Cleaned code structure

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

@@ -7,6 +7,7 @@ from openflexure_microscope.common.flask_labthings.decorators import (
     doc,
     doc_response,
 )
+
 from openflexure_microscope.common.flask_labthings import fields
 from openflexure_microscope.utilities import filter_dict
 

openflexure_microscope/api/v2/views/state.py

@@ -1,5 +1,10 @@
 from openflexure_microscope.api.utilities import JsonResponse
-from openflexure_microscope.utilities import get_by_path, set_by_path, create_from_path
+
+from openflexure_microscope.common.labthings_core.utilities import (
+    get_by_path,
+    set_by_path,
+    create_from_path,
+)
 
 from openflexure_microscope.common.flask_labthings.find import find_device
 from openflexure_microscope.common.flask_labthings.resource import Resource

openflexure_microscope/api/v2/views/streams.py

@@ -1,5 +1,10 @@
 from openflexure_microscope.api.utilities import gen, JsonResponse
-from openflexure_microscope.utilities import get_by_path, set_by_path, create_from_path
+
+from openflexure_microscope.common.labthings_core.utilities import (
+    get_by_path,
+    set_by_path,
+    create_from_path,
+)
 
 from openflexure_microscope.common.flask_labthings.find import find_device
 from openflexure_microscope.common.flask_labthings.resource import Resource

openflexure_microscope/common/flask_labthings/decorators.py

@@ -2,8 +2,10 @@ from webargs import flaskparser
 from functools import wraps, update_wrapper
 from flask import make_response
 
-from .utilities import rupdate
-from .spec import update_spec
+from openflexure_microscope.common.labthings_core.utilities import rupdate
+from openflexure_microscope.common.labthings_core.spec import update_spec
+
+from openflexure_microscope.common.labthings_core.decorators import doc, doc_response
 
 
 def unpack(value):
@@ -74,27 +76,3 @@ class use_kwargs(use_args):
         """
         kwargs["as_kwargs"] = True
         use_args.__init__(self, schema, **kwargs)
-
-
-class doc(object):
-    def __init__(self, **kwargs):
-        self.kwargs = kwargs
-
-    def __call__(self, f):
-        # Pass params to call function attribute for external access
-        update_spec(f, self.kwargs)
-        return f
-
-
-class doc_response(object):
-    def __init__(self, code, description, **kwargs):
-        self.code = code
-        self.description = description
-        self.kwargs = kwargs
-
-    def __call__(self, f):
-        # Pass params to call function attribute for external access
-        f.__apispec__ = f.__dict__.get("__apispec__", {})
-        d = {"responses": {self.code: {"description": self.description, **self.kwargs}}}
-        rupdate(f.__apispec__, d)
-        return f

openflexure_microscope/common/flask_labthings/extensions.py

@@ -7,8 +7,14 @@ import sys
 import os
 import glob
 
-from openflexure_microscope.common.labthings_core.utilities import get_docstring
-from openflexure_microscope.utilities import camel_to_snake, snake_to_spine
+from openflexure_microscope.common.labthings_core.utilities import (
+    get_docstring,
+    camel_to_snake,
+    snake_to_spine,
+)
+
+
+# TODO: Move into core?
 
 
 class BaseExtension:
@@ -134,7 +140,7 @@ def find_instances_in_module(module, class_to_find):
     return objs
 
 
-def find_extensions_in_file(extension_path, module_name="extensions"):
+def find_extensions_in_file(extension_path: str, module_name="extensions"):
     logging.debug(f"Loading extensions from {extension_path}")
 
     spec = util.spec_from_file_location(module_name, extension_path)
@@ -149,7 +155,7 @@ def find_extensions_in_file(extension_path, module_name="extensions"):
         return find_instances_in_module(mod, BaseExtension)
 
 
-def find_extensions(extension_dir, module_name="extensions"):
+def find_extensions(extension_dir: str, module_name="extensions"):
     logging.debug(f"Loading extensions from {extension_dir}")
 
     extensions = []

openflexure_microscope/common/flask_labthings/fields.py

@@ -1,175 +1 @@
-from marshmallow.fields import *
-from marshmallow import missing
-import re
-from flask import url_for
-from flask.views import View
-
-_tpl_pattern = re.compile(r"\s*<\s*(\S*)\s*>\s*")
-
-
-def _tpl(val):
-    """Return value within ``< >`` if possible, else return ``None``."""
-    match = _tpl_pattern.match(val)
-    if match:
-        return match.groups()[0]
-    return None
-
-
-def _get_value(obj, key, default=missing):
-    """Slightly-modified version of marshmallow.utils.get_value.
-    If a dot-delimited ``key`` is passed and any attribute in the
-    path is `None`, return `None`.
-    """
-    if "." in key:
-        return _get_value_for_keys(obj, key.split("."), default)
-    else:
-        return _get_value_for_key(obj, key, default)
-
-
-def _get_value_for_keys(obj, keys, default):
-    if len(keys) == 1:
-        return _get_value_for_key(obj, keys[0], default)
-    else:
-        value = _get_value_for_key(obj, keys[0], default)
-        # XXX This differs from the marshmallow implementation
-        if value is None:
-            return None
-        return _get_value_for_keys(value, keys[1:], default)
-
-
-def _get_value_for_key(obj, key, default):
-    if not hasattr(obj, "__getitem__"):
-        return getattr(obj, key, default)
-
-    try:
-        return obj[key]
-    except (KeyError, IndexError, TypeError, AttributeError):
-        return getattr(obj, key, default)
-
-
-class URLFor(Field):
-    """Field that outputs the URL for an endpoint. Acts identically to
-    Flask's ``url_for`` function, except that arguments can be pulled from the
-    object to be serialized.
-    Usage: ::
-        url = URLFor('author_get', id='<id>')
-        https_url = URLFor('author_get', id='<id>', _scheme='https', _external=True)
-    :param str endpoint: Flask endpoint name.
-    :param kwargs: Same keyword arguments as Flask's url_for, except string
-        arguments enclosed in `< >` will be interpreted as attributes to pull
-        from the object.
-    """
-
-    _CHECK_ATTRIBUTE = False
-
-    def __init__(self, endpoint, **kwargs):
-        # Handle the case where endpoint is an attached flask View of any kind
-        if isinstance(endpoint, type) and issubclass(endpoint, View):
-            self.view_class = endpoint
-            self.endpoint = None
-        # Handle cases where endpoint is passed directly as a string
-        elif type(endpoint) == str:
-            self.view_class = None
-            self.endpoint = endpoint
-        else:
-            raise RuntimeError(
-                f"Endpoint {endpoint} is not a valid Flask view or endpoint string."
-            )
-        self.params = kwargs
-        Field.__init__(self, **kwargs)
-
-    def _serialize(self, value, key, obj):
-        """Output the URL for the endpoint, given the kwargs passed to
-        ``__init__``.
-        """
-        # Get endpoint from view_class, if needed
-        if self.view_class and not self.endpoint:
-            if hasattr(self.view_class, "endpoint"):
-                self.endpoint = self.view_class.endpoint
-            else:
-                raise RuntimeError(
-                    f"Resource {self.endpoint} has not been added to a LabThing application. Unable to generate URL."
-                )
-
-        # Generate URL for
-        param_values = {}
-        for name, attr_tpl in self.params.items():
-            attr_name = _tpl(str(attr_tpl))
-            if attr_name:
-                attribute_value = _get_value(obj, attr_name, default=missing)
-                if attribute_value is None:
-                    return None
-                if attribute_value is not missing:
-                    param_values[name] = attribute_value
-                else:
-                    raise AttributeError(
-                        "{attr_name!r} is not a valid "
-                        "attribute of {obj!r}".format(attr_name=attr_name, obj=obj)
-                    )
-            else:
-                param_values[name] = attr_tpl
-        return url_for(self.endpoint, **param_values)
-
-
-UrlFor = URLFor
-
-
-class AbsoluteURLFor(URLFor):
-    """Field that outputs the absolute URL for an endpoint."""
-
-    def __init__(self, endpoint, **kwargs):
-        kwargs["_external"] = True
-        URLFor.__init__(self, endpoint=endpoint, **kwargs)
-
-
-AbsoluteUrlFor = AbsoluteURLFor
-
-
-def _rapply(d, func, *args, **kwargs):
-    """Apply a function to all values in a dictionary or list of dictionaries, recursively."""
-    if isinstance(d, (tuple, list)):
-        return [_rapply(each, func, *args, **kwargs) for each in d]
-    if isinstance(d, dict):
-        return {key: _rapply(value, func, *args, **kwargs) for key, value in d.items()}
-    else:
-        return func(d, *args, **kwargs)
-
-
-def _url_val(val, key, obj, **kwargs):
-    """Function applied by `HyperlinksField` to get the correct value in the
-    schema.
-    """
-    if isinstance(val, URLFor):
-        return val.serialize(key, obj, **kwargs)
-    else:
-        return val
-
-
-class Hyperlinks(Field):
-    """Field that outputs a dictionary of hyperlinks,
-    given a dictionary schema with :class:`~flask_marshmallow.fields.URLFor`
-    objects as values.
-    Example: ::
-        _links = Hyperlinks({
-            'self': URLFor('author', id='<id>'),
-            'collection': URLFor('author_list'),
-        })
-    `URLFor` objects can be nested within the dictionary. ::
-        _links = Hyperlinks({
-            'self': {
-                'href': URLFor('book', id='<id>'),
-                'title': 'book detail'
-            }
-        })
-    :param dict schema: A dict that maps names to
-        :class:`~fields.URLFor` fields.
-    """
-
-    _CHECK_ATTRIBUTE = False
-
-    def __init__(self, schema, **kwargs):
-        self.schema = schema
-        Field.__init__(self, **kwargs)
-
-    def _serialize(self, value, attr, obj):
-        return _rapply(self.schema, _url_val, key=attr, obj=obj)
+from openflexure_microscope.common.labthings_core.fields import *

openflexure_microscope/common/flask_labthings/labthing.py

@@ -3,14 +3,13 @@ from apispec import APISpec
 from apispec.ext.marshmallow import MarshmallowPlugin
 
 from .extensions import BaseExtension
-from .views.extensions import ExtensionListResource
-from .views.tasks import TaskList, TaskResource
-
-from .spec import view2path
-
 from .utilities import description_from_view
 
+from .views.extensions import ExtensionList
+from .views.tasks import TaskList, TaskResource
+
 from openflexure_microscope.common.labthings_core.utilities import get_docstring
+from openflexure_microscope.common.labthings_core.spec import view2path
 
 from . import EXTENSION_NAME
 
@@ -114,8 +113,8 @@ class LabThing(object):
         )
 
         # Add extension overview
-        self.add_resource(ExtensionListResource, "/extensions")
-        self.register_property(ExtensionListResource)
+        self.add_resource(ExtensionList, "/extensions")
+        self.register_property(ExtensionList)
         # Add task routes
         self.add_resource(TaskList, "/tasks")
         self.register_property(TaskList)
@@ -320,8 +319,8 @@ class LabThing(object):
                     "methods": ["GET"],
                 },
                 "extensions": {
-                    "href": self.url_for(ExtensionListResource, _external=True),
-                    **description_from_view(ExtensionListResource),
+                    "href": self.url_for(ExtensionList, _external=True),
+                    **description_from_view(ExtensionList),
                 },
                 "tasks": {
                     "href": self.url_for(TaskList, _external=True),

openflexure_microscope/common/flask_labthings/resource.py

@@ -1,23 +1,12 @@
 from flask.views import MethodView
+from openflexure_microscope.common.labthings_core.resource import BaseResource
 
 
-class Resource(MethodView):
+class Resource(MethodView, BaseResource):
     """Currently identical to MethodView
     """
 
     endpoint = None
-    methods = ["get", "post", "put", "delete"]
 
     def __init__(self, *args, **kwargs):
         MethodView.__init__(self, *args, **kwargs)
-
-    def doc(self):
-        docs = {"operations": {}}
-        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] = {}
-                docs["operations"][meth] = getattr(self, meth).__apispec__
-        return docs

openflexure_microscope/common/flask_labthings/schema.py

@@ -1,39 +1 @@
-# -*- coding: utf-8 -*-
-import flask
-import marshmallow
-
-MARSHMALLOW_VERSION_INFO = tuple(
-    [int(part) for part in marshmallow.__version__.split(".") if part.isdigit()]
-)
-
-sentinel = object()
-
-
-class Schema(marshmallow.Schema):
-    """Base serializer with which to define custom serializers.
-    See `marshmallow.Schema` for more details about the `Schema` API.
-    """
-
-    def jsonify(self, obj, many=sentinel, *args, **kwargs):
-        """Return a JSON response containing the serialized data.
-        :param obj: Object to serialize.
-        :param bool many: Whether `obj` should be serialized as an instance
-            or as a collection. If unset, defaults to the value of the
-            `many` attribute on this Schema.
-        :param kwargs: Additional keyword arguments passed to `flask.jsonify`.
-        .. versionchanged:: 0.6.0
-            Takes the same arguments as `marshmallow.Schema.dump`. Additional
-            keyword arguments are passed to `flask.jsonify`.
-        .. versionchanged:: 0.6.3
-            The `many` argument for this method defaults to the value of
-            the `many` attribute on the Schema. Previously, the `many`
-            argument of this method defaulted to False, regardless of the
-            value of `Schema.many`.
-        """
-        if many is sentinel:
-            many = self.many
-        if MARSHMALLOW_VERSION_INFO[0] >= 3:
-            data = self.dump(obj, many=many)
-        else:
-            data = self.dump(obj, many=many).data
-        return flask.jsonify(data, *args, **kwargs)
+from openflexure_microscope.common.labthings_core.schema import *

openflexure_microscope/common/flask_labthings/utilities.py

@@ -2,10 +2,6 @@ from openflexure_microscope.common.labthings_core.utilities import (
     get_docstring,
     get_summary,
 )
-from .schema import Schema, marshmallow, MARSHMALLOW_VERSION_INFO
-import collections.abc
-
-import logging
 
 
 def description_from_view(view_class):
@@ -18,14 +14,3 @@ def description_from_view(view_class):
     d = {"methods": methods, "description": summary}
 
     return d
-
-
-def rupdate(d, u):
-    for k, v in u.items():
-        if isinstance(v, collections.abc.Mapping):
-            if not k in d:
-                d[k] = {}
-            d[k] = rupdate(d.get(k, {}), v)
-        else:
-            d[k] = v
-    return d

openflexure_microscope/common/flask_labthings/views/extensions.py

@@ -3,13 +3,15 @@ Top-level representation of attached and enabled Extensions
 """
 
 from openflexure_microscope.common.labthings_core.utilities import get_docstring
+from openflexure_microscope.common.labthings_core.schema import Schema
+from openflexure_microscope.common.labthings_core import fields
+
 from ..utilities import description_from_view
 
-from openflexure_microscope.common.flask_labthings.resource import Resource
-from openflexure_microscope.common.flask_labthings.find import registered_extensions
-from openflexure_microscope.common.flask_labthings.schema import Schema
-from openflexure_microscope.common.flask_labthings.decorators import marshal_with
-from openflexure_microscope.common.flask_labthings import fields
+from ..resource import Resource
+from ..find import registered_extensions
+
+from ..decorators import marshal_with
 from marshmallow import pre_dump
 
 from flask import jsonify, url_for
@@ -48,7 +50,7 @@ class ExtensionSchema(Schema):
         return data
 
 
-class ExtensionListResource(Resource):
+class ExtensionList(Resource):
     """
     List and basic documentation for all enabled Extensions
     """

openflexure_microscope/common/flask_labthings/views/tasks.py

@@ -1,14 +1,15 @@
 from flask import abort, url_for
 
-from openflexure_microscope.common.flask_labthings.schema import Schema
 from openflexure_microscope.common.flask_labthings.decorators import marshal_with
-from openflexure_microscope.common.flask_labthings import fields
-from openflexure_microscope.common.labthings_core import tasks
 from openflexure_microscope.common.flask_labthings.resource import Resource
 from openflexure_microscope.common.flask_labthings.utilities import (
     description_from_view,
 )
 
+from openflexure_microscope.common.labthings_core import tasks
+from openflexure_microscope.common.labthings_core.schema import Schema
+from openflexure_microscope.common.labthings_core import fields
+
 from marshmallow import pre_dump
 
 

openflexure_microscope/common/labthings_core/decorators.py

@@ -0,0 +1,26 @@
+from .spec import update_spec
+from .utilities import rupdate
+
+
+class doc(object):
+    def __init__(self, **kwargs):
+        self.kwargs = kwargs
+
+    def __call__(self, f):
+        # Pass params to call function attribute for external access
+        update_spec(f, self.kwargs)
+        return f
+
+
+class doc_response(object):
+    def __init__(self, code, description, **kwargs):
+        self.code = code
+        self.description = description
+        self.kwargs = kwargs
+
+    def __call__(self, f):
+        # Pass params to call function attribute for external access
+        f.__apispec__ = f.__dict__.get("__apispec__", {})
+        d = {"responses": {self.code: {"description": self.description, **self.kwargs}}}
+        rupdate(f.__apispec__, d)
+        return f

openflexure_microscope/common/labthings_core/fields.py

@@ -0,0 +1 @@
+from marshmallow.fields import *

openflexure_microscope/common/labthings_core/resource.py

@@ -0,0 +1,20 @@
+class BaseResource:
+    """
+    A LabThing Resource class should, regardless of the underlying framework, make use of
+    functions get(), put(), post(), and delete() corresponding to HTTP methods.
+
+    These functions will allow for automated documentation generation
+    """
+
+    methods = ["get", "post", "put", "delete"]
+
+    def doc(self):
+        docs = {"operations": {}}
+        if hasattr(self, "__apispec__"):
+            docs.update(self.__apispec__)
+
+        for meth in BaseResource.methods:
+            if hasattr(self, meth) and hasattr(getattr(self, meth), "__apispec__"):
+                docs["operations"][meth] = {}
+                docs["operations"][meth] = getattr(self, meth).__apispec__
+        return docs

openflexure_microscope/common/labthings_core/schema.py

@@ -0,0 +1,39 @@
+# -*- coding: utf-8 -*-
+import flask
+import marshmallow
+
+MARSHMALLOW_VERSION_INFO = tuple(
+    [int(part) for part in marshmallow.__version__.split(".") if part.isdigit()]
+)
+
+sentinel = object()
+
+
+class Schema(marshmallow.Schema):
+    """Base serializer with which to define custom serializers.
+    See `marshmallow.Schema` for more details about the `Schema` API.
+    """
+
+    def jsonify(self, obj, many=sentinel, *args, **kwargs):
+        """Return a JSON response containing the serialized data.
+        :param obj: Object to serialize.
+        :param bool many: Whether `obj` should be serialized as an instance
+            or as a collection. If unset, defaults to the value of the
+            `many` attribute on this Schema.
+        :param kwargs: Additional keyword arguments passed to `flask.jsonify`.
+        .. versionchanged:: 0.6.0
+            Takes the same arguments as `marshmallow.Schema.dump`. Additional
+            keyword arguments are passed to `flask.jsonify`.
+        .. versionchanged:: 0.6.3
+            The `many` argument for this method defaults to the value of
+            the `many` attribute on the Schema. Previously, the `many`
+            argument of this method defaulted to False, regardless of the
+            value of `Schema.many`.
+        """
+        if many is sentinel:
+            many = self.many
+        if MARSHMALLOW_VERSION_INFO[0] >= 3:
+            data = self.dump(obj, many=many)
+        else:
+            data = self.dump(obj, many=many).data
+        return flask.jsonify(data, *args, **kwargs)

openflexure_microscope/common/labthings_core/spec.py

@@ -1,4 +1,4 @@
-from .resource import Resource
+from .resource import BaseResource
 from .utilities import rupdate
 from apispec import APISpec
 from apispec.ext.marshmallow import MarshmallowPlugin
@@ -20,7 +20,7 @@ def update_spec(obj, spec):
     return obj.__apispec__
 
 
-def view2path(rule: str, view: Resource, spec: APISpec):
+def view2path(rule: str, view: BaseResource, spec: APISpec):
     params = {
         "path": rule,  # TODO: Validate this slightly (leading / etc)
         "operations": view2operations(view, spec),
@@ -35,9 +35,9 @@ def view2path(rule: str, view: Resource, spec: APISpec):
     return params
 
 
-def view2operations(view: Resource, spec: APISpec, populate_default: bool = True):
+def view2operations(view: BaseResource, spec: APISpec, populate_default: bool = True):
     ops = {}
-    for method in Resource.methods:
+    for method in BaseResource.methods:
         if hasattr(view, method):
             # Populate with default responses
             if populate_default:

openflexure_microscope/common/labthings_core/utilities.py

@@ -1,3 +1,10 @@
+import collections.abc
+import re
+import base64
+import operator
+from functools import reduce
+
+
 def get_docstring(obj):
     ds = obj.__doc__
     if ds:
@@ -8,3 +15,49 @@ def get_docstring(obj):
 
 def get_summary(obj):
     return get_docstring(obj).partition("\n")[0].strip()
+
+
+def rupdate(d, u):
+    for k, v in u.items():
+        if isinstance(v, collections.abc.Mapping):
+            if not k in d:
+                d[k] = {}
+            d[k] = rupdate(d.get(k, {}), v)
+        else:
+            d[k] = v
+    return d
+
+
+def get_by_path(root, items):
+    """Access a nested object in root by item sequence."""
+    return reduce(operator.getitem, items, root)
+
+
+def set_by_path(root, items, value):
+    """Set a value in a nested object in root by item sequence."""
+    get_by_path(root, items[:-1])[items[-1]] = value
+
+
+def create_from_path(items):
+    tree_dict = {}
+    for key in reversed(items):
+        tree_dict = {key: tree_dict}
+    return tree_dict
+
+
+def bottom_level_name(obj):
+    return obj.__name__.split(".")[-1]
+
+
+def camel_to_snake(name):
+    s1 = re.sub("(.)([A-Z][a-z]+)", r"\1_\2", name)
+    return re.sub("([a-z0-9])([A-Z])", r"\1_\2", s1).lower()
+
+
+def camel_to_spine(name):
+    s1 = re.sub("(.)([A-Z][a-z]+)", r"\1-\2", name)
+    return re.sub("([a-z0-9])([A-Z])", r"\1-\2", s1).lower()
+
+
+def snake_to_spine(name):
+    return name.replace("_", "-")

openflexure_microscope/microscope.py

@@ -12,9 +12,10 @@ from openflexure_microscope.camera.base import BaseCamera
 from openflexure_microscope.camera.mock import MockStreamer
 
 from openflexure_microscope.utilities import serialise_array_b64
-from openflexure_microscope.common.labthings_core.lock import CompositeLock
 from openflexure_microscope.config import user_settings
 
+from openflexure_microscope.common.labthings_core.lock import CompositeLock
+
 
 class Microscope:
     """

openflexure_microscope/utilities.py

@@ -20,41 +20,6 @@ def serialise_array_b64(npy_arr):
     return b64_string, dtype, shape
 
 
-def get_by_path(root, items):
-    """Access a nested object in root by item sequence."""
-    return reduce(operator.getitem, items, root)
-
-
-def set_by_path(root, items, value):
-    """Set a value in a nested object in root by item sequence."""
-    get_by_path(root, items[:-1])[items[-1]] = value
-
-
-def create_from_path(items):
-    tree_dict = {}
-    for key in reversed(items):
-        tree_dict = {key: tree_dict}
-    return tree_dict
-
-
-def bottom_level_name(obj):
-    return obj.__name__.split(".")[-1]
-
-
-def camel_to_snake(name):
-    s1 = re.sub("(.)([A-Z][a-z]+)", r"\1_\2", name)
-    return re.sub("([a-z0-9])([A-Z])", r"\1_\2", s1).lower()
-
-
-def camel_to_spine(name):
-    s1 = re.sub("(.)([A-Z][a-z]+)", r"\1-\2", name)
-    return re.sub("([a-z0-9])([A-Z])", r"\1-\2", s1).lower()
-
-
-def snake_to_spine(name):
-    return name.replace("_", "-")
-
-
 @contextmanager
 def set_properties(obj, **kwargs):
     """A context manager to set, then reset, certain properties of an object.