Versioning potion-client solves simplejson issue (#111)

.circleci/config.yml

@@ -27,7 +27,7 @@ jobs:
           name: Run tests
           command: |
             . venv/bin/activate
-            py.test --ignore tests/test_minimal.py --ignore tests/test_simplejson.py tests/
+            py.test --ignore tests/test_minimal.py tests/
   test-py2:
     docker:
       - image: circleci/python:2.7-stretch
@@ -44,7 +44,7 @@ jobs:
           name: Run tests
           command: |
             . venv/bin/activate
-            py.test --ignore tests/test_minimal.py --ignore tests/test_simplejson.py tests/
+            py.test --ignore tests/test_minimal.py tests/
   test-minimal:
     docker:
       - image: circleci/python:3.4-stretch
@@ -79,7 +79,7 @@ jobs:
           name: Run tests
           command: |
             . venv/bin/activate
-            py.test tests/test_simplejson.py
+            py.test --ignore tests/test_minimal.py tests/
   lint:
     docker:
       - image: circleci/python:2.7-stretch
@@ -112,6 +112,6 @@ jobs:
           name: Run flake8
           command: |
             . venv/bin/activate
-            py.test --cov-report=html --cov=onecodex --ignore tests/test_minimal.py --ignore tests/test_simplejson.py tests/
+            py.test --cov-report=html --cov=onecodex --ignore tests/test_minimal.py tests/
             coveralls
 

.coveragerc

@@ -23,6 +23,7 @@ ignore_errors = True
 
 omit =
     onecodex/version.py
+    onecodex/vendored/*
 
 [html]
 directory = htmlcov

onecodex/api.py

@@ -12,11 +12,11 @@
 import warnings
 import errno
 
-from potion_client import Client as PotionClient
-from potion_client.converter import PotionJSONSchemaDecoder, PotionJSONDecoder, PotionJSONEncoder
-from potion_client.utils import upper_camel_case
 from requests.auth import HTTPBasicAuth
 
+from onecodex.vendored.potion_client import Client as PotionClient
+from onecodex.vendored.potion_client.converter import PotionJSONSchemaDecoder, PotionJSONDecoder, PotionJSONEncoder
+from onecodex.vendored.potion_client.utils import upper_camel_case
 from onecodex.lib.auth import BearerTokenAuth
 from onecodex.models import _model_lookup
 from onecodex.utils import ModuleAlias, get_raven_client, collapse_user

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)
+                            warn_if_insecure_platform, telemetry)
 from onecodex.api import Api
 from onecodex.exceptions import (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()
-
     # handle checking insecure platform, we let upload command do it by itself
     if ctx.invoked_subcommand != "upload":
         warn_if_insecure_platform()

onecodex/models/__init__.py

@@ -7,10 +7,10 @@
 from dateutil.parser import parse
 import pytz
 from requests.exceptions import HTTPError
-from potion_client.converter import PotionJSONEncoder
-from potion_client.resource import Resource
 import six
 
+from onecodex.vendored.potion_client.converter import PotionJSONEncoder
+from onecodex.vendored.potion_client.resource import Resource
 from onecodex.exceptions import MethodNotSupported, PermissionDenied, ServerError
 from onecodex.models.helpers import (check_bind, generate_potion_sort_clause,
                                      generate_potion_keyword_where)

onecodex/utils.py

@@ -25,8 +25,8 @@
 
 import requests
 from click import BadParameter, Context, echo
-from potion_client.converter import PotionJSONEncoder
 
+from onecodex.vendored.potion_client.converter import PotionJSONEncoder
 from onecodex.exceptions import OneCodexException, UploadException
 from onecodex.version import __version__
 
@@ -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):

onecodex/vendored/__init__.py

@@ -0,0 +1,5 @@
+"""
+Modules created by others. Versioned and distributed by One Codex
+"""
+
+__all__ = ['potion_client']

onecodex/vendored/potion_client/LICENSE

@@ -0,0 +1,18 @@
+Copyright (c) 2016 The Novo Nordisk Foundation Center for Biosustainability
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+the Software, and to permit persons to whom the Software is furnished to do so,
+subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

onecodex/vendored/potion_client/README.rst

@@ -0,0 +1,86 @@
+
+=============
+Potion client
+=============
+
+
+.. image:: https://img.shields.io/travis/biosustain/potion-client/new-potion-client.svg?style=flat-square
+    :target: https://travis-ci.org/biosustain/potion-client
+
+.. image:: https://img.shields.io/coveralls/biosustain/potion-client/new-potion-client.svg?style=flat-square
+    :target: https://coveralls.io/r/biosustain/potion-client
+
+.. image:: https://img.shields.io/pypi/v/Potion-Client.svg?style=flat-square
+    :target: https://pypi.python.org/pypi/Potion-Client
+
+.. image:: https://img.shields.io/pypi/l/Potion-Client.svg?style=flat-square
+    :target: https://pypi.python.org/pypi/Potion-Client
+
+.. image:: https://badges.gitter.im/Join%20Chat.svg
+   :alt: Join the chat at https://gitter.im/biosustain/potion
+   :target: https://gitter.im/biosustain/potion?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge
+
+Description
+===========
+
+This is a Python client for APIs written in `Flask-Potion <https://github.com/biosustain/potion>`_ (a powerful Flask extension for self-documenting JSON APIs).
+
+The package uses `Requests <https://github.com/kennethreitz/requests>`_ to provide a super-simple interface to Potion APIs that
+works with all common authentication methods. It generates classes for each of the resources in the API and automatically handles pagination
+and resolving and serializing references. It also has some basic `IPython Notebook <http://ipython.org/notebook.html>`_ support.
+
+Example
+=======
+
+.. code-block:: python
+
+    from potion_client import Client
+    from potion_client.auth import HTTPBearerAuth
+    from potion_client.exceptions import ItemNotFound
+
+    client = Client('http://localhost/api', auth=HTTPBearerAuth('79054025255fb1a26e4bc422aef54eb4'))
+
+    u123 = client.User(123)
+
+    chomp = client.Animal()
+    chomp.owner = u123
+    chomp.name = "Chomp"
+    chomp.species = "hamster"
+    chomp.save()
+
+    pets = client.Animal.instances(where={"owner": u123}, sort={"created_at": True})
+
+    print("{} has {} pet(s)".format(u123.first_name, len(pets))
+
+    for pet in pets:
+        if pet is not chomp:
+            pet.add_friend(chomp)
+            print("{} is now friends with Chomp".format(pet.name)))
+
+    try:
+        foo = client.User.first(where={"username": "foo"})
+    except ItemNotFound:
+        print("User 'foo' does not exist!")
+    else:
+        chomp.update(owner=foo)
+        print("Chomp has been sold to {}".format(foo.name))
+
+    chomp.destroy()
+    print("RIP, Chomp. You lived a happy life.")
+
+Installation
+============
+
+To install ``potion-client``, run:
+
+::
+
+    pip install potion-client
+
+
+
+
+Authors
+=======
+
+Potion-client was written by `João Cardoso <https://github.com/joaocardoso>`_ and `Lars Schöning <https://github.com/lyschoening>`_.

onecodex/vendored/potion_client/__init__.py

@@ -0,0 +1,148 @@
+# flake8: noqa
+from functools import partial
+from operator import getitem, delitem, setitem
+from six.moves.urllib.parse import urlparse, urljoin
+from weakref import WeakValueDictionary
+import collections
+import requests
+
+from .converter import PotionJSONDecoder, PotionJSONSchemaDecoder
+from .resource import Reference, Resource, uri_for
+from .links import Link
+from .utils import upper_camel_case, snake_case
+
+
+class Client(object):
+    # TODO optional HTTP/2 support: this makes multiple queries simultaneously.
+
+    def __init__(self, api_root_url, schema_path='/schema', fetch_schema=True, **session_kwargs):
+        self._instances = WeakValueDictionary()
+        self._resources = {}
+
+        self.session = session = requests.Session()
+        for key, value in session_kwargs.items():
+            setattr(session, key, value)
+
+        parse_result = urlparse(api_root_url)
+        self._root_url = '{}://{}'.format(parse_result.scheme, parse_result.netloc)
+        self._api_root_url = api_root_url  # '{}://{}'.format(parse_result.scheme, parse_result.netloc)
+        self._root_path = parse_result.path
+        self._schema_url = api_root_url + schema_path
+
+        if fetch_schema:
+            self._fetch_schema()
+
+    def _fetch_schema(self):
+        schema = self.session \
+            .get(self._schema_url) \
+            .json(cls=PotionJSONSchemaDecoder,
+                  referrer=self._schema_url,
+                  client=self)
+
+        # NOTE these should perhaps be definitions in Flask-Potion
+        for name, resource_schema in schema['properties'].items():
+            resource = self.resource_factory(name, resource_schema)
+            setattr(self, upper_camel_case(name), resource)
+
+    def instance(self, uri, cls=None, default=None, **kwargs):
+        instance = self._instances.get(uri, None)
+
+        if instance is None:
+            if cls is None:
+                try:
+                    cls = self._resources[uri[:uri.rfind('/')]]
+                except KeyError:
+                    cls = Reference
+
+            if isinstance(default, Resource) and default._uri is None:
+                default._status = 200
+                default._uri = uri
+                instance = default
+            else:
+                instance = cls(uri=uri, **kwargs)
+            self._instances[uri] = instance
+        return instance
+
+    def fetch(self, uri, cls=PotionJSONDecoder, **kwargs):
+        # TODO handle URL fragments (#properties/id etc.)
+        response = self.session \
+            .get(urljoin(self._root_url, uri, True))
+
+        response.raise_for_status()
+
+        return response.json(cls=cls,
+                             client=self,
+                             referrer=uri,
+                             **kwargs)
+
+    def resource_factory(self, name, schema, resource_cls=None):
+        """
+        Registers a new resource with a given schema. The schema must not have any unresolved references
+        (such as `{"$ref": "#"}` for self-references, or otherwise). A subclass of :class:`Resource`
+        may be provided to add specific functionality to the resulting :class:`Resource`.
+
+        :param str name:
+        :param dict schema:
+        :param Resource resource_cls: a subclass of :class:`Resource` or None
+        :return: The new :class:`Resource`.
+        """
+        cls = type(str(upper_camel_case(name)), (resource_cls or Resource, collections.MutableMapping), {
+            '__doc__': schema.get('description', '')
+        })
+
+        cls._schema = schema
+        cls._client = self
+        cls._links = links = {}
+
+        for link_schema in schema['links']:
+            link = Link(self,
+                        rel=link_schema['rel'],
+                        href=link_schema['href'],
+                        method=link_schema['method'],
+                        schema=link_schema.get('schema', None),
+                        target_schema=link_schema.get('targetSchema', None))
+
+            # Set Resource._self, etc. for the special methods as they are managed by the Resource class
+            if link.rel in ('self', 'instances', 'create', 'update', 'destroy'):
+                setattr(cls, '_{}'.format(link.rel), link)
+            links[link.rel] = link
+
+            if link.rel != 'update':  # 'update' is a special case because of MutableMapping.update()
+                setattr(cls, snake_case(link.rel), link)
+
+        # TODO routes (instance & non-instance)
+
+        for property_name, property_schema in schema.get('properties', {}).items():
+            # skip $uri and $id as these are already implemented in Resource and overriding them causes unnecessary
+            # fetches.
+            if property_name.startswith('$'):
+                continue
+
+            if property_schema.get('readOnly', False):
+                # TODO better error message. Raises AttributeError("can't set attribute")
+                setattr(cls,
+                        property_name,
+                        property(fget=partial((lambda name, obj: getitem(obj, name)), property_name),
+                                 doc=property_schema.get('description', None)))
+            else:
+                setattr(cls,
+                        property_name,
+                        property(fget=partial((lambda name, obj: getitem(obj, name)), property_name),
+                                 fset=partial((lambda name, obj, value: setitem(obj, name, value)), property_name),
+                                 fdel=partial((lambda name, obj: delitem(obj, name)), property_name),
+                                 doc=property_schema.get('description', None)))
+
+        root = None
+        if 'instances' in links:
+            root = cls._instances.href
+        elif 'self' in links:
+            root = cls._self.href[:cls._self.href.rfind('/')]
+        else:
+            root = self._root_path + '/' + name.replace('_', '-')
+
+        self._resources[root] = cls
+        return cls
+
+
+ASC = ASCENDING = False
+DESC = DESCENDING = True