dcicutils 8.5.0.1b6__tar.gz → 8.5.0.1b7__tar.gz

{dcicutils-8.5.0.1b6 → dcicutils-8.5.0.1b7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcicutils
-Version: 8.5.0.1b6
+Version: 8.5.0.1b7
 Summary: Utility package for interacting with the 4DN Data Portal and other 4DN resources
 Home-page: https://github.com/4dn-dcic/utils
 License: MIT

{dcicutils-8.5.0.1b6 → dcicutils-8.5.0.1b7}/dcicutils/portal_utils.py

@@ -1,13 +1,17 @@
 from collections import deque
 import io
 import json
-from pyramid.paster import get_app
-from pyramid.router import Router
+from pyramid.config import Configurator as PyramidConfigurator
+from pyramid.paster import get_app as pyramid_get_app
+from pyramid.response import Response as PyramidResponse
+from pyramid.router import Router as PyramidRouter
 import os
 import re
 import requests
 from requests.models import Response as RequestResponse
-from typing import Optional, Type, Union
+from typing import Callable, Dict, List, Optional, Type, Union
+from uuid import uuid4 as uuid
+# from waitress import serve
 from webtest.app import TestApp, TestResponse
 from dcicutils.common import OrchestratedApp, ORCHESTRATED_APPS
 from dcicutils.ff_utils import get_metadata, get_schema, patch_metadata, post_metadata
@@ -37,7 +41,7 @@ class Portal:
     KEYS_FILE_DIRECTORY = os.path.expanduser(f"~")
 
     def __init__(self,
-                 arg: Optional[Union[Portal, TestApp, VirtualApp, Router, dict, tuple, str]] = None,
+                 arg: Optional[Union[Portal, TestApp, VirtualApp, PyramidRouter, dict, tuple, str]] = None,
                  env: Optional[str] = None, server: Optional[str] = None,
                  app: Optional[OrchestratedApp] = None) -> None:
 
@@ -69,14 +73,14 @@ class Portal:
             self._app = portal._app
             self._vapp = portal._vapp
 
-        def init_from_vapp(vapp: Union[TestApp, VirtualApp, Router], unspecified: Optional[list] = []) -> None:
+        def init_from_vapp(vapp: Union[TestApp, VirtualApp, PyramidRouter], unspecified: Optional[list] = []) -> None:
             init(unspecified)
-            self._vapp = Portal._create_testapp(vapp)
+            self._vapp = Portal._create_vapp(vapp)
 
         def init_from_ini_file(ini_file: str, unspecified: Optional[list] = []) -> None:
             init(unspecified)
             self._ini_file = ini_file
-            self._vapp = Portal._create_testapp(ini_file)
+            self._vapp = Portal._create_vapp(ini_file)
 
         def init_from_key(key: dict, server: Optional[str], unspecified: Optional[list] = []) -> None:
             init(unspecified)
@@ -138,7 +142,7 @@ class Portal:
 
         if isinstance(arg, Portal):
             init_from_portal(arg, unspecified=[env, server, app])
-        elif isinstance(arg, (TestApp, VirtualApp, Router)):
+        elif isinstance(arg, (TestApp, VirtualApp, PyramidRouter)):
             init_from_vapp(arg, unspecified=[env, server, app])
         elif isinstance(arg, str) and arg.endswith(".ini"):
             init_from_ini_file(arg, unspecified=[env, server, app])
@@ -201,35 +205,36 @@ class Portal:
     def patch_metadata(self, object_id: str, data: str) -> Optional[dict]:
         if self._key:
             return patch_metadata(obj_id=object_id, patch_item=data, key=self._key)
-        return self.patch(f"/{object_id}", data)
+        return self.patch(f"/{object_id}", data).json()
 
     def post_metadata(self, object_type: str, data: str) -> Optional[dict]:
         if self._key:
             return post_metadata(schema_name=object_type, post_item=data, key=self._key)
-        return self.post(f"/{object_type}", data)
+        return self.post(f"/{object_type}", data).json()
 
     def get(self, uri: str, follow: bool = True, **kwargs) -> Optional[Union[RequestResponse, TestResponse]]:
-        if self._vapp:
-            response = self._vapp.get(self.url(uri), **self._kwargs(**kwargs))
-            if response and response.status_code in [301, 302, 303, 307, 308] and follow:
-                response = response.follow()
-            return self._response(response)
-        return requests.get(self.url(uri), allow_redirects=follow, **self._kwargs(**kwargs))
+        if not self._vapp:
+            return requests.get(self.url(uri), allow_redirects=follow, **self._kwargs(**kwargs))
+        response = self._vapp.get(self.url(uri), **self._kwargs(**kwargs))
+        if response and response.status_code in [301, 302, 303, 307, 308] and follow:
+            response = response.follow()
+        return self._response(response)
 
     def patch(self, uri: str, data: Optional[dict] = None,
               json: Optional[dict] = None, **kwargs) -> Optional[Union[RequestResponse, TestResponse]]:
-        if self._vapp:
-            return self._vapp.patch_json(self.url(uri), json or data, **self._kwargs(**kwargs))
-        return requests.patch(self.url(uri), data=data, json=json, **self._kwargs(**kwargs))
+        if not self._vapp:
+            return requests.patch(self.url(uri), data=data, json=json, **self._kwargs(**kwargs))
+        return self._response(self._vapp.patch_json(self.url(uri), json or data, **self._kwargs(**kwargs)))
 
     def post(self, uri: str, data: Optional[dict] = None, json: Optional[dict] = None,
              files: Optional[dict] = None, **kwargs) -> Optional[Union[RequestResponse, TestResponse]]:
-        if self._vapp:
-            if files:
-                return self._vapp.post(self.url(uri), json or data, upload_files=files, **self._kwargs(**kwargs))
-            else:
-                return self._vapp.post_json(self.url(uri), json or data, upload_files=files, **self._kwargs(**kwargs))
-        return requests.post(self.url(uri), data=data, json=json, files=files, **self._kwargs(**kwargs))
+        if not self._vapp:
+            return requests.post(self.url(uri), data=data, json=json, files=files, **self._kwargs(**kwargs))
+        if files:
+            response = self._vapp.post(self.url(uri), json or data, upload_files=files, **self._kwargs(**kwargs))
+        else:
+            response = self._vapp.post_json(self.url(uri), json or data, upload_files=files, **self._kwargs(**kwargs))
+        return self._response(response)
 
     def get_schema(self, schema_name: str) -> Optional[dict]:
         return get_schema(self.schema_name(schema_name), portal_vapp=self._vapp, key=self._key)
@@ -311,7 +316,7 @@ class Portal:
         if is_valid_app(app) or (app := infer_app_from_env(env)):
             return os.path.join(Portal.KEYS_FILE_DIRECTORY, f".{app.lower()}-keys.json")
 
-    def _response(self, response) -> Optional[RequestResponse]:
+    def _response(self, response: TestResponse) -> Optional[RequestResponse]:
         if response and isinstance(getattr(response.__class__, "json"), property):
             class RequestResponseWrapper:  # For consistency change json property to method.
                 def __init__(self, response, **kwargs):
@@ -325,51 +330,72 @@ class Portal:
         return response
 
     @staticmethod
-    def create_for_testing(ini_file: Optional[str] = None) -> Portal:
-        if isinstance(ini_file, str):
-            return Portal(Portal._create_testapp(ini_file))
-        minimal_ini_for_unit_testing = "[app:app]\nuse = egg:encoded\nsqlalchemy.url = postgresql://dummy\n"
-        with temporary_file(content=minimal_ini_for_unit_testing, suffix=".ini") as ini_file:
-            return Portal(Portal._create_testapp(ini_file))
-
-    @staticmethod
-    def create_for_testing_local(ini_file: Optional[str] = None) -> Portal:
-        if isinstance(ini_file, str) and ini_file:
-            return Portal(Portal._create_testapp(ini_file))
-        minimal_ini_for_testing_local = "\n".join([
-            "[app:app]\nuse = egg:encoded\nfile_upload_bucket = dummy",
-            "sqlalchemy.url = postgresql://postgres@localhost:5441/postgres?host=/tmp/snovault/pgdata",
-            "multiauth.groupfinder = encoded.authorization.smaht_groupfinder",
-            "multiauth.policies = auth0 session remoteuser accesskey",
-            "multiauth.policy.session.namespace = mailto",
-            "multiauth.policy.session.use = encoded.authentication.NamespacedAuthenticationPolicy",
-            "multiauth.policy.session.base = pyramid.authentication.SessionAuthenticationPolicy",
-            "multiauth.policy.remoteuser.namespace = remoteuser",
-            "multiauth.policy.remoteuser.use = encoded.authentication.NamespacedAuthenticationPolicy",
-            "multiauth.policy.remoteuser.base = pyramid.authentication.RemoteUserAuthenticationPolicy",
-            "multiauth.policy.accesskey.namespace = accesskey",
-            "multiauth.policy.accesskey.use = encoded.authentication.NamespacedAuthenticationPolicy",
-            "multiauth.policy.accesskey.base = encoded.authentication.BasicAuthAuthenticationPolicy",
-            "multiauth.policy.accesskey.check = encoded.authentication.basic_auth_check",
-            "multiauth.policy.auth0.use = encoded.authentication.NamespacedAuthenticationPolicy",
-            "multiauth.policy.auth0.namespace = auth0",
-            "multiauth.policy.auth0.base = encoded.authentication.Auth0AuthenticationPolicy"
-        ])
-        with temporary_file(content=minimal_ini_for_testing_local, suffix=".ini") as minimal_ini_file:
-            return Portal(Portal._create_testapp(minimal_ini_file))
+    def create_for_testing(arg: Optional[Union[str, bool, List[dict], dict, Callable]] = None) -> Portal:
+        if isinstance(arg, list) or isinstance(arg, dict) or isinstance(arg, Callable):
+            return Portal(Portal._create_router_for_testing(arg))
+        if isinstance(arg, str) and arg.endswith(".ini"):
+            return Portal(Portal._create_vapp(arg))
+        if arg == "local" or arg is True:
+            minimal_ini_for_testing = "\n".join([
+                "[app:app]\nuse = egg:encoded\nfile_upload_bucket = dummy",
+                "sqlalchemy.url = postgresql://postgres@localhost:5441/postgres?host=/tmp/snovault/pgdata",
+                "multiauth.groupfinder = encoded.authorization.smaht_groupfinder",
+                "multiauth.policies = auth0 session remoteuser accesskey",
+                "multiauth.policy.session.namespace = mailto",
+                "multiauth.policy.session.use = encoded.authentication.NamespacedAuthenticationPolicy",
+                "multiauth.policy.session.base = pyramid.authentication.SessionAuthenticationPolicy",
+                "multiauth.policy.remoteuser.namespace = remoteuser",
+                "multiauth.policy.remoteuser.use = encoded.authentication.NamespacedAuthenticationPolicy",
+                "multiauth.policy.remoteuser.base = pyramid.authentication.RemoteUserAuthenticationPolicy",
+                "multiauth.policy.accesskey.namespace = accesskey",
+                "multiauth.policy.accesskey.use = encoded.authentication.NamespacedAuthenticationPolicy",
+                "multiauth.policy.accesskey.base = encoded.authentication.BasicAuthAuthenticationPolicy",
+                "multiauth.policy.accesskey.check = encoded.authentication.basic_auth_check",
+                "multiauth.policy.auth0.use = encoded.authentication.NamespacedAuthenticationPolicy",
+                "multiauth.policy.auth0.namespace = auth0",
+                "multiauth.policy.auth0.base = encoded.authentication.Auth0AuthenticationPolicy"
+            ])
+        else:
+            minimal_ini_for_testing = "[app:app]\nuse = egg:encoded\nsqlalchemy.url = postgresql://dummy\n"
+        with temporary_file(content=minimal_ini_for_testing, suffix=".ini") as ini_file:
+            return Portal(Portal._create_vapp(ini_file))
 
     @staticmethod
-    def _create_testapp(arg: Union[TestApp, VirtualApp, Router, str] = None, app_name: Optional[str] = None) -> TestApp:
+    def _create_vapp(arg: Union[TestApp, VirtualApp, PyramidRouter, str] = None) -> TestApp:
         if isinstance(arg, TestApp):
             return arg
         elif isinstance(arg, VirtualApp):
             if not isinstance(arg.wrapped_app, TestApp):
-                raise Exception("Portal._create_testapp VirtualApp argument error.")
+                raise Exception("Portal._create_vapp VirtualApp argument error.")
             return arg.wrapped_app
-        if isinstance(arg, Router):
+        if isinstance(arg, PyramidRouter):
             router = arg
-        elif isinstance(arg, str) or arg is None:
-            router = get_app(arg or "development.ini", app_name or "app")
+        elif isinstance(arg, str) or not arg:
+            router = pyramid_get_app(arg or "development.ini", "app")
         else:
-            raise Exception("Portal._create_testapp argument error.")
+            raise Exception("Portal._create_vapp argument error.")
         return TestApp(router, {"HTTP_ACCEPT": "application/json", "REMOTE_USER": "TEST"})
+
+    @staticmethod
+    def _create_router_for_testing(endpoints: Optional[List[Dict[str, Union[str, Callable]]]] = None):
+        if isinstance(endpoints, dict):
+            endpoints = [endpoints]
+        elif isinstance(endpoints, Callable):
+            endpoints = [{"path": "/", "method": "GET", "function": endpoints}]
+        if not isinstance(endpoints, list) or not endpoints:
+            endpoints = [{"path": "/", "method": "GET", "function": lambda request: {"status": "OK"}}]
+        with PyramidConfigurator() as config:
+            nendpoints = 0
+            for endpoint in endpoints:
+                if (endpoint_path := endpoint.get("path")) and (endpoint_function := endpoint.get("function")):
+                    endpoint_method = endpoint.get("method", "GET")
+                    def endpoint_wrapper(request):  # noqa
+                        response = endpoint_function(request)
+                        return PyramidResponse(json.dumps(response), content_type="application/json; charset=utf-8")
+                    endpoint_id = str(uuid())
+                    config.add_route(endpoint_id, endpoint_path)
+                    config.add_view(endpoint_wrapper, route_name=endpoint_id, request_method=endpoint_method)
+                    nendpoints += 1
+            if nendpoints == 0:
+                return Portal._create_router_for_testing([])
+            return config.make_wsgi_app()

{dcicutils-8.5.0.1b6 → dcicutils-8.5.0.1b7}/dcicutils/structured_data.py

@@ -616,12 +616,9 @@ class Portal(PortalBase):
         return self.get_metadata(f"/{type_name}/{value}") is not None
 
     @staticmethod
-    def create_for_testing(ini_file: Optional[str] = None, schemas: Optional[List[dict]] = None) -> Portal:
-        return Portal(PortalBase.create_for_testing(ini_file), schemas=schemas)
-
-    @staticmethod
-    def create_for_testing_local(ini_file: Optional[str] = None, schemas: Optional[List[dict]] = None) -> Portal:
-        return Portal(PortalBase.create_for_testing_local(ini_file), schemas=schemas)
+    def create_for_testing(arg: Optional[Union[str, bool, List[dict], dict, Callable]] = None,
+                           schemas: Optional[List[dict]] = None) -> Portal:
+        return Portal(PortalBase.create_for_testing(arg), schemas=schemas)
 
 
 def _split_dotted_string(value: str):

{dcicutils-8.5.0.1b6 → dcicutils-8.5.0.1b7}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.5.0.1b6"  # TODO: To become 8.6.0
+version = "8.5.0.1b7"  # TODO: To become 8.6.0
 description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources"
 authors = ["4DN-DCIC Team <support@4dnucleome.org>"]
 license = "MIT"