From 1c37eb20c85d45ccf7acb08462bc4a1d0d27bc25 Mon Sep 17 00:00:00 2001
From: BUI Van Tuan <buivantuan07@gmail.com>
Date: Fri, 8 Dec 2023 14:10:37 +0100
Subject: [PATCH] fix flake8
---
dnadna/utils/config.py | 44 ++++++++++++++----------------
dnadna/utils/jsonschema.py | 44 +++++++++++++-----------------
dnadna/utils/jsonschema_pyref.py | 4 +--
dnadna/utils/torch_plugin_mixin.py | 3 +-
4 files changed, 44 insertions(+), 51 deletions(-)
diff --git a/dnadna/utils/config.py b/dnadna/utils/config.py
index 6c8524cb..25a649b5 100644
--- a/dnadna/utils/config.py
+++ b/dnadna/utils/config.py
@@ -16,7 +16,8 @@ from referencing import Resource
from .. import DEFAULTS_DIR
from .decorators import cached_classproperty, lru_cache_with_dict
-from .jsonschema import make_config_validator, normpath, SCHEMA_DIRS, CustomValidationError, REGISTRY
+from .jsonschema import make_config_validator, normpath, SCHEMA_DIRS, \
+ CustomValidationError, REGISTRY
from .serializers import DictSerializer, JSONSerializer, YAMLSerializer
from .yaml import CommentedMapping, CommentedYAMLDumper
@@ -179,7 +180,7 @@ def save_dict_annotated(obj, filename, schema=None, validate=False,
resource = Resource.from_contents(parent_schema, DRAFT7)
# Resolver with a specific root resource in case '$ref' is relative
schema = validator.registry.resolver_with_root(resource).lookup(ref).contents
-
+
if not ref.startswith('#'):
return get_comment(schema, schema)
else:
@@ -215,7 +216,7 @@ def save_dict_annotated(obj, filename, schema=None, validate=False,
resource = Resource.from_contents(parent_schema, DRAFT7)
# Resolver with a specific root resource in case '$ref' is relative
schema = validator.registry.resolver_with_root(resource).lookup(ref).contents
-
+
if not ref.startswith('#'):
get_comments_recursive(schema, schema)
else:
@@ -1487,8 +1488,8 @@ def _get_config_key_path(config, key):
class ConfigValidator():
"""
- A custom validator wrapping `jsonschema.Draft7Validator` class which supports special validation
- functionality for DNADNA `Config` objects::
+ A custom validator wrapping `jsonschema.Draft7Validator` class which
+ supports special validation functionality for DNADNA `Config` objects::
* Recognizes `Config` objects as JSON ``object`` s.
@@ -1546,7 +1547,7 @@ class ConfigValidator():
Config({'abspath': '/bar/baz/qux', 'relpath': '/foo/bar/fred',
'nonpath': 'barney', 'has_default_2': 'c', 'has_default_1': 'a'})
"""
-
+
def __init__(self, schema, *args, resolve_plugins=True,
resolve_defaults=True, resolve_filenames=True,
posixify_filenames=False, **kwargs):
@@ -1554,23 +1555,22 @@ class ConfigValidator():
self._resolve_defaults = resolve_defaults
self._resolve_filenames = resolve_filenames
self._posixify_filenames = posixify_filenames
-
+
# Creates a new `jsonschema.Draft7Validator` class fully overriding the built in of the
# `jsonschema.Draft7Validator` by default
- validator = make_config_validator(get_path=_get_config_key_path,
+ validator = make_config_validator(get_path=_get_config_key_path,
resolve_plugins=self._resolve_plugins,
resolve_defaults=self._resolve_defaults,
resolve_filenames=self._resolve_filenames,
posixify_filenames=self._posixify_filenames)
-
- self.validator = validator(schema, registry=REGISTRY, format_checker=validator.FORMAT_CHECKER)
+
+ self.validator = validator(schema, registry=REGISTRY,
+ format_checker=validator.FORMAT_CHECKER)
self.registry = REGISTRY
-
-
+
def iter_errors(self, config, *args, **kwargs):
return self.validator.iter_errors(config, *args, **kwargs)
-
-
+
@staticmethod
def relevance_with_const_select(error):
"""
@@ -1735,17 +1735,16 @@ class ConfigValidator():
return (True,) + rank
else:
return (False,) + rank
-
-
+
def best_match(self, errors, key=relevance_with_const_select):
"""
Wraps the `jsonschema.exceptions.best_match` to return `CustomValidatonError`
See the `relevance_with_const_select` documentation above
"""
-
+
error = best_match(errors,
key=key)
-
+
if error is None:
return
else:
@@ -1757,8 +1756,7 @@ class ConfigValidator():
error = CustomValidationError.create_from(error)
error.message = errormsg
return error
-
-
+
def validate(self, config, *args, **kwargs):
"""
Validate the config against the schema and raise a `ConfigError` if
@@ -1875,10 +1873,10 @@ class ConfigValidator():
try:
error = best_match(self.iter_errors(config, *args, **kwargs),
key=self.relevance_with_const_select)
-
+
if error is None:
return
-
+
raise error
except jsonschema.ValidationError as exc:
# if the error came from a sub-schema in a one/all/anyOf then the
@@ -1892,7 +1890,7 @@ class ConfigValidator():
if errormsg is not None:
exc = CustomValidationError.create_from(exc)
exc.message = errormsg
-
+
path = ()
while parent is not None:
if len(parent.path) > len(path):
diff --git a/dnadna/utils/jsonschema.py b/dnadna/utils/jsonschema.py
index cc376608..40a6a206 100644
--- a/dnadna/utils/jsonschema.py
+++ b/dnadna/utils/jsonschema.py
@@ -127,7 +127,7 @@ def make_config_validator(validator_cls=jsonschema.Draft7Validator,
``validator_cls`` (`jsonschema.Draft7Validator` by default) which supports
special functionality for DNADNA `.Config` objects, though it can be adapted
to other types.
-
+
The new validator has additional options for controlling how to resolve
relative filenames in the schema and how to handle the ``default`` property
in schemas.
@@ -151,16 +151,16 @@ def make_config_validator(validator_cls=jsonschema.Draft7Validator,
# "between releases of jsonschema. Instead, prefer "
# "composition of validators, wrapping them in an object "
# "owned entirely by the downstream library."
-
- # From now on, the attributs 'resolves' are to be passed to ConfigValidaror class
+
+ # From now on, the attributs 'resolves' are to be passed to ConfigValidaror class
# that wraps the new Draft7Validator
def resolve_filename(instance, prop, subschema, get_path=None,
posixify=False):
errors = []
-
+
if subschema is True:
return []
-
+
# Handle format: filename
format_ = subschema.get('format')
if (subschema.get('type') == 'string' and
@@ -203,7 +203,7 @@ def make_config_validator(validator_cls=jsonschema.Draft7Validator,
err_occurred = False
orig_instance = copy.deepcopy(instance)
-
+
# If there are no errors then the instance matches this schema or
# sub-schema (in the case of a oneOf/allOf/anyOf); now we assign any
# defaults so that defaults are only added from a schema that this
@@ -215,19 +215,19 @@ def make_config_validator(validator_cls=jsonschema.Draft7Validator,
for prop, subschema in properties.items():
if subschema is True:
continue
-
+
# Fill missing props with their defaults
if (isinstance(instance, (dict, Mapping)) and
'default' in subschema and prop not in instance):
instance[prop] = subschema['default']
added_defaults = True
-
+
if added_defaults:
# We only need to re-validate if any defaults were actually
# assigned
errors = validate_properties(validator, properties, instance,
schema)
-
+
try:
for error in errors:
err_occurred = True
@@ -240,7 +240,6 @@ def make_config_validator(validator_cls=jsonschema.Draft7Validator,
if err_occurred:
instance.clear()
instance.update(orig_instance)
-
# Create the format checker; filename and filename! are already handled
# specially in validate_config_properties since it requires special support
@@ -254,18 +253,16 @@ def make_config_validator(validator_cls=jsonschema.Draft7Validator,
__import__(instance)
return True
-
+
# supports special functionality for DNADNA `.Config` objects
def is_config(checker, instance):
return (
isinstance(instance, (dict, Mapping))
)
- type_checker = validator_cls.TYPE_CHECKER.redefine(
- "object", is_config,
- )
-
+ type_checker = validator_cls.TYPE_CHECKER.redefine("object", is_config)
+
# Creates a new `jsonschema.Draft7Validator` class fully overriding the built in of the
- # ``validator_cls`` (`jsonschema.Draft7Validator` by default)
+ # ``validator_cls`` (`jsonschema.Draft7Validator` by default)
# This is to work around the issue in
# https://github.com/python-jsonschema/jsonschema/issues/1197
validator_cls = jsonschema.validators.create(
@@ -326,7 +323,7 @@ def _resolver_file_handler(uri):
Slightly hackish, but supported workaround to the larger issue discussed at
https://github.com/Julian/jsonschema/issues/420
"""
-
+
filename = url2pathname(urlparse(uri).path)
return DictSerializer.load(filename)
@@ -348,30 +345,27 @@ def _retrieve(uri: str):
"""
base_url = f'file:///{SCHEMA_DIRS[0].as_posix()}/'
-
+
scheme = urlparse(uri).scheme
if not scheme:
uri = base_url + uri
scheme = urlparse(uri).scheme
if scheme == 'file':
- try:
- contents = _resolver_file_handler(uri)
- except:
- contents = {}
+ contents = _resolver_file_handler(uri)
elif scheme == 'py-obj':
contents = _resolve_url_py_obj(uri)
else:
contents = {}
-
+
if not contents.get('$id'):
contents['$id'] = 'urn:unknown-dialect'
-
+
return Resource.from_contents(contents, DRAFT7)
# a specific immutable set of in-memory schemas to be available in addition to the dynamic schemas
REGISTRY = Registry(retrieve=_retrieve)
-# include all in-memory schemas in the directory SCHEMA_DIRS,
+# include all in-memory schemas in the directory SCHEMA_DIRS,
# making them available for use during validation.
for schema_dir in SCHEMA_DIRS:
for curdir, dirs, files in os.walk(schema_dir):
diff --git a/dnadna/utils/jsonschema_pyref.py b/dnadna/utils/jsonschema_pyref.py
index 88802399..38e5f9a8 100644
--- a/dnadna/utils/jsonschema_pyref.py
+++ b/dnadna/utils/jsonschema_pyref.py
@@ -10,8 +10,8 @@ try:
import yaml # type: ignore
except ImportError:
yaml = None
-
-
+
+
__all__ = ['urljoin', 'urlparse']
diff --git a/dnadna/utils/torch_plugin_mixin.py b/dnadna/utils/torch_plugin_mixin.py
index 9f441c95..94f7eb18 100644
--- a/dnadna/utils/torch_plugin_mixin.py
+++ b/dnadna/utils/torch_plugin_mixin.py
@@ -291,7 +291,8 @@ class TorchPluginMixin:
param_schema = {'type': 'array'}
# param_schema['items'] = [cls._schema_from_default(v, False)
# for v in value]
- # the items keyword to a single schema that will be used to validate all of the items in the array.
+ # the items keyword to a single schema that will be used to
+ # validate all of the items in the array.
param_schema['items'] = cls._schema_from_default(value[0], False)
value = list(value)
elif value is None:
--
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