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

dnastack/client/workbench/samples/models.py

@@ -10,33 +10,33 @@ from dnastack.client.workbench.storage.models import PlatformType
 
 class OntologyClass(BaseModel):
     id: str
-    label: Optional[str]
+    label: Optional[str] = None
 
 
 class PhenotypicFeature(BaseModel):
-    created_at: Optional[datetime]
-    last_updated_at: Optional[datetime]
-    type: Optional[OntologyClass]
+    created_at: Optional[datetime] = None
+    last_updated_at: Optional[datetime] = None
+    type: Optional[OntologyClass] = None
 
 
 class SampleMetrics(BaseModel):
-    file_count: Optional[int]
-    instrument_types: Optional[List[str]]
+    file_count: Optional[int] = None
+    instrument_types: Optional[List[str]] = None
 
 
 class RunMetadata(BaseModel):
-    run_id: Optional[str]
-    state: Optional[State]
-    start_time: Optional[datetime]
-    end_time: Optional[datetime]
-    updated_time: Optional[datetime]
-    submitted_by: Optional[str]
-    workflow_id: Optional[str]
-    workflow_version_id: Optional[str]
-    workflow_name: Optional[str]
-    workflow_version: Optional[str]
-    last_recorded_event_time: Optional[datetime]
-    tags: Optional[dict[str, str]]
+    run_id: Optional[str] = None
+    state: Optional[State] = None
+    start_time: Optional[datetime] = None
+    end_time: Optional[datetime] = None
+    updated_time: Optional[datetime] = None
+    submitted_by: Optional[str] = None
+    workflow_id: Optional[str] = None
+    workflow_version_id: Optional[str] = None
+    workflow_name: Optional[str] = None
+    workflow_version: Optional[str] = None
+    last_recorded_event_time: Optional[datetime] = None
+    tags: Optional[dict[str, str]] = None
 
 
 class Sex(str, CaseInsensitiveEnum):
@@ -76,27 +76,27 @@ class SampleListOptions(BaseListOptions):
 class SampleFile(BaseModel):
     sample_id: str
     path: str
-    storage_account_id: Optional[str]
-    platform_type: Optional[PlatformType]
-    instrument_id: Optional[str]
-    created_at: Optional[datetime]
-    last_updated_at: Optional[datetime]
-    size: Optional[int]
+    storage_account_id: Optional[str] = None
+    platform_type: Optional[PlatformType] = None
+    instrument_id: Optional[str] = None
+    created_at: Optional[datetime] = None
+    last_updated_at: Optional[datetime] = None
+    size: Optional[int] = None
 
 
 class Sample(BaseModel):
     id: str
-    created_at: Optional[datetime]
-    last_updated_at: Optional[datetime]
-    father_id: Optional[str]
-    mother_id: Optional[str]
-    family_id: Optional[str]
-    sex: Optional[str]
-    metrics: Optional[SampleMetrics]
-    phenotypes: Optional[List[PhenotypicFeature]]
-    runs: Optional[List[RunMetadata]]
-    affected_status: Optional[AffectedStatus]
-    has_been_analyzed: Optional[bool]
+    created_at: Optional[datetime] = None
+    last_updated_at: Optional[datetime] = None
+    father_id: Optional[str] = None
+    mother_id: Optional[str] = None
+    family_id: Optional[str] = None
+    sex: Optional[str] = None
+    metrics: Optional[SampleMetrics] = None
+    phenotypes: Optional[List[PhenotypicFeature]] = None
+    runs: Optional[List[RunMetadata]] = None
+    affected_status: Optional[AffectedStatus] = None
+    has_been_analyzed: Optional[bool] = None
 
 
 class SampleListResponse(PaginatedResource):
@@ -107,10 +107,10 @@ class SampleListResponse(PaginatedResource):
 
 
 class SampleFilesListOptions(BaseListOptions):
-    storage_id: Optional[str]
-    platform_type: Optional[PlatformType]
-    instrument_id: Optional[str]
-    search: Optional[str]
+    storage_id: Optional[str] = None
+    platform_type: Optional[PlatformType] = None
+    instrument_id: Optional[str] = None
+    search: Optional[str] = None
 
 
 class SampleFileListResponse(PaginatedResource):
@@ -121,7 +121,7 @@ class SampleFileListResponse(PaginatedResource):
 
 
 class InstrumentListOptions(BaseListOptions):
-    platform_type: Optional[PlatformType]
+    platform_type: Optional[PlatformType] = None
 
 
 class Instrument(BaseModel):

dnastack/client/workbench/storage/client.py

@@ -53,7 +53,7 @@ class StorageClient(BaseWorkbenchClient):
         with self.create_http_session() as session:
             response = session.post(
                 urljoin(self.endpoint.url, f'{self.namespace}/storage'),
-                json=storage_account.dict()
+                json=storage_account.model_dump()
             )
         return StorageAccount(**response.json())
 
@@ -62,7 +62,7 @@ class StorageClient(BaseWorkbenchClient):
         with self.create_http_session() as session:
             response = session.submit("PUT",
                                       urljoin(self.endpoint.url, f'{self.namespace}/storage/{storage_account_id}'),
-                                      json=storage_account.dict(),
+                                      json=storage_account.model_dump(),
                                       headers={"If-Match": if_match}
                                       )
         return StorageAccount(**response.json())

dnastack/client/workbench/storage/models.py

@@ -20,16 +20,16 @@ class PlatformType(str, CaseInsensitiveEnum):
 
 class AwsStorageAccountCredentials(BaseModel):
     type: Literal['AWS_ACCESS_KEY'] = 'AWS_ACCESS_KEY'
-    access_key_id: Optional[str]
-    secret_access_key: Optional[str]
-    region: Optional[str]
+    access_key_id: Optional[str] = None
+    secret_access_key: Optional[str] = None
+    region: Optional[str] = None
 
 
 class GcpStorageAccountCredentials(BaseModel):
     type: Literal['GCP_SERVICE_ACCOUNT'] = 'GCP_SERVICE_ACCOUNT'
-    service_account_json: Optional[str]
-    region: Optional[str]
-    project_id: Optional[str]
+    service_account_json: Optional[str] = None
+    region: Optional[str] = None
+    project_id: Optional[str] = None
 
 
 class AzureCredentialsType(str, CaseInsensitiveEnum):
@@ -40,30 +40,30 @@ class AzureCredentialsType(str, CaseInsensitiveEnum):
 
 class AzureStorageAccountCredentials(BaseModel):
     type: Literal['AZURE_CREDENTIALS'] = 'AZURE_CREDENTIALS'
-    sas_url: Optional[str]
-    access_key: Optional[str]
-    tenant_id: Optional[str]
-    client_id: Optional[str]
-    client_secret: Optional[str]
-    storage_account_name: Optional[str]
-    azure_credentials_type: Optional[AzureCredentialsType]
+    sas_url: Optional[str] = None
+    access_key: Optional[str] = None
+    tenant_id: Optional[str] = None
+    client_id: Optional[str] = None
+    client_secret: Optional[str] = None
+    storage_account_name: Optional[str] = None
+    azure_credentials_type: Optional[AzureCredentialsType] = None
 
 
 class StorageAccount(BaseModel):
-    id: Optional[str]
-    namespace: Optional[str]
-    name: Optional[str]
-    etag: Optional[str]
-    provider: Optional[Provider]
-    created_at: Optional[str]
-    last_updated_at: Optional[str]
-    bucket: Optional[str]
-    credentials: Optional[Union[AwsStorageAccountCredentials, GcpStorageAccountCredentials, AzureStorageAccountCredentials]]
+    id: Optional[str] = None
+    namespace: Optional[str] = None
+    name: Optional[str] = None
+    etag: Optional[str] = None
+    provider: Optional[Provider] = None
+    created_at: Optional[str] = None
+    last_updated_at: Optional[str] = None
+    bucket: Optional[str] = None
+    credentials: Optional[Union[AwsStorageAccountCredentials, GcpStorageAccountCredentials, AzureStorageAccountCredentials]] = None
 
 
 class StorageListOptions(BaseListOptions):
-    provider: Optional[Provider]
-    sort: Optional[str]
+    provider: Optional[Provider] = None
+    sort: Optional[str] = None
 
 
 class StorageListResponse(PaginatedResource):

dnastack/client/workbench/workflow/client.py

@@ -259,7 +259,7 @@ class WorkflowClient(BaseWorkbenchClient):
 
     def update_workflow(self, workflow_id: str, etag: str, updates: List[JsonPatch]) -> Workflow:
         with self.create_http_session() as session:
-            updates = [update.dict() for update in updates]
+            updates = [update.model_dump() for update in updates]
             response = session.json_patch(
                 urljoin(self.endpoint.url, f'{self.namespace}/workflows/{workflow_id}'),
                 headers={'If-Match': etag},
@@ -270,7 +270,7 @@ class WorkflowClient(BaseWorkbenchClient):
     def update_workflow_version(self, workflow_id: str, version_id: str, etag: str,
                                 updates: List[JsonPatch]) -> WorkflowVersion:
         with self.create_http_session() as session:
-            updates = [update.dict() for update in updates]
+            updates = [update.model_dump() for update in updates]
             response = session.json_patch(
                 urljoin(self.endpoint.url, f'{self.namespace}/workflows/{workflow_id}/versions/{version_id}'),
                 headers={'If-Match': etag},
@@ -325,7 +325,7 @@ class WorkflowClient(BaseWorkbenchClient):
             response = session.post(
                 urljoin(self.endpoint.url,
                         f'{self.namespace}/workflows/{workflow_id}/versions/{version_id}/defaults'),
-                json=workflow_defaults.dict()
+                json=workflow_defaults.model_dump()
             )
             return WorkflowDefaults(**response.json())
 
@@ -343,7 +343,7 @@ class WorkflowClient(BaseWorkbenchClient):
             response = session.submit("PUT",
                 urljoin(self.endpoint.url,
                         f'{self.namespace}/workflows/{workflow_id}/versions/{version_id}/defaults/{default_id}'),
-                json=workflow_defaults.dict(),
+                json=workflow_defaults.model_dump(),
                 headers={"If-Match": if_match}
             )
             return WorkflowDefaults(**response.json())
@@ -378,7 +378,7 @@ class WorkflowClient(BaseWorkbenchClient):
         with self.create_http_session() as session:
             response = session.post(
                 urljoin(self.endpoint.url, f'{self.namespace}/workflows/{workflow_id}/versions/{workflow_version_id}/transformations'),
-                json=workflow_transformation_create_request.dict()
+                json=workflow_transformation_create_request.model_dump()
             )
         return WorkflowTransformation(**response.json())
 
@@ -411,7 +411,7 @@ class WorkflowClient(BaseWorkbenchClient):
         with self.create_http_session() as session:
             response = session.post(
                 urljoin(self.endpoint.url, f'{self.namespace}/workflows/{workflow_id}/versions/{workflow_version_id}/dependencies'),
-                json=workflow_dependency_create_request.dict(),
+                json=workflow_dependency_create_request.model_dump(),
                 headers=headers
             )
         return WorkflowDependency(**response.json())
@@ -426,7 +426,7 @@ class WorkflowClient(BaseWorkbenchClient):
         with self.create_http_session() as session:
             response = session.submit("PUT",
                 urljoin(self.endpoint.url, f'{self.namespace}/workflows/{workflow_id}/versions/{workflow_version_id}/dependencies/{dependency_id}'),
-                json=workflow_dependency_update_request.dict(),
+                json=workflow_dependency_update_request.model_dump(),
                 headers=headers
             )
         return WorkflowDependency(**response.json())

dnastack/client/workbench/workflow/models.py

@@ -12,17 +12,17 @@ class WorkflowDescriptor(BaseModel):
     input_schema: Dict
     output_schema: Dict
     wdl_version: str
-    errors: Optional[Any]
+    errors: Optional[Any] = None
 
 
 class WorkflowVersion(BaseModel):
-    workflowId: Optional[str]
+    workflowId: Optional[str] = None
     id: str
-    externalId: Optional[str]
+    externalId: Optional[str] = None
     versionName: str
     workflowName: str
-    createdAt: Optional[str]
-    lastUpdatedAt: Optional[str]
+    createdAt: Optional[str] = None
+    lastUpdatedAt: Optional[str] = None
     descriptorType: str
     authors: Optional[List[str]] = None
     description: Optional[str] = None
@@ -34,14 +34,14 @@ class Workflow(BaseModel):
     internalId: str
     source: str
     name: str
-    description: Optional[str]
-    lastUpdatedAt: Optional[str]
+    description: Optional[str] = None
+    lastUpdatedAt: Optional[str] = None
     latestVersion: str
-    authors: Optional[List[str]]
-    versions: Optional[List[WorkflowVersion]]
-    deleted: Optional[bool]
-    etag: Optional[str]
-    labels: Optional[List[str]]
+    authors: Optional[List[str]] = None
+    versions: Optional[List[WorkflowVersion]] = None
+    deleted: Optional[bool] = None
+    etag: Optional[str] = None
+    labels: Optional[List[str]] = None
 
 
 class WorkflowFileType(str, Enum):
@@ -83,12 +83,12 @@ class WorkflowVersionCreate(BaseModel):
 
 
 class WorkflowListOptions(BaseListOptions):
-    search: Optional[str]
-    source: Optional[WorkflowSource]
-    deleted: Optional[bool]
-    sort: Optional[str]
+    search: Optional[str] = None
+    source: Optional[WorkflowSource] = None
+    deleted: Optional[bool] = None
+    sort: Optional[str] = None
     order: Optional[str] = Field(default=None, deprecated=True)
-    direction: Optional[str]
+    direction: Optional[str] = None
 
 
 class WorkflowListResponse(PaginatedResource):
@@ -99,7 +99,7 @@ class WorkflowListResponse(PaginatedResource):
 
 
 class WorkflowVersionListOptions(BaseListOptions):
-    deleted: Optional[bool]
+    deleted: Optional[bool] = None
 
 
 class WorkflowVersionListResponse(PaginatedResource):
@@ -113,42 +113,42 @@ class ResolvedWorkflow(BaseModel):
     internalId: str
     source: str
     name: str
-    description: Optional[str]
-    lastUpdatedAt: Optional[str]
-    versionId: Optional[str]
-    version: Optional[WorkflowVersion]
-    authors: Optional[List[str]]
-    etag: Optional[str]
+    description: Optional[str] = None
+    lastUpdatedAt: Optional[str] = None
+    versionId: Optional[str] = None
+    version: Optional[WorkflowVersion] = None
+    authors: Optional[List[str]] = None
+    etag: Optional[str] = None
 
 class WorkflowDefaultsSelector(BaseModel):
-    engine: Optional[str]
-    provider: Optional[str]
-    region: Optional[str]
+    engine: Optional[str] = None
+    provider: Optional[str] = None
+    region: Optional[str] = None
 
 
 class WorkflowDefaults(BaseModel):
-    id: Optional[str]
-    name: Optional[str]
-    workflow_id: Optional[str]
-    workflow_version_id: Optional[str]
-    created_at: Optional[str]
-    updated_at: Optional[str]
-    selector: Optional[WorkflowDefaultsSelector]
-    values: Optional[Dict]
-    etag: Optional[str]
+    id: Optional[str] = None
+    name: Optional[str] = None
+    workflow_id: Optional[str] = None
+    workflow_version_id: Optional[str] = None
+    created_at: Optional[str] = None
+    updated_at: Optional[str] = None
+    selector: Optional[WorkflowDefaultsSelector] = None
+    values: Optional[Dict] = None
+    etag: Optional[str] = None
 
 
 class WorkflowDefaultsCreateRequest(BaseModel):
-    id: Optional[str]
-    name: Optional[str]
-    selector: Optional[WorkflowDefaultsSelector]
-    values: Optional[Dict]
+    id: Optional[str] = None
+    name: Optional[str] = None
+    selector: Optional[WorkflowDefaultsSelector] = None
+    values: Optional[Dict] = None
 
 
 class WorkflowDefaultsUpdateRequest(BaseModel):
-    name: Optional[str]
-    selector: Optional[WorkflowDefaultsSelector]
-    values: Optional[Dict]
+    name: Optional[str] = None
+    selector: Optional[WorkflowDefaultsSelector] = None
+    values: Optional[Dict] = None
 
 
 class WorkflowDefaultsListResponse(PaginatedResource):
@@ -159,24 +159,24 @@ class WorkflowDefaultsListResponse(PaginatedResource):
 
 
 class WorkflowDefaultsListOptions(BaseListOptions):
-    sort: Optional[str]
+    sort: Optional[str] = None
 
 
 class WorkflowTransformationCreate(BaseModel):
-    id: Optional[str]
-    next_transformation_id: Optional[str]
-    script: Optional[str]
-    labels: Optional[List[str]]
+    id: Optional[str] = None
+    next_transformation_id: Optional[str] = None
+    script: Optional[str] = None
+    labels: Optional[List[str]] = None
 
 
 class WorkflowTransformation(BaseModel):
-    id: Optional[str]
-    workflow_id: Optional[str]
-    workflow_version_id: Optional[str]
-    next_transformation_id: Optional[str]
-    script: Optional[str]
-    labels: Optional[List[str]]
-    created_at: Optional[str]
+    id: Optional[str] = None
+    workflow_id: Optional[str] = None
+    workflow_version_id: Optional[str] = None
+    next_transformation_id: Optional[str] = None
+    script: Optional[str] = None
+    labels: Optional[List[str]] = None
+    created_at: Optional[str] = None
 
 
 class WorkflowTransformationListOptions(BaseListOptions):
@@ -191,20 +191,20 @@ class WorkflowTransformationListResponse(PaginatedResource):
 
 
 class WorkflowDependencyPrerequisite(BaseModel):
-    workflow_id: Optional[str]
-    workflow_version_id: Optional[str]
+    workflow_id: Optional[str] = None
+    workflow_version_id: Optional[str] = None
 
 
 class WorkflowDependency(BaseModel):
-    namespace: Optional[str]
-    id: Optional[str]
-    workflow_id: Optional[str]
-    workflow_version_id: Optional[str]
-    name: Optional[str]
+    namespace: Optional[str] = None
+    id: Optional[str] = None
+    workflow_id: Optional[str] = None
+    workflow_version_id: Optional[str] = None
+    name: Optional[str] = None
     dependencies: Optional[List[WorkflowDependencyPrerequisite]] = []
     global_: Optional[bool] = Field(default=None, alias="global")
-    created_at: Optional[str]
-    updated_at: Optional[str]
+    created_at: Optional[str] = None
+    updated_at: Optional[str] = None
 
 
 class WorkflowDependencyCreateRequest(BaseModel):

dnastack/client/workbench/workflow/utils.py

@@ -42,10 +42,10 @@ class WorkflowSourceLoader(object):
             if import_path not in _visited:
                 _visited.append(import_path)
             else:
-                return list()
+                return []
 
-            resolved_content = list()
-            all_imported_contents = list()
+            resolved_content = []
+            all_imported_contents = []
             if path.name.endswith(".wdl"):
                 pattern = re.compile(r'^\s*import\s["\'](?!http)(.+)["\'].*$')
                 with import_path.open('r') as fp:
@@ -67,8 +67,8 @@ class WorkflowSourceLoader(object):
             os.chdir(cwd)
 
     def _load_files(self):
-        path_and_contents: List[Tuple[Path, bytes]] = list()
-        _visited = list()
+        path_and_contents: List[Tuple[Path, bytes]] = []
+        _visited = []
         for path in self.source_files:
             path_and_contents.extend(self._resolve_content(None, Path(path), _visited))
         wdl_files = [wdl_file for wdl_file in path_and_contents if wdl_file[0].name.endswith(".wdl")]

dnastack/common/auth_manager.py

@@ -64,12 +64,8 @@ class AuthManager:
             if state.session_info and state.session_info.get('scope'):
                 granted_scopes.extend(sorted(str(state.session_info.get('scope')).split(r' ')))
 
-            basic_event_info = dict(session_id=authenticator.session_id,
-                                    index=index,
-                                    total=total,
-                                    state=state,
-                                    endpoint_ids=affected_endpoint_ids,
-                                    scopes=granted_scopes)
+            basic_event_info = {'session_id': authenticator.session_id, 'index': index, 'total': total, 'state': state,
+                                'endpoint_ids': affected_endpoint_ids, 'scopes': granted_scopes}
 
             self.events.dispatch('revoke-begin', basic_event_info)
 
@@ -91,7 +87,7 @@ class AuthManager:
         endpoints = self.get_filtered_endpoints(endpoint_ids)
         for authenticator in self.get_authenticators(endpoint_ids):
             auth_state = authenticator.get_state()
-            state = ExtendedAuthState(**auth_state.dict())
+            state = ExtendedAuthState(**auth_state.model_dump())
 
             # Simplify the auth info.
             simplified_auth_info = self._remove_none_entry_from(auth_state.auth_info)
@@ -144,10 +140,7 @@ class AuthManager:
                 index += 1
                 continue
             
-            basic_event_info = dict(session_id=authenticator.session_id,
-                                    state=state,
-                                    index=index,
-                                    total=total)
+            basic_event_info = {'session_id': authenticator.session_id, 'state': state, 'index': index, 'total': total}
 
             self.events.dispatch('auth-begin', basic_event_info)
 
@@ -166,7 +159,7 @@ class AuthManager:
                     with trace.new_span({'actor': 'auth_manager', 'action': 'revoke_session'}):
                         authenticator.revoke()
 
-                state.session_info = authenticator.initialize(trace_context=trace).dict()
+                state.session_info = authenticator.initialize(trace_context=trace).model_dump()
                 session = state.session_info
 
                 if (
@@ -196,7 +189,7 @@ class AuthManager:
     def handle_block_response_required_event(self, event: Event):
         if event.details.get('kind') == 'user_verification':
             self._logger.debug(f'Intercepting the "blocking-response-required" event for user verification ({event.details})...')
-            self.events.dispatch('user-verification-required', dict(url=event.details.get('url')))
+            self.events.dispatch('user-verification-required', {'url': event.details.get('url')})
         else:
             self._logger.error(f'Intercepted the "blocking-response-required" event but FAILED to handle {event.details}.')
 

dnastack/common/class_decorator.py

@@ -1,6 +1,6 @@
 from collections.abc import Callable
 from dataclasses import dataclass
-from typing import Optional, Any, Dict, get_origin, get_args, Union, Type
+from typing import Any, Dict, get_origin, get_args, Union, Type
 
 
 @dataclass(repr=True)
@@ -20,11 +20,11 @@ class UndefinedInitializedPropertyError(RuntimeError):
         return f'{self.__cls.__module__}.{self.__cls.__name__}: "{self.__property_name}" not defined'
 
 
-def simple_constructor(overwrite_init: Optional[bool] = None):
+def simple_constructor():
     """ Provide a simple constructor by turning all annotated properties into non-static instance variables. """
 
     def wrapper(cls):
-        property_map: Dict[str, _Property] = dict()
+        property_map: Dict[str, _Property] = {}
 
         for p, a in cls.__annotations__.items():
             special_type = get_origin(a)

dnastack/common/events.py

@@ -17,7 +17,7 @@ class Event(BaseModel):
 
     @classmethod
     def make(cls, details: Optional[Dict[str, Any]] = None):
-        return Event(details=deepcopy(details) if details else dict())
+        return Event(details=deepcopy(details) if details else {})
 
 
 class EventHandler:
@@ -70,8 +70,8 @@ class EventSource(AbstractEventSource):
                 self._alias = f'{type(self._origin).__name__}/{hash(self._origin)}/{self._alias}'
 
         self._event_logger = get_logger(self._alias, logging.WARNING)
-        self._event_handlers: Dict[str, List[Union[EventHandler, Callable[[Event], None]]]] = dict()
-        self._fixed_types = fixed_types or list()
+        self._event_handlers: Dict[str, List[Union[EventHandler, Callable[[Event], None]]]] = {}
+        self._fixed_types = fixed_types or []
 
         self._event_logger.debug('Initialized')
 
@@ -110,7 +110,7 @@ class EventSource(AbstractEventSource):
         self._raise_error_for_non_registered_event_type(event_type)
 
         if event_type not in self._event_handlers:
-            self._event_handlers[event_type] = list()
+            self._event_handlers[event_type] = []
 
         if handler in self._event_handlers[event_type]:
             self._event_logger.debug(f'E/{event_type}: IGNORE BINDING {handler} (duplicate)')
@@ -124,7 +124,7 @@ class EventSource(AbstractEventSource):
         self._raise_error_for_non_registered_event_type(event_type)
 
         if event_type not in self._event_handlers:
-            self._event_handlers[event_type] = list()
+            self._event_handlers[event_type] = []
 
         new_handlers = [
             existing_handler
@@ -166,9 +166,9 @@ class EventSource(AbstractEventSource):
     def _compute_event_hash(obj: Event) -> str:
         h = hashlib.new('sha1')
         try:
-            h.update(obj.json().encode('utf-8'))
+            h.update(obj.model_dump_json().encode('utf-8'))
         except TypeError:
-            h.update(str(obj.dict()).encode('utf-8'))
+            h.update(str(obj.model_dump()).encode('utf-8'))
         return h.hexdigest()[:8]
 
     def __repr__(self):

dnastack/common/json_argument_parser.py

@@ -160,7 +160,7 @@ def get_argument_type(argument: str) -> str:
 
 def parse_kv_arguments(arguments: List[str]) -> Union[List[JSONType], Dict[str, JSONType]]:
     arg_types = KeyValueArgType(*SEPARATOR_GROUP_NESTED_JSON_ITEMS)
-    kv_pairs = list()
+    kv_pairs = []
     for argument in arguments:
         arg_type = arg_types(argument)
         if arg_type.sep == SEPARATOR_DATA_EMBED_FILE_CONTENTS:
@@ -180,8 +180,8 @@ def parse_kv_arguments(arguments: List[str]) -> Union[List[JSONType], Dict[str,
 
 
 def parse_and_merge_arguments(arguments: List[JsonLike]) -> Dict[str, JSONType]:
-    arguments_results = dict()
-    kv_arguments = list()
+    arguments_results = {}
+    kv_arguments = []
     for argument in arguments:
         if argument.argument_type == ArgumentType.KV_PARAM_TYPE:
             kv_arguments.extend(split_arguments_list(argument.value()))
@@ -198,7 +198,7 @@ def parse_and_merge_arguments(arguments: List[JsonLike]) -> Dict[str, JSONType]:
 
 def merge_param_json_data(kv_pairs_list: List[str], json_literals_list: List[str],
                           files_list: List[str]) -> Dict[str, JSONType]:
-    param_presets = dict()
+    param_presets = {}
 
     # in this ordering the JSON content of the file will be overwritten by any keys with the same values
     if files_list:

dnastack/common/model_mixin.py

@@ -6,7 +6,7 @@ import json
 class JsonModelMixin:
     def get_content_hash(self):
         # noinspection PyUnresolvedReferences
-        return self.hash(self.dict(exclude_none=True))
+        return self.hash(self.model_dump(exclude_none=True))
 
     @classmethod
     def hash(self, content):