Gross monkey patch to fix simplejson issue (#66)

onecodex/api.py

@@ -11,9 +11,8 @@
 import os
 import warnings
 
-from potion_client import Client as PotionClient
-from potion_client.converter import PotionJSONSchemaDecoder, PotionJSONDecoder, PotionJSONEncoder
-from potion_client.utils import upper_camel_case
+import potion_client
+
 from requests.auth import HTTPBasicAuth
 
 from onecodex.lib.auth import BearerTokenAuth
@@ -23,6 +22,60 @@
 log = logging.getLogger(__name__)
 
 
+# begin gross monkey patch (see #66)
+class MPPotionJSONSchemaDecoder(potion_client.converter.PotionJSONSchemaDecoder):
+    def __init__(*args, **kwargs):
+        if 'encoding' in kwargs:
+            del kwargs['encoding']
+
+        potion_client.converter.PotionJSONSchemaDecoder.__init__(*args, **kwargs)
+
+
+class MPPotionJSONDecoder(potion_client.converter.PotionJSONDecoder):
+    def __init__(*args, **kwargs):
+        if 'encoding' in kwargs:
+            del kwargs['encoding']
+
+        potion_client.converter.PotionJSONDecoder.__init__(*args, **kwargs)
+
+
+class MPPotionJSONEncoder(potion_client.converter.PotionJSONEncoder):
+    def __init__(*args, **kwargs):
+        if 'encoding' in kwargs:
+            del kwargs['encoding']
+
+        potion_client.converter.PotionJSONEncoder.__init__(*args, **kwargs)
+
+
+class MPJSONSchemaReference(potion_client.resource.Reference):
+    @classmethod
+    def _resolve(self, client, uri):
+        return client.fetch(uri, cls=MPPotionJSONSchemaDecoder)
+
+
+def mp_make_request(self, data, params):
+    req = self.request_factory(data, params)
+    prepared_request = self.owner._client.session.prepare_request(req)
+
+    response = self.owner._client.session.send(prepared_request)
+
+    # return error for some error conditions
+    self.raise_for_status(response)
+
+    if response.status_code == 204:
+        return response, None
+
+    return response, response.json(cls=MPPotionJSONDecoder,
+                                   client=self.owner._client,
+                                   default_instance=self.instance)
+
+
+potion_client.converter.JSONSchemaReference = MPJSONSchemaReference
+potion_client.links.LinkBinding.make_request = mp_make_request
+PotionClient = potion_client.Client
+# end gross monkey patch
+
+
 class Api(object):
     """
     This is the base One Codex Api object class. It instantiates a Potion-Client
@@ -121,7 +174,7 @@ class ExtendedPotionClient(PotionClient):
     DATE_FORMAT = "%Y-%m-%d %H:%M"
     SCHEMA_SAVE_DURATION = 1  # day
 
-    def fetch(self, uri, cls=PotionJSONDecoder, **kwargs):
+    def fetch(self, uri, cls=MPPotionJSONDecoder, **kwargs):
         if uri in self._cached_schema:
             return self._cached_schema[uri]
         return super(ExtendedPotionClient, self).fetch(uri, cls=cls, **kwargs)
@@ -154,19 +207,19 @@ def _fetch_schema(self, cache_schema=False, creds_file=None):
             # Catch schema caching issues and fall back to remote URL
             try:
                 base_schema = serialized_schema.pop(self._schema_url)
-                schema = json.loads(base_schema, cls=PotionJSONSchemaDecoder,
+                schema = json.loads(base_schema, cls=MPPotionJSONSchemaDecoder,
                                     referrer=self._schema_url, client=self)
 
                 for route, route_schema in serialized_schema.items():
-                    object_schema = json.loads(route_schema, cls=PotionJSONSchemaDecoder,
+                    object_schema = json.loads(route_schema, cls=MPPotionJSONSchemaDecoder,
                                                referrer=self._schema_url, client=self)
                     self._cached_schema[route] = object_schema
             except KeyError:  # Caches issue with schema_url not existing
                 pass
 
         if schema is None:
             # if the schema wasn't cached or if it was expired, get it anew
-            schema = self.session.get(self._schema_url).json(cls=PotionJSONSchemaDecoder,
+            schema = self.session.get(self._schema_url).json(cls=MPPotionJSONSchemaDecoder,
                                                              referrer=self._schema_url,
                                                              client=self)
             if cache_schema:
@@ -175,12 +228,12 @@ def _fetch_schema(self, cache_schema=False, creds_file=None):
 
                 # serialize the main schema
                 serialized_schema = {}
-                serialized_schema[self._schema_url] = json.dumps(schema, cls=PotionJSONEncoder)
+                serialized_schema[self._schema_url] = json.dumps(schema, cls=MPPotionJSONEncoder)
 
                 # serialize the object schemas
                 for schema_ref in schema['properties'].values():
                     serialized_schema[schema_ref._uri] = json.dumps(schema_ref._properties,
-                                                                    cls=PotionJSONEncoder)
+                                                                    cls=MPPotionJSONEncoder)
 
                 creds['schema'] = serialized_schema
             else:
@@ -194,5 +247,5 @@ def _fetch_schema(self, cache_schema=False, creds_file=None):
             json.dump(creds, open(creds_fp, mode='w'))
 
         for name, resource_schema in schema['properties'].items():
-            class_name = upper_camel_case(name)
+            class_name = potion_client.utils.upper_camel_case(name)
             setattr(self, class_name, self.resource_factory(name, resource_schema))

onecodex/cli.py

@@ -13,8 +13,7 @@
 
 from onecodex.utils import (cli_resource_fetcher, download_file_helper,
                             valid_api_key, OPTION_HELP, pprint, pretty_errors,
-                            warn_if_insecure_platform, is_simplejson_installed,
-                            warn_simplejson, telemetry, snake_case)
+                            warn_if_insecure_platform, telemetry, snake_case)
 from onecodex.api import Api
 from onecodex.exceptions import (OneCodexException, ValidationWarning,
                                  ValidationError, UploadException)
@@ -63,10 +62,6 @@ def onecodex(ctx, api_key, no_pprint, verbose, telemetry):
     if verbose:
         log.setLevel(logging.INFO)
 
-    # Show a warning if simplejson is installed
-    if is_simplejson_installed():
-        warn_simplejson()
-
     # create the api
     no_api_subcommands = ["login", "logout"]
     if ctx.invoked_subcommand not in no_api_subcommands:

onecodex/utils.py

@@ -187,33 +187,6 @@ def warn_if_insecure_platform():
         return False
 
 
-def is_simplejson_installed():
-    try:
-        import simplejson  # noqa
-    except ImportError:
-        return False
-    else:
-        return True
-
-
-def warn_simplejson():
-    """
-    Right now, potion-client is incompatible with requests when simplejson is
-    installed. Until this is patched upstream, we display this warning to
-    users when simplejson is installed.
-    """
-    m = ("\n"
-         "######################################################################################\n"  # noqa
-         "#                                                                                    #\n"  # noqa
-         "#  You currently have simplejson installed. Unfortunately, this library does not     #\n"  # noqa
-         "#  work properly alongside simplejson. Please install this library in a separate     #\n"  # noqa
-         "#  virtual environment using a tool such as virtualenv or uninstall simplejson.      #\n"  # noqa
-         "#  For more information, see https://virtualenv.pypa.io/en/stable/.                  #\n"  # noqa
-         "#                                                                                    #\n"  # noqa
-         "######################################################################################\n")  # noqa)
-    echo(m, err=True)
-
-
 def get_download_dest(input_path, url):
     original_filename = urlparse(url).path.split("/")[-1]
     if os.path.isdir(input_path):