Blackened

openflexure_microscope/api/app.py

@@ -169,7 +169,7 @@ atexit.register(cleanup)
 
 if __name__ == "__main__":
     app.run(host="0.0.0.0", port="5000", threaded=True, debug=True, use_reloader=False)
-    #from pprint import pprint
+    # from pprint import pprint
-    #pprint(labthing.spec.to_dict())
+    # pprint(labthing.spec.to_dict())
-    #with open('spec.yaml', 'w') as f:
+    # with open('spec.yaml', 'w') as f:
-    #    f.write(labthing.spec.to_yaml())
+    #    f.write(labthing.spec.to_yaml())

openflexure_microscope/api/v2/views/actions/camera.py

@@ -1,7 +1,12 @@
 from openflexure_microscope.api.utilities import get_bool, JsonResponse
 from openflexure_microscope.common.flask_labthings.resource import Resource
 from openflexure_microscope.common.flask_labthings.find import find_device
-from openflexure_microscope.common.flask_labthings.decorators import use_args, marshal_with, doc, doc_response
+from openflexure_microscope.common.flask_labthings.decorators import (
+    use_args,
+    marshal_with,
+    doc,
+    doc_response,
+)
 from openflexure_microscope.common.flask_labthings import fields
 from openflexure_microscope.utilities import filter_dict
 
@@ -10,6 +15,7 @@ from openflexure_microscope.api.v2.views.captures import capture_schema
 import logging
 from flask import jsonify, request, abort, url_for, redirect, send_file
 
+
 @doc(tags=["actions"])
 class CaptureAPI(Resource):
     """

openflexure_microscope/api/v2/views/captures.py

@@ -18,7 +18,9 @@ from marshmallow import pre_dump
 
 class CaptureSchema(Schema):
     id = fields.String()
-    file = fields.String(data_key="path", description="Path of file on microscope device")
+    file = fields.String(
+        data_key="path", description="Path of file on microscope device"
+    )
     exists = fields.Bool(data_key="available")
     filename = fields.String()
     metadata = fields.Dict()

openflexure_microscope/common/flask_labthings/decorators.py

@@ -5,6 +5,7 @@ from flask import make_response
 from .utilities import rupdate
 from .spec import update_spec
 
+
 def unpack(value):
     """Return a three tuple of data, code, and headers"""
     if not isinstance(value, tuple):
@@ -93,14 +94,7 @@ class doc_response(object):
 
     def __call__(self, f):
         # Pass params to call function attribute for external access
-        f.__apispec__ = f.__dict__.get('__apispec__', {})
+        f.__apispec__ = f.__dict__.get("__apispec__", {})
-        d = {
+        d = {"responses": {self.code: {"description": self.description, **self.kwargs}}}
-            "responses": {
-                self.code: {
-                    "description": self.description,
-                    **self.kwargs
-                }
-            }
-        }
         rupdate(f.__apispec__, d)
-        return f
+        return f

openflexure_microscope/common/flask_labthings/labthing.py

@@ -17,6 +17,7 @@ from . import EXTENSION_NAME
 
 import logging
 
+
 class LabThing(object):
     def __init__(
         self,
@@ -60,32 +61,31 @@ class LabThing(object):
             self.init_app(app)
 
     @property
-    def description(self, ):
+    def description(self,):
         return self._description
-    
+
     @description.setter
     def description(self, description: str):
         self._description = description
         self.spec.description = description
-    
+
     @property
-    def title(self, ):
+    def title(self,):
         return self._title
-    
+
     @title.setter
     def title(self, title: str):
         self._title = title
         self.spec.title = title
-    
+
     @property
-    def version(self, ):
+    def version(self,):
         return str(self._version)
-    
+
     @version.setter
     def version(self, version: str):
         self._version = version
         self.spec.version = version
-    
 
     ### Flask stuff
 
@@ -117,7 +117,9 @@ class LabThing(object):
         # Add thing description
         self.app.add_url_rule(self._complete_url("/td", ""), "td", self.td)
         # Add swagger spec
-        self.app.add_url_rule(self._complete_url("/swagger", ""), "swagger", self.swagger)
+        self.app.add_url_rule(
+            self._complete_url("/swagger", ""), "swagger", self.swagger
+        )
 
         # Add plugin overview
         self.add_resource(PluginListResource, "/plugins")
@@ -212,7 +214,7 @@ class LabThing(object):
 
         if self.app is not None:
             self._register_view(self.app, resource, *urls, endpoint=endpoint, **kwargs)
-        
+
         self.resources.append((resource, urls, endpoint, kwargs))
 
     def resource(self, *urls, **kwargs):
@@ -261,9 +263,7 @@ class LabThing(object):
             # Add the url to the application or blueprint
             app.add_url_rule(rule, view_func=resource_func, **kwargs)
             # Add the resource to our API spec
-            self.spec.path(
+            self.spec.path(**view2path(rule, resource, self.spec))
-                **view2path(rule, resource, self.spec)
-            )
 
     ### Utilities
 
@@ -334,8 +334,8 @@ class LabThing(object):
                 "tasks": {
                     "href": self.url_for(TaskList, _external=True),
                     **description_from_view(TaskList),
-                }
+                },
-            }
+            },
         }
 
         return jsonify(rr)
@@ -344,4 +344,4 @@ class LabThing(object):
         """
         OpenAPI v3 documentation
         """
-        return jsonify(self.spec.to_dict())
+        return jsonify(self.spec.to_dict())

openflexure_microscope/common/flask_labthings/resource.py

@@ -4,6 +4,7 @@ from flask.views import MethodView
 class Resource(MethodView):
     """Currently identical to MethodView
     """
+
     endpoint = None
     methods = ["get", "post", "put", "delete"]
 
@@ -15,7 +16,6 @@ class Resource(MethodView):
         if hasattr(self, "__apispec__"):
             docs.update(self.__apispec__)
 
-
         for meth in Resource.methods:
             if hasattr(self, meth) and hasattr(getattr(self, meth), "__apispec__"):
                 docs["operations"][meth] = {}

openflexure_microscope/common/flask_labthings/spec.py

@@ -1,27 +1,31 @@
-
 from .resource import Resource
 from .utilities import rupdate
 from apispec import APISpec
 from apispec.ext.marshmallow import MarshmallowPlugin
 
-from openflexure_microscope.common.labthings_core.utilities import get_docstring, get_summary
+from openflexure_microscope.common.labthings_core.utilities import (
+    get_docstring,
+    get_summary,
+)
 
 from .fields import Field
 from marshmallow import Schema as BaseSchema
 
 from collections import Mapping
 
+
 def update_spec(obj, spec):
-        obj.__apispec__ = obj.__dict__.get('__apispec__', {})
+    obj.__apispec__ = obj.__dict__.get("__apispec__", {})
-        rupdate(obj.__apispec__, spec)
+    rupdate(obj.__apispec__, spec)
-        return obj.__apispec__
+    return obj.__apispec__
+
 
 def view2path(rule: str, view: Resource, spec: APISpec):
     params = {
         "path": rule,  # TODO: Validate this slightly (leading / etc)
         "operations": view2operations(view, spec),
         "description": get_docstring(view),
-        "summary": get_summary(view)
+        "summary": get_summary(view),
     }
 
     if hasattr(view, "__apispec__"):
@@ -30,6 +34,7 @@ def view2path(rule: str, view: Resource, spec: APISpec):
 
     return params
 
+
 def view2operations(view: Resource, spec: APISpec, populate_default: bool = True):
     ops = {}
     for method in Resource.methods:
@@ -39,58 +44,67 @@ def view2operations(view: Resource, spec: APISpec, populate_default: bool = True
                 ops[method] = {
                     "responses": {
                         200: {
-                            "description": get_summary(getattr(view, method)) or "Success"
+                            "description": get_summary(getattr(view, method))
+                            or "Success"
                         },
-                        404: {
+                        404: {"description": "Resource not found"},
-                            "description": "Resource not found"
+                    }
-                        }
-                    },
                 }
             else:
                 ops[method] = {}
-            
+
-            rupdate(ops[method], {
+            rupdate(
-                "description": get_docstring(getattr(view, method)),
+                ops[method],
-                "summary": get_summary(getattr(view, method))
+                {
-            })
+                    "description": get_docstring(getattr(view, method)),
-        
+                    "summary": get_summary(getattr(view, method)),
+                },
+            )
+
             if hasattr(getattr(view, method), "__apispec__"):
-                rupdate(ops[method], doc2operation(getattr(view, method).__apispec__, spec))
+                rupdate(
-    
+                    ops[method], doc2operation(getattr(view, method).__apispec__, spec)
+                )
+
     return ops
 
 
 def doc2operation(apispec: dict, spec: APISpec):
     op = {}
     if "_params" in apispec:
-        rupdate(op, {
+        rupdate(
-            "requestBody": {
+            op,
-                "content": {
+            {
-                    "application/json": {
+                "requestBody": {
-                        "schema": convert_schema(apispec.get("_params"), spec)
-                    }
-                }
-            }
-        })
-
-    if "_schema" in apispec:
-        rupdate(op, 
-        {
-            "responses": {
-                200: {
                     "content": {
                         "application/json": {
-                            "schema": convert_schema(apispec.get("_schema"), spec)
+                            "schema": convert_schema(apispec.get("_params"), spec)
                         }
-                    },
+                    }
                 }
-            }
+            },
-        })
+        )
+
+    if "_schema" in apispec:
+        rupdate(
+            op,
+            {
+                "responses": {
+                    200: {
+                        "content": {
+                            "application/json": {
+                                "schema": convert_schema(apispec.get("_schema"), spec)
+                            }
+                        }
+                    }
+                }
+            },
+        )
 
     for key, val in apispec.items():
         if not key in ["_params", "_schema"]:
             op[key] = val
-    
+
     return op
 
 
@@ -100,12 +114,14 @@ def convert_schema(schema, spec: APISpec):
     elif isinstance(schema, Mapping):
         return map2properties(schema, spec)
     else:
-        raise TypeError("Unsupported schema type. Ensure schema is a Schema class, or dictionary of Field objects")
+        raise TypeError(
+            "Unsupported schema type. Ensure schema is a Schema class, or dictionary of Field objects"
+        )
+
 
 def map2properties(schema, spec: APISpec):
     marshmallow_plugin = next(
-        plugin for plugin in spec.plugins
+        plugin for plugin in spec.plugins if isinstance(plugin, MarshmallowPlugin)
-        if isinstance(plugin, MarshmallowPlugin)
     )
     converter = marshmallow_plugin.converter
 
@@ -118,4 +134,4 @@ def map2properties(schema, spec: APISpec):
         else:
             d[k] = v
 
-    return {"properties": d}
+    return {"properties": d}

openflexure_microscope/common/flask_labthings/utilities.py

@@ -1,4 +1,7 @@
-from openflexure_microscope.common.labthings_core.utilities import get_docstring, get_summary
+from openflexure_microscope.common.labthings_core.utilities import (
+    get_docstring,
+    get_summary,
+)
 from .schema import Schema, marshmallow, MARSHMALLOW_VERSION_INFO
 import collections.abc
 
@@ -25,4 +28,4 @@ def rupdate(d, u):
             d[k] = rupdate(d.get(k, {}), v)
         else:
             d[k] = v
-    return d
+    return d

openflexure_microscope/common/flask_labthings/views/plugins.py

@@ -48,6 +48,7 @@ class PluginListResource(Resource):
     """
     List and basic documentation for all enabled plugins
     """
+
     @marshal_with(PluginSchema(many=True))
     def get(self):
         """

openflexure_microscope/common/flask_labthings/views/tasks.py

@@ -39,6 +39,7 @@ class TaskList(Resource):
     """
     List and basic documentation for all session tasks
     """
+
     @marshal_with(TaskSchema(many=True))
     def get(self):
         return tasks.tasks()

openflexure_microscope/common/labthings_core/utilities.py

@@ -5,5 +5,6 @@ def get_docstring(obj):
     else:
         return ""
 
+
 def get_summary(obj):
-    return get_docstring(obj).partition("\n")[0].strip()
+    return get_docstring(obj).partition("\n")[0].strip()