dnastack-client-library 3.1.178__py3-none-any.whl → 3.1.204__py3-none-any.whl

dnastack/client/collections/client.py

@@ -58,7 +58,7 @@ class CollectionItemListResultLoader(ResultLoader):
         self.__max_results = int(max_results) if max_results else None
         self.__loaded_results = 0
         self.__active = True
-        self.__visited_urls: List[str] = list()
+        self.__visited_urls: List[str] = []
         self.__trace = trace
         self.__next_page_url = None
 
@@ -119,7 +119,7 @@ class CollectionItemListResultLoader(ResultLoader):
             response_text = response.text
 
             try:
-                response_body = response.json() if response_text else dict()
+                response_body = response.json() if response_text else {}
             except Exception:
                 self.logger.error(f'{self.__service_url}: Unexpectedly non-JSON response body from {current_url}')
                 raise PageableApiError(
@@ -208,7 +208,7 @@ class CollectionServiceClient(BaseServiceClient):
         trace = trace or Span(origin=self)
         with self.create_http_session() as session:
             res = session.post(urljoin(self.url, 'collections') + '?includeInternalItemsQuery=true',
-                               json=collection.dict(),
+                               json=collection.model_dump(),
                                trace_context=trace)
             return Collection(**res.json())
 
@@ -245,7 +245,7 @@ class CollectionServiceClient(BaseServiceClient):
         trace = trace or Span(origin=self)
         with self.create_http_session() as session:
             session.post(urljoin(self.url, f'collections/{collection_id_or_slug_name_or_db_schema_name}/items'),
-                         json=create_items_request.dict(), trace_context=trace)
+                         json=create_items_request.model_dump(), trace_context=trace)
             return None
 
     def delete_collection_items(self,

dnastack/client/collections/model.py

@@ -10,7 +10,7 @@ from dnastack.client.base_exceptions import ApiError
 
 
 class Tag(BaseModel):
-    id: Optional[str]
+    id: Optional[str] = None
     label: str
 
 
@@ -40,9 +40,9 @@ class Collection(BaseModel):
     slugName: str
     metadata: Optional[Dict[str, Any]] = Field(default_factory=dict)
     description: Optional[str] = None
-    itemsQuery: Optional[str]
+    itemsQuery: Optional[str] = None
     tags: Optional[List[Tag]] = Field(default_factory=list)
-    createdAt: Optional[datetime]
+    createdAt: Optional[datetime] = None
     updatedAt: Optional[datetime] = None
     dbSchemaName: Optional[str] = None
     itemsChangedAt: Optional[datetime] = None
@@ -69,53 +69,53 @@ class PageableApiError(ApiError):
 
 
 class Pagination(BaseModel):
-    nextPageUrl: Optional[str]
+    nextPageUrl: Optional[str] = None
 
 
 class PaginatedResource(BaseModel):
-    pagination: Optional[Pagination]
+    pagination: Optional[Pagination] = None
 
     def items(self) -> List[Any]:
         pass
 
 class CollectionItem(BaseModel):
     id: str
-    collectionId: Optional[str]
-    type: Optional[str]
-    name: Optional[str]
-    displayName: Optional[str]
-    dataSourceName: Optional[str]
-    dataSourceType: Optional[str]
-    cachedAt: Optional[str]
-    createdTime: Optional[str]
-    updatedTime: Optional[str]
-    itemUpdatedTime: Optional[str]
-    sourceKey: Optional[str]
-    metadataUrl: Optional[str]
-    dataSourceUrl: Optional[str]
-    sizeUnit: Optional[str]
-    size: Optional[int]
+    collectionId: Optional[str] = None
+    type: Optional[str] = None
+    name: Optional[str] = None
+    displayName: Optional[str] = None
+    dataSourceName: Optional[str] = None
+    dataSourceType: Optional[str] = None
+    cachedAt: Optional[str] = None
+    createdTime: Optional[str] = None
+    updatedTime: Optional[str] = None
+    itemUpdatedTime: Optional[str] = None
+    sourceKey: Optional[str] = None
+    metadataUrl: Optional[str] = None
+    dataSourceUrl: Optional[str] = None
+    sizeUnit: Optional[str] = None
+    size: Optional[int] = None
 
 
 class CollectionItemListResponse(BaseModel):
     items: List[CollectionItem]
-    pagination: Optional[Pagination]
+    pagination: Optional[Pagination] = None
 
 
 class CollectionItemListOptions(BaseModel):
-    type: Optional[str]
-    limit: Optional[int]
+    type: Optional[str] = None
+    limit: Optional[int] = None
 
 
 class CreateCollectionItemsRequest(BaseModel):
     dataSourceId: str
-    dataSourceType: Optional[str]
+    dataSourceType: Optional[str] = None
     sourceKeys: List[str]
 
 
 class DeleteCollectionItemRequest(BaseModel):
     dataSourceId: str
-    dataSourceType: Optional[str]
+    dataSourceType: Optional[str] = None
     sourceKey: str
 
 
@@ -127,11 +127,11 @@ class CollectionValidationStatus(str, Enum):
 
 
 class CollectionValidationMissingItems(BaseModel):
-    files: Optional[int]
-    tables: Optional[int]
+    files: Optional[int] = None
+    tables: Optional[int] = None
 
 
 class CollectionStatus(BaseModel):
     validationsStatus: CollectionValidationStatus
-    lastChecked: Optional[datetime]
-    missingItems: Optional[int]
+    lastChecked: Optional[datetime] = None
+    missingItems: Optional[int] = None

dnastack/client/data_connect.py

@@ -40,7 +40,7 @@ class DataConversionError(RuntimeError):
 
 class Error(BaseModel):
     """ Error representation """
-    status: Any
+    status: Any = None
     title: str
     details: Optional[str] = None
 
@@ -91,7 +91,7 @@ class PageableResultLoader(ResultLoader):
         self._initial_url = initial_url
         self._current_url: Optional[str] = None
         self._active = True
-        self._visited_urls: List[str] = list()
+        self._visited_urls: List[str] = []
 
     def _post_request(self, api_response: Union[ListTablesResponse, TableDataResponse]):
         if api_response.errors:
@@ -161,7 +161,7 @@ class TableListLoader(PageableResultLoader):
             response_text = response.text
 
             try:
-                response_body = response.json() if response_text else dict()
+                response_body = response.json() if response_text else {}
             except Exception:
                 self.logger.error(f'{self._initial_url}: Unexpectedly non-JSON response body from {current_url}')
                 raise DataConnectError(
@@ -425,7 +425,7 @@ class QueryLoader(PageableResultLoader):
         super(QueryLoader, self).__init__(initial_url=initial_url, http_session=http_session)
 
         self.__query = query
-        self.__schema: Dict[str, Any] = dict()
+        self.__schema: Dict[str, Any] = {}
         self.__trace = trace
 
     def load(self) -> List[Dict[str, Any]]:
@@ -456,11 +456,7 @@ class QueryLoader(PageableResultLoader):
                     self._visited_urls.append(self._current_url)
             except ClientError as e:
                 status_code = e.response.status_code
-                common_error_properties = dict(
-                    visited_urls=self._visited_urls,
-                    response=e.response,
-                    trace=e.trace,
-                )
+                common_error_properties = {'visited_urls': self._visited_urls, 'response': e.response, 'trace': e.trace}
                 if status_code == 400:
                     if not self._current_url:
                         if self.__query:

dnastack/client/datasources/model.py

@@ -6,6 +6,6 @@ class DataSourceListOptions(BaseModel):
     pass
 
 class DataSource(BaseModel):
-    id: Optional[str]
-    name: Optional[str]
-    type: Optional[str]
+    id: Optional[str] = None
+    name: Optional[str] = None
+    type: Optional[str] = None

dnastack/client/drs.py

@@ -141,8 +141,8 @@ class DrsObjectAccessMethod(BaseModel):
 
 
 class DrsObjectChecksum(BaseModel):
-    checksum: Optional[str]
-    type: Optional[str]
+    checksum: Optional[str] = None
+    type: Optional[str] = None
 
 
 class DrsObject(BaseModel):
@@ -314,7 +314,7 @@ class Blob(AbstractContextManager):
     def get_access_url_object(self) -> DrsObjectAccessUrl:
         """ Get the DRS Access URL Object """
         drs_obj = self.get_object()
-        self._logger.debug(f'DRS Object:\n\n{drs_obj.json(indent=2)}\n')
+        self._logger.debug(f'DRS Object:\n\n{drs_obj.model_dump_json(indent=2)}\n')
 
         if drs_obj.access_methods:
             for access_method in drs_obj.access_methods:
@@ -538,7 +538,7 @@ class DrsClient(BaseServiceClient):
         if max_worker_count < 2:
             max_worker_count = 2
 
-        future_to_url_map: Dict[Future, str] = dict()
+        future_to_url_map: Dict[Future, str] = {}
 
         with ThreadPoolExecutor(max_workers=max_worker_count) as pool:
             for url in unique_urls:

dnastack/client/explorer/client.py

@@ -210,7 +210,7 @@ class FederatedQuestionQueryResultLoader(ResultLoader):
             try:
                 response = session.post(
                     self.__service_url,
-                    json=self.__request_payload.dict(),
+                    json=self.__request_payload.model_dump(),
                     trace_context=self.__trace
                 )
                 

dnastack/client/explorer/models.py

@@ -1,5 +1,5 @@
 from typing import List, Optional, Dict, Any
-from pydantic import BaseModel, Field
+from pydantic import ConfigDict, BaseModel, Field
 
 
 class QuestionParam(BaseModel):
@@ -21,9 +21,7 @@ class QuestionParam(BaseModel):
     table: Optional[str] = None
     column: Optional[str] = None
     values: Optional[str] = None
-
-    class Config:
-        allow_population_by_field_name = True
+    model_config = ConfigDict(populate_by_name=True)
 
 
 class QuestionCollection(BaseModel):
@@ -34,9 +32,7 @@ class QuestionCollection(BaseModel):
     slug: str
     name: str
     question_id: str = Field(alias="questionId")
-
-    class Config:
-        allow_population_by_field_name = True
+    model_config = ConfigDict(populate_by_name=True)
 
 
 class FederatedQuestion(BaseModel):

dnastack/client/factory.py

@@ -65,7 +65,7 @@ class EndpointRepository:
         self.__cacheable = cacheable
         self.__endpoints = self.__set_endpoints(endpoints)
         self.__additional_service_client_classes = additional_service_client_classes
-        self.__default_event_interceptors = default_event_interceptors or dict()
+        self.__default_event_interceptors = default_event_interceptors or {}
 
         self.__logger.debug('Initialized')
 

dnastack/client/models.py

@@ -41,21 +41,21 @@ class ServiceEndpoint(BaseModel, HashableModel):
         This is in junction with GA4GH Service Information.
     """
 
-    type: Optional[ServiceType]
+    type: Optional[ServiceType] = None
     """ Service Type """
 
     url: str
     """ Base URL """
 
     # DEPRECATED: It is here only for the migration.
-    mode: Optional[str]
+    mode: Optional[str] = None
     """ Client mode ("standard" or "explorer") - only applicable if the client supports.
-    
+
         DO NOT USE THIS. This is replaced by "type" in model version 2.0.
     """
 
     # DEPRECATED: It is here only for the migration.
-    source: Optional[EndpointSource]
+    source: Optional[EndpointSource] = None
     """ The source of the endpoint configuration (e.g., service registry) """
 
     def get_authentications(self) -> List[Dict[str, Any]]:
@@ -70,12 +70,12 @@ class ServiceEndpoint(BaseModel, HashableModel):
         return [self.__convert_to_dict(raw_auth) for raw_auth in raw_auths]
 
     def __convert_to_dict(self, model: Union[Dict[str, Any], BaseModel]) -> Dict[str, Any]:
-        converted_model: Dict[str, Any] = dict()
+        converted_model: Dict[str, Any] = {}
 
         if isinstance(model, dict):
             converted_model.update(model)
         elif isinstance(model, BaseModel):
-            converted_model.update(model.dict())
+            converted_model.update(model.model_dump())
         else:
             raise NotImplementedError(f'No interpretation for {model}')
 

dnastack/client/service_registry/factory.py

@@ -88,7 +88,7 @@ class ClientFactory:
             yield entry
 
     def _merge_auth_info_list(self, entries: List[RegisteredServiceInfo]):
-        auth_info_groups: Dict[str, List[Dict[str, Any]]] = dict()
+        auth_info_groups: Dict[str, List[Dict[str, Any]]] = {}
         for entry in entries:
             for auth_info in (entry.info.authentication or []):
                 if auth_info.get('type') is None or auth_info.get('type') == 'oauth2':
@@ -103,7 +103,7 @@ class ClientFactory:
 
                 group_key = self._make_auth_info_group_key(auth_info)
                 if group_key not in auth_info_groups:
-                    auth_info_groups[group_key] = list()
+                    auth_info_groups[group_key] = []
                 auth_info_groups[group_key].append(auth_info)
 
         for group_key, auth_info_list in auth_info_groups.items():
@@ -118,7 +118,7 @@ class ClientFactory:
         # The current implementation makes an optimistic assumption that when the client has authorization for
         # a resource at the root level, i.e., https://foo.io/, it will have access to all resources as long as
         # all necessary scopes are requested.
-        url_to_scopes_map: Dict[str, Set[str]] = dict()
+        url_to_scopes_map: Dict[str, Set[str]] = {}
 
         # Separate scopes per domain
         for auth_info in auth_info_list:

dnastack/client/service_registry/helper.py

@@ -15,7 +15,7 @@ def parse_ga4gh_service_info(service: Service, alternate_service_id: Optional[st
 
     authentications = [
         _parse_authentication_info(auth_info)
-        for auth_info in (service.authentication or list())
+        for auth_info in (service.authentication or [])
     ]
 
     if authentications:
@@ -26,16 +26,9 @@ def parse_ga4gh_service_info(service: Service, alternate_service_id: Optional[st
 
 
 def _parse_authentication_info(auth_info: Dict[str, Any]) -> Dict[str, Any]:
-    return dict(
-        type='oauth2',
-        authorization_endpoint=auth_info.get('authorizationUrl'),
-        client_id=auth_info.get('clientId'),
-        client_secret=auth_info.get('clientSecret'),
-        device_code_endpoint=auth_info.get('deviceCodeUrl'),
-        grant_type=auth_info.get('grantType'),
-        redirect_url=auth_info.get('redirectUrl'),
-        resource_url=auth_info.get('resource'),
-        scope=auth_info.get('scope'),
-        token_endpoint=auth_info.get('accessTokenUrl'),
-        platform_credentials=auth_info.get('grantType') == GRANT_TYPE_TOKEN_EXCHANGE,
-    )
+    return {'type': 'oauth2', 'authorization_endpoint': auth_info.get('authorizationUrl'),
+            'client_id': auth_info.get('clientId'), 'client_secret': auth_info.get('clientSecret'),
+            'device_code_endpoint': auth_info.get('deviceCodeUrl'), 'grant_type': auth_info.get('grantType'),
+            'redirect_url': auth_info.get('redirectUrl'), 'resource_url': auth_info.get('resource'),
+            'scope': auth_info.get('scope'), 'token_endpoint': auth_info.get('accessTokenUrl'),
+            'platform_credentials': auth_info.get('grantType') == GRANT_TYPE_TOKEN_EXCHANGE}

dnastack/client/service_registry/manager.py

@@ -75,7 +75,7 @@ class ServiceRegistryManager:
 
         # Add the registry endpoint.
         self.__context.endpoints.append(registry_endpoint)
-        self.events.dispatch('endpoint-sync', dict(action='add', endpoint=registry_endpoint))
+        self.events.dispatch('endpoint-sync', {'action': 'add', 'endpoint': registry_endpoint})
 
         # Initiate the first sync.
         return self.__synchronize_endpoints_with(ServiceRegistry.make(registry_endpoint))
@@ -133,7 +133,7 @@ class ServiceRegistryManager:
             if sync_operation.action in ('add', 'update', 'keep'):
                 new_endpoint_list.append(endpoint)
 
-            self.events.dispatch('endpoint-sync', dict(action=sync_operation.action, endpoint=endpoint))
+            self.events.dispatch('endpoint-sync', {'action': sync_operation.action, 'endpoint': endpoint})
 
         endpoints.clear()
         endpoints.extend(sorted([endpoint for endpoint in new_endpoint_list], key=lambda e: e.id))
@@ -183,11 +183,11 @@ class ServiceRegistryManager:
                     endpoint.id == registry_endpoint_id
                     or (endpoint.source and endpoint.source.source_id == registry_endpoint_id)
             ):
-                self.events.dispatch('endpoint-sync', dict(action='remove', endpoint=endpoint))
+                self.events.dispatch('endpoint-sync', {'action': 'remove', 'endpoint': endpoint})
                 continue
             else:
                 new_endpoint_list.append(endpoint)
-                self.events.dispatch('endpoint-sync', dict(action='keep', endpoint=endpoint))
+                self.events.dispatch('endpoint-sync', {'action': 'keep', 'endpoint': endpoint})
 
         endpoints.clear()
         endpoints.extend(new_endpoint_list)

dnastack/client/workbench/base_client.py

@@ -74,7 +74,7 @@ class WorkbenchResultLoader(ResultLoader):
         self.__max_results = int(max_results) if max_results else None
         self.__loaded_results = 0
         self.__active = True
-        self.__visited_urls: List[str] = list()
+        self.__visited_urls: List[str] = []
         self.__trace = trace
         self.__next_page_url = None
 
@@ -135,7 +135,7 @@ class WorkbenchResultLoader(ResultLoader):
             response_text = response.text
 
             try:
-                response_body = response.json() if response_text else dict()
+                response_body = response.json() if response_text else {}
             except Exception:
                 self.logger.error(f'{self.__service_url}: Unexpectedly non-JSON response body from {current_url}')
                 raise PageableApiError(

dnastack/client/workbench/ewes/client.py

@@ -195,14 +195,14 @@ class EWesClient(BaseWorkbenchClient):
         trace = trace or Span(origin=self)
         with self.create_http_session() as session:
             response = session.post(urljoin(self.endpoint.url, f'{self.namespace}/ga4gh/wes/v1/runs'),
-                                    json=data.dict(),
+                                    json=data.model_dump(),
                                     trace_context=trace)
         return MinimalExtendedRun(**response.json())
 
     def submit_batch(self, data: BatchRunRequest, trace: Optional[Span] = None) -> BatchRunResponse:
         with self.create_http_session() as session:
             response = session.post(urljoin(self.endpoint.url, f'{self.namespace}/ga4gh/wes/v1/batch'),
-                                    json=data.dict(),
+                                    json=data.model_dump(),
                                     trace_context=trace)
         return BatchRunResponse(**response.json())
 
@@ -240,7 +240,7 @@ class EWesClient(BaseWorkbenchClient):
                        trace: Optional[Span] = None) -> Iterable[bytes]:
         trace = trace or Span()
 
-        params = dict()
+        params = {}
         if max_bytes:
             params['max'] = max_bytes