dnastack-client-library 3.1.179__py3-none-any.whl → 3.1.205__py3-none-any.whl

dnastack/common/parser.py

@@ -27,7 +27,7 @@ class DotPropertiesParser:
         self.allow_value_overriding = allow_value_overriding
 
     def parse(self, content: str) -> Dict[str, Any]:
-        data: Dict[str, Any] = dict()
+        data: Dict[str, Any] = {}
 
         for line in re.split(r'\r\n|\r|\n', content):
             truncated_line = line.strip()
@@ -99,11 +99,11 @@ class DotPropertiesParser:
                                                                    '.'.join([path[i] for i in range(depth + 1)]))
 
                     if is_array:
-                        node[p_name_without_array] = list()
+                        node[p_name_without_array] = []
                         node = node[p_name_without_array]
                     else:
                         if p_name not in node:
-                            node[p_name] = dict()
+                            node[p_name] = {}
                         node = node[p_name]
 
             self.__logger.debug(f'PARSED: {path} = {value}')

dnastack/common/simple_stream.py

@@ -38,7 +38,7 @@ class SimpleStream:
         return [item for item in self._run()]
 
     def to_map(self, key_mapper: Callable[[X], Y], value_mapper: Callable[[X], Z]) -> Dict[Y, Z]:
-        result: Dict[Y, Z] = dict()
+        result: Dict[Y, Z] = {}
 
         for item in self._run():
             result[key_mapper(item)] = value_mapper(item)

dnastack/configuration/manager.py

@@ -51,10 +51,14 @@ class ConfigurationManager:
         """ Load the configuration object """
         self.__logger.debug(f'Reading the configuration from {self.__file_path}...')
         raw_config = self.load_raw()
-        if not raw_config:
+        if not raw_config or raw_config.strip() in ('', '{}'):
             return Configuration()
         try:
-            config = Configuration(**yaml.load(raw_config, Loader=yaml.SafeLoader))
+            parsed_config = yaml.load(raw_config, Loader=yaml.SafeLoader)
+            # Handle empty or None yaml results
+            if not parsed_config or parsed_config == {}:
+                return Configuration()
+            config = Configuration(**parsed_config)
             return self.migrate(config)
         except ValidationError as e:
             raise InvalidExistingConfigurationError(f'The existing configuration file at {self.__file_path} is invalid.') from e
@@ -69,7 +73,7 @@ class ConfigurationManager:
 
         # Perform sanity checks
         for context_name, context in configuration.contexts.items():
-            duplicate_endpoint_id_count_map = dict()
+            duplicate_endpoint_id_count_map = {}
             for endpoint in context.endpoints:
                 if endpoint.id not in duplicate_endpoint_id_count_map:
                     duplicate_endpoint_id_count_map[endpoint.id] = 0
@@ -80,7 +84,7 @@ class ConfigurationManager:
                 f'in the "{context_name}" context'
 
         # Save the changes.
-        new_content = yaml.dump(configuration.dict(exclude_none=True), Dumper=yaml.SafeDumper)
+        new_content = yaml.dump(configuration.model_dump(exclude_none=True), Dumper=yaml.SafeDumper)
         if not os.path.exists(os.path.dirname(self.__swap_file_path)):
             os.makedirs(os.path.dirname(self.__swap_file_path), exist_ok=True)
         with open(self.__swap_file_path, 'w') as f:

dnastack/configuration/models.py

@@ -29,5 +29,5 @@ class Configuration(BaseModel):
     ###############################################################
     # Version 3 (for object migration and backward compatibility) #
     ###############################################################
-    defaults: Optional[Dict[str, str]]
-    endpoints: Optional[List[Endpoint]]
+    defaults: Optional[Dict[str, str]] = None
+    endpoints: Optional[List[Endpoint]] = None

dnastack/constants.py

@@ -1,5 +1,5 @@
 import os
 
-__version__ = "v3.1.179"
+__version__ = "3.1.205"
 
 LOCAL_STORAGE_DIRECTORY = os.path.join(os.path.expanduser("~"), '.dnastack')

dnastack/context/manager.py

@@ -81,7 +81,7 @@ class InMemoryContextMap(ContextMap):
         self._current_context_name: Optional[str] = None
 
         # Internal context maps
-        self._reference_contexts: Dict[str, Context] = reference_contexts or dict()
+        self._reference_contexts: Dict[str, Context] = reference_contexts or {}
 
     def all(self) -> Dict[str, Context]:
         return self._reference_contexts
@@ -327,7 +327,7 @@ class BaseContextManager:
         # Initiate the authentication procedure.
         if no_auth:
             self._logger.debug('AUTH disabled')
-            self.events.dispatch('auth-disabled', dict())
+            self.events.dispatch('auth-disabled', {})
         else:
             self._logger.debug('AUTH enabled')
             auth_manager = AuthManager(context=self._contexts.current_context)

dnastack/context/models.py

@@ -13,9 +13,9 @@ class Context(BaseModel):
     guid:  str = Field(default_factory=lambda: str(uuid4()))
 
     # This is the short-type-to-service-id map.
-    defaults: Dict[str, str] = Field(default_factory=lambda: dict())
+    defaults: Dict[str, str] = Field(default_factory=lambda: {})
 
-    endpoints: List[Endpoint] = Field(default_factory=lambda: list())
+    endpoints: List[Endpoint] = Field(default_factory=lambda: [])
     
     # Store subject token for token exchange authentication if provided
     platform_subject_token: Optional[str] = Field(default=None)

dnastack/feature_flags.py

@@ -3,8 +3,8 @@ from typing import Callable, List, Dict
 
 from dnastack.common.environments import flag
 
-__FLAG_CACHE_MAP: Dict[str, bool] = dict()
-__DEBUG_MODE_HOOKS: List[Callable[[bool], None]] = list()
+__FLAG_CACHE_MAP: Dict[str, bool] = {}
+__DEBUG_MODE_HOOKS: List[Callable[[bool], None]] = []
 
 
 def currently_in_debug_mode():

dnastack/http/authenticators/abstract.py

@@ -39,7 +39,7 @@ class RefreshRequired(RuntimeError):
 
     def __init__(self, session: Optional[SessionInfo]):
         super().__init__('Session refresh required')
-        self.__session = session.copy(deep=True)
+        self.__session = session.model_copy(deep=True)
 
     @property
     def session(self):
@@ -141,7 +141,7 @@ class Authenticator(AuthBase, ABC):
 
     def initialize(self, trace_context: Span) -> SessionInfo:
         """ Initialize the authenticator """
-        self.events.dispatch('initialization-before', dict(origin=f'{self.class_name}'))
+        self.events.dispatch('initialization-before', {'origin': f'{self.class_name}'})
         logger = trace_context.create_span_logger(self._logger)
         try:
             logger.debug('initialize: Restoring the session...')

dnastack/http/authenticators/factory.py

@@ -37,13 +37,13 @@ class HttpAuthenticatorFactory:
 
             # NOTE: Should raise a custom exception if it fails the model validation.
 
-            return config.dict()
+            return config.model_dump()
         else:
             raise UnsupportedAuthenticationInformationError(auth_info)
 
     @staticmethod
     def get_unique_auth_info_list(endpoints: List[ServiceEndpoint]) -> List[Dict[str, Any]]:
-        unique_auth_info_map: Dict[str, Dict[str, Any]] = dict()
+        unique_auth_info_map: Dict[str, Dict[str, Any]] = {}
 
         for endpoint in endpoints:
             for auth_info in endpoint.get_authentications():

dnastack/http/authenticators/oauth2.py

@@ -55,7 +55,7 @@ class OAuth2Authenticator(Authenticator):
         self._session_info: Optional[SessionInfo] = None
 
     def _get_logger_name(self):
-        metadata = dict()
+        metadata = {}
 
         if self._auth_info:
             auth_info = OAuth2Authentication(**self._auth_info)
@@ -81,14 +81,14 @@ class OAuth2Authenticator(Authenticator):
 
     def get_state(self) -> AuthState:
         status = AuthStateStatus.READY
-        session_info: Dict[str, Any] = dict()
+        session_info: Dict[str, Any] = {}
 
         try:
             session = self.restore_session()
-            session_info.update(session.dict())
+            session_info.update(session.model_dump())
         except RefreshRequired as e:
             status = AuthStateStatus.REFRESH_REQUIRED
-            session_info.update(e.session.dict())
+            session_info.update(e.session.model_dump())
         except AuthenticationRequired:
             status = AuthStateStatus.UNINITIALIZED
         except (ReauthenticationRequiredDueToConfigChange, ReauthenticationRequired):
@@ -137,7 +137,7 @@ class OAuth2Authenticator(Authenticator):
             self.events.relay_from(adapter.events, auth_event_type)
 
         raw_response = adapter.exchange_tokens(trace_context)
-        self._session_info = self._convert_token_response_to_session(auth_info.dict(), raw_response)
+        self._session_info = self._convert_token_response_to_session(auth_info.model_dump(), raw_response)
         self._session_manager.save(session_id, self._session_info)
 
         event_details['session_info'] = self._session_info
@@ -227,7 +227,7 @@ class OAuth2Authenticator(Authenticator):
                 refresh_token_json['refresh_token'] = refresh_token
 
                 # Update the session
-                updated_session_info = self._convert_token_response_to_session(auth_info.dict(), refresh_token_json)
+                updated_session_info = self._convert_token_response_to_session(auth_info.model_dump(), refresh_token_json)
                 session_info.access_token = updated_session_info.access_token
                 session_info.token_type = updated_session_info.token_type
                 session_info.valid_until = updated_session_info.valid_until
@@ -280,7 +280,7 @@ class OAuth2Authenticator(Authenticator):
 
                 if currently_in_debug_mode():
                     exception_details['_internal'] = {
-                        'session_info': session_info.dict(),
+                        'session_info': session_info.model_dump(),
                         'session_manager': str(self._session_manager),
                     }
 
@@ -420,7 +420,7 @@ class OAuth2Authenticator(Authenticator):
             self.events.relay_from(adapter.events, auth_event_type)
 
         token_response = adapter.exchange_tokens(trace_context)
-        self._session_info = self._convert_token_response_to_session(auth_info.dict(), token_response)
+        self._session_info = self._convert_token_response_to_session(auth_info.model_dump(), token_response)
         self._session_manager.save(session_id, self._session_info)
 
         event_details['session_info'] = self._session_info

dnastack/http/authenticators/oauth2_adapter/client_credential.py

@@ -31,22 +31,13 @@ class ClientCredentialAdapter(OAuth2Adapter):
         auth_info = self._auth_info
         resource_urls = self._prepare_resource_urls_for_request(auth_info.resource_url)
 
-        trace_info = dict(
-            oauth='client-credentials',
-            token_url=auth_info.token_endpoint,
-            client_id=auth_info.client_id,
-            grant_type=self.__grant_type,
-            resource_urls=resource_urls,
-            scope=auth_info.scope,
-        )
+        trace_info = {'oauth': 'client-credentials', 'token_url': auth_info.token_endpoint,
+                      'client_id': auth_info.client_id, 'grant_type': self.__grant_type, 'resource_urls': resource_urls,
+                      'scope': auth_info.scope}
         logger.debug(f'exchange_token: Authenticating with {trace_info}')
 
-        auth_params = dict(
-            client_id=auth_info.client_id,
-            client_secret=auth_info.client_secret,
-            grant_type=self.__grant_type,
-            resource=resource_urls,
-        )
+        auth_params = {'client_id': auth_info.client_id, 'client_secret': auth_info.client_secret,
+                       'grant_type': self.__grant_type, 'resource': resource_urls}
 
         if auth_info.scope:
             auth_params['scope'] = auth_info.scope

dnastack/http/authenticators/oauth2_adapter/models.py

@@ -10,21 +10,21 @@ GRANT_TYPE_TOKEN_EXCHANGE = 'urn:ietf:params:oauth:grant-type:token-exchange'
 
 class OAuth2Authentication(BaseModel, HashableModel):
     """OAuth2 Authentication Information"""
-    authorization_endpoint: Optional[str]
-    client_id: Optional[str]
-    client_secret: Optional[str]
-    device_code_endpoint: Optional[str]
+    authorization_endpoint: Optional[str] = None
+    client_id: Optional[str] = None
+    client_secret: Optional[str] = None
+    device_code_endpoint: Optional[str] = None
     grant_type: str
-    personal_access_endpoint: Optional[str]
-    personal_access_email: Optional[str]
-    personal_access_token: Optional[str]
-    redirect_url: Optional[str]
+    personal_access_endpoint: Optional[str] = None
+    personal_access_email: Optional[str] = None
+    personal_access_token: Optional[str] = None
+    redirect_url: Optional[str] = None
     resource_url: str
-    scope: Optional[str]
-    token_endpoint: Optional[str]
+    scope: Optional[str] = None
+    token_endpoint: Optional[str] = None
     type: str = 'oauth2'
-    subject_token: Optional[str]
-    subject_token_type: Optional[str]
-    requested_token_type: Optional[str]
-    audience: Optional[str]
-    cloud_provider: Optional[str]  # Currently supported: 'gcp'
+    subject_token: Optional[str] = None
+    subject_token_type: Optional[str] = None
+    requested_token_type: Optional[str] = None
+    audience: Optional[str] = None
+    cloud_provider: Optional[str] = None  # Currently supported: 'gcp'

dnastack/http/session.py

@@ -164,7 +164,7 @@ class HttpSession(AbstractContextManager):
                **kwargs) -> Response | None | Any:
         trace_context = trace_context or Span(origin=self)
 
-        retry_history = retry_history or list()
+        retry_history = retry_history or []
         session = self._session
 
         logger = trace_context.create_span_logger(self.__logger)
@@ -211,7 +211,7 @@ class HttpSession(AbstractContextManager):
 
             sub_logger.debug(f'Request/{http_method.upper()} {url}')
 
-            existing_headers = kwargs.get('headers') or dict()
+            existing_headers = kwargs.get('headers') or {}
             existing_headers.update(sub_span.create_http_headers())
             kwargs['headers'] = existing_headers
 
@@ -369,7 +369,7 @@ class HttpSession(AbstractContextManager):
         final_comments = [
             f'Platform/{platform.platform()}',  # OS information + CPU architecture
             'Python/{}.{}.{}'.format(*sys.version_info),  # Python version
-            *(comments or list()),
+            *(comments or []),
             *[
                 f'Module/{interested_module_name}'
                 for interested_module_name in interested_module_names

dnastack/http/session_info.py

@@ -111,7 +111,7 @@ class InMemorySessionStorage(BaseSessionStorage):
 
     def __init__(self):
         self.__logger = get_logger(type(self).__name__)
-        self.__cache_map: Dict[str, SessionInfo] = dict()
+        self.__cache_map: Dict[str, SessionInfo] = {}
 
     def __contains__(self, id: str) -> bool:
         return id in self.__cache_map
@@ -164,7 +164,7 @@ class FileSessionStorage(BaseSessionStorage):
         final_file_path = self.__get_file_path(id)
         temp_file_path = f'{final_file_path}.{time()}.swap'
 
-        content: str = session.json(indent=2)
+        content: str = session.model_dump_json(indent=2)
 
         os.makedirs(os.path.dirname(final_file_path), exist_ok=True)
         with open(temp_file_path, 'w') as f:
@@ -210,7 +210,7 @@ class SessionManager:
                  static_session_file: Optional[str] = None):
         self.__logger = get_logger(type(self).__name__)
         self.__storage = storage
-        self.__change_locks: Dict[str, Lock] = dict()
+        self.__change_locks: Dict[str, Lock] = {}
         self.__static_session: Optional[SessionInfo] = None
 
         self.__logger.debug('Session Storage: %s', self.__storage)

{dnastack_client_library-3.1.179.dist-info → dnastack_client_library-3.1.205.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dnastack-client-library
-Version: 3.1.179
+Version: 3.1.205
 Summary: DNAstack's GA4GH library and CLI
 Author-email: DNAstack <devs@dnastack.com>
 License: Apache License, Version 2.0
@@ -18,7 +18,7 @@ Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: click<8.2,>=8.0.3
-Requires-Dist: pydantic<2,>=1.9.0
+Requires-Dist: pydantic>=2.0
 Requires-Dist: pyjwt<3,>=2.1.0
 Requires-Dist: pyyaml>=5.4.1
 Requires-Dist: requests<3,>=2.23.0