests/remote/test_globus.py

@@ -175,7 +175,8 @@ def test_get_lab_from_endpoint_id(self):
             self.assertEqual(len(globus.get_lab_from_endpoint_id('123', ac)), 2)
 
         # Check behaviour when no input ID returned
-        with mock.patch('one.remote.globus.get_local_endpoint_id', return_value=endpoint_id):
+        uid = uuid.UUID(endpoint_id)
+        with mock.patch('one.remote.globus.get_local_endpoint_id', return_value=uid):
             name = globus.get_lab_from_endpoint_id(alyx=ac)[0]
             self.assertEqual(name, 'mainenlab')
 

one/tests/test_alyxclient.py

@@ -4,6 +4,7 @@
 import urllib.parse
 import random
 import weakref
+import uuid
 import os
 import one.webclient as wc
 import one.params
@@ -170,7 +171,7 @@ def setUp(self):
             'users': [TEST_DB_1['username']],
         }) for _ in range(2)]
 
-        self.eids = [x['url'].split('/')[-1] for x in sessions]
+        self.eids = [uuid.UUID(x['url'].split('/')[-1]) for x in sessions]
         self.endpoint = 'sessions'
         self.field_name = 'extended_qc'
         # We filter by key value so we use randint to avoid race condition in concurrent tests
@@ -253,6 +254,14 @@ def test_empty(self):
             modified = self.ac.json_field_remove_key(self.endpoint, eid, self.field_name)
         self.assertIsNone(modified)
 
+    def test_uuid_serialize(self):
+        """Check that UUID objects are serialized to JSON."""
+        data = {'uid': self.eids[-1], **self.data_dict}
+        written = self.ac.json_field_write(self.endpoint, self.eids[0], self.field_name, data)
+        self.assertIsInstance(written, dict)
+        # Encoder should have cast uuid to str
+        self.assertEqual(str(self.eids[-1]), written.get('uid'))
+
     def tearDown(self):
         self.ac.rest('subjects', 'delete', id=self.subj['nickname'])
 
@@ -581,6 +590,17 @@ def _check_get_query(self, call_args, limit, offset):
         expected = {'foo': ['bar'], 'offset': [str(offset)], 'limit': [str(limit)]}
         self.assertDictEqual(query, expected)
 
+    def test_json_encoder(self):
+        """Test that the JSONEncoder subclass serializes UUID objects."""
+        uid = uuid.uuid4()
+        data = {'foo': 12, 'bar': uid}
+        # First check that the default encoder raises;
+        # python could add support for UUID objects in the future
+        self.assertRaises(TypeError, json.dumps, data)
+        serialized = json.dumps(data, cls=wc._JSONEncoder)
+        expected = '{"foo": 12, "bar": "' + str(uid) + '"}'
+        self.assertEqual(expected, serialized)
+
 
 if __name__ == '__main__':
     unittest.main(exit=False, verbosity=2)

one/webclient.py

@@ -30,6 +30,7 @@
 >>> local_path = alyx.download_file(url, target_dir='zadorlab/Subjects/flowers/2018-07-13/1/')
 
 """
+from uuid import UUID
 import json
 import logging
 import math
@@ -62,6 +63,16 @@
 _logger = logging.getLogger(__name__)
 
 
+class _JSONEncoder(json.JSONEncoder):
+    """A JSON encoder that handles UUID objects."""
+
+    def default(self, o):
+        """Cast UUID objects to str before serializing."""
+        if isinstance(o, UUID):
+            return str(o)
+        return super().default(o)
+
+
 def _cache_response(method):
     """Decorator for the generic request method for caching REST reponses.
 
@@ -139,7 +150,7 @@ def wrapper_decorator(alyx_client, *args, expires=None, clobber=False, **kwargs)
         _logger.debug('caching REST response')
         expiry_datetime = datetime.now() + (timedelta() if expires is True else expires)
         with open(rest_cache / name, 'w') as f:
-            json.dump((response, expiry_datetime.isoformat()), f)
+            json.dump((response, expiry_datetime.isoformat()), f, cls=_JSONEncoder)
         return response
 
     return wrapper_decorator
@@ -646,7 +657,8 @@ def _generic_request(self, reqfunction, rest_query, data=None, files=None):
         _logger.debug(f'{self.base_url + rest_query}, headers: {self._headers}')
         headers = self._headers.copy()
         if files is None:
-            data = json.dumps(data) if isinstance(data, dict) or isinstance(data, list) else data
+            to_json = functools.partial(json.dumps, cls=_JSONEncoder)
+            data = to_json(data) if isinstance(data, dict) or isinstance(data, list) else data
             headers['Content-Type'] = 'application/json'
         if rest_query.startswith('/docs'):
             # the mixed accept application may cause errors sometimes, only necessary for the docs