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

dnastack/alpha/app/explorer.py

@@ -58,7 +58,7 @@ class Collection(PerCollectionApiMixin, BlobApiMixin):
         url = urljoin(endpoint.url, f'collections/{self._collection.slugName}/tables/{table_name}/filter/query'
                                     '?includeSharedQueryUrl=true')
         headers = {'Content-Type': 'application/json'}
-        return FilterInfo(**session.post(url, data=json.dumps(filters), headers=headers).json())
+        return FilterInfo(**session.post(url, data=json.dumps(filters), headers=headers).model_dump_json())
 
     def data_connect(self):
         default_no_auth_properties = {'authentication': None, 'fallback_authentications': None}

dnastack/alpha/app/workbench.py

@@ -145,7 +145,7 @@ class Workbench:
 		return self._get_ewes_client().list_runs(list_options=ExtendedRunListOptions(tag=[f"batch_id:{batch_id}"]))
 
 	def submit_batch(self, batch: BatchRunRequest, batch_id:Optional[str]=None) -> str:
-		self._logger.debug("Submitting batch request: "+json.dumps(batch.dict()))
+		self._logger.debug("Submitting batch request: "+json.dumps(batch.model_dump()))
 		if batch_id is None:
 			batch_id = self._get_short_uuid()
 
@@ -164,7 +164,7 @@ class Workbench:
 			raise WorkbenchRunException("Could not submit run, unexpected run state '"+result.state)
 		return result.run_id
 
-	def cancel_batch(self, batch_id: str) -> RunStatus:
+	def cancel_batch(self, batch_id: str) -> None:
 		bad_run_ids=[]
 		for run_status in self.describe_batch(batch_id):
 			r=RunStatus(run_status.state)
@@ -173,7 +173,7 @@ class Workbench:
 					self.cancel_run(run_status.run_id)
 				except Exception:
 					bad_run_ids.append(run_status.run_id)
-		if(len(bad_run_ids) > 0):
+		if len(bad_run_ids) > 0:
 			raise WorkbenchRunException("Could not cancel all runs in batch "+batch_id+".  Run IDs: "+"\n".join(bad_run_ids), run_ids=bad_run_ids)
 
 	def cancel_run(self, run_id) -> RunStatus:
@@ -181,7 +181,7 @@ class Workbench:
 		if type(result) is RunId:
 			return RunStatus(RunId.state)
 		else:
-			raise WorkbenchRunException("Run "+run_id+" could not be canceled: "+json.dumps(result.dict()))
+			raise WorkbenchRunException("Run "+run_id+" could not be canceled: "+json.dumps(result.model_dump()))
 
 	# Returns the state that all of the runs are in unless:
 	# - If any run has a failed status, then that status is returned, otherwise

dnastack/alpha/cli/wes.py

@@ -115,7 +115,7 @@ def submit(context: Optional[str],
 
         dnastack alpha wes submit --endpoint-id testing_wes -u hello_world.wdl -a samples/workflows/no_input/hello_world.wdl
     """
-    actual_params = dict()
+    actual_params = {}
 
     re_parameter = re.compile(r'^(?P<key>[a-zA-Z0-9_\.]+)(?P<op>:?=@?)(?P<value>.+)$')
 
@@ -138,7 +138,7 @@ def submit(context: Optional[str],
 
         param_counter += 1
 
-    actual_tags = dict(agent=f'dnastack-client-library/{__version__}')
+    actual_tags = {'agent': f'dnastack-client-library/{__version__}'}
     if tags:
         tag_counter = 0
         for tag in tags:
@@ -192,7 +192,7 @@ def submit(context: Optional[str],
                     'this run request will not be submitted to the service endpoint.',
                     fg='yellow',
                     err=True)
-        click.secho(run_request.json(indent=2), dim=True)
+        click.secho(run_request.model_dump_json(indent=2), dim=True)
     else:
         _execute(context=context,
                  endpoint_id=endpoint_id,

dnastack/alpha/client/collections/client.py

@@ -37,9 +37,9 @@ class CollectionServiceClient(StandardCollectionServiceClient):
 
         collection_id = collection.id if collection else id
 
-        given_overriding_properties = (collection.dict() if collection else (attrs or dict()))
+        given_overriding_properties = (collection.model_dump() if collection else (attrs or {}))
         update_patches = [
-            JsonPatch(op='replace', path=f'/{k}', value=v).dict()
+            JsonPatch(op='replace', path=f'/{k}', value=v).model_dump()
             for k, v in given_overriding_properties.items()
             if k not in COLLECTION_READ_ONLY_PROPERTIES and v is not None
         ]
@@ -52,7 +52,6 @@ class CollectionServiceClient(StandardCollectionServiceClient):
             resource_url = self._get_single_collection_url(collection_id)
             get_response = session.get(resource_url, trace_context=trace)
 
-            # trace_logger = trace.create_span_logger(self._logger)
             assert get_response.status_code == 200, 'Unexpected Response'
 
             etag = (get_response.headers.get('etag') or '').replace('"', '')

dnastack/alpha/client/wes/client.py

@@ -74,10 +74,7 @@ class RunRequest(BaseModel):
                         )
                     ))
 
-        return dict(
-            # data=form_data,
-            files=multipart_data
-        )
+        return {'files': multipart_data}
 
 
 class _Id(BaseModel):
@@ -165,7 +162,7 @@ class RunListLoader(ResultLoader):
         with self.__http_session as session:
             current_url = self.__initial_url
 
-            params = dict()
+            params = {}
             if self.__page_size:
                 params['page_size'] = self.__page_size
             if self.__page_token:
@@ -195,7 +192,7 @@ class RunListLoader(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.__initial_url}: Unexpectedly non-JSON response body from {current_url}')
                 raise DataConnectError(
@@ -254,7 +251,7 @@ class Run:
 
     def info(self) -> _Run:
         # GET /runs/{id}
-        raw_data = self.__session.get(self.__base_url).json()
+        raw_data = self.__session.get(self.__base_url).model_dump_json()
         try:
             return _Run(**raw_data)
         except ValidationError:
@@ -328,7 +325,7 @@ class WesClient(BaseServiceClient):
 
     def submit(self, run: RunRequest) -> str:
         workflow_url_is_external = run.workflow_url.startswith('http://') or run.workflow_url.startswith('https://')
-        workflow_url_is_in_attachments = run.workflow_url in [os.path.basename(p) for p in (run.attachments or list())]
+        workflow_url_is_in_attachments = run.workflow_url in [os.path.basename(p) for p in (run.attachments or [])]
         if not workflow_url_is_external and not workflow_url_is_in_attachments:
             if not workflow_url_is_in_attachments:
                 raise RuntimeError('The workflow file from the local drive is defined but it is apparently not in the '

dnastack/cli/commands/collections/commands.py

@@ -126,10 +126,9 @@ def init_collections_commands(group: Group):
     
             logger.debug(f'Item Simplifier: given: {to_json(row)}')
     
-            item = dict(
-                id=row['id'],
-                name=row.get('qualified_table_name') or row.get('preferred_name') or row.get('display_name') or row['name'],
-            )
+            item = {'id': row['id'],
+                    'name': row.get('qualified_table_name') or row.get('preferred_name') or row.get('display_name') or
+                            row['name']}
     
             if row['type'] == 'blob':
                 property_names.extend([

dnastack/cli/commands/collections/tables.py

@@ -54,4 +54,4 @@ def get_table_info(context: Optional[str],
     """ List all accessible tables """
     client = _switch_to_data_connect(_get_context(context), _get(context, endpoint_id), collection, no_auth=no_auth)
     obj = client.table(table_name, no_auth=no_auth).info
-    click.echo((to_json if output == 'json' else to_yaml)(obj.dict()))
+    click.echo((to_json if output == 'json' else to_yaml)(obj.model_dump()))

dnastack/cli/commands/collections/utils.py

@@ -110,7 +110,7 @@ def _abort_with_collection_list(collection_service_client: CollectionServiceClie
 def _transform_to_public_collection(collection: Collection) -> Dict[str, Any]:
     return {
         field_name: value
-        for field_name, value in (collection.dict() if isinstance(collection, Collection) else collection).items()
+        for field_name, value in (collection.model_dump() if isinstance(collection, Collection) else collection).items()
         if field_name not in ['itemsQuery', 'accessTypeLabels']
     }
 

dnastack/cli/commands/config/commands.py

@@ -17,7 +17,7 @@ def init_config_commands(group: Group):
     )
     def config_schema():
         """Show the schema of the configuration file"""
-        click.echo(json.dumps(Configuration.schema(), indent=2, sort_keys=True))
+        click.echo(json.dumps(Configuration.model_json_schema(), indent=2, sort_keys=True))
 
 
     @formatted_command(

dnastack/cli/commands/config/endpoints.py

@@ -83,10 +83,10 @@ def show_schema():
     This is mainly for development.
     """
     echo_header('Service Endpoint')
-    click.echo(to_json(ServiceEndpoint.schema()))
+    click.echo(to_json(ServiceEndpoint.model_json_schema()))
 
     echo_header('OAuth2 Authentication Information')
-    click.echo(to_json(OAuth2Authentication.schema()))
+    click.echo(to_json(OAuth2Authentication.model_json_schema()))
 
 
 @formatted_command(
@@ -109,7 +109,7 @@ def list_endpoints(context: Optional[str],
     handler = EndpointCommandHandler(context_name=context)
     full_type = handler.parse_given_service_type(short_or_full_type)[1] if short_or_full_type else None
     show_iterator(output_format=output, iterator=[
-        endpoint.dict(exclude_none=True)
+        endpoint.model_dump(exclude_none=True)
         for endpoint in handler.list_endpoints()
         if not full_type or endpoint.type == full_type
     ])
@@ -282,7 +282,7 @@ def unset_default(context: Optional[str],
 class EndpointCommandHandler:
     def __init__(self, context_name: Optional[str] = None):
         self.__logger = get_logger(type(self).__name__)
-        self.__schema: Dict[str, Any] = self.__resolve_json_reference(ServiceEndpoint.schema())
+        self.__schema: Dict[str, Any] = self.__resolve_json_reference(ServiceEndpoint.model_json_schema())
         self.__config_manager: ConfigurationManager = container.get(ConfigurationManager)
         self.__config = self.__config_manager.load()
         self.__context_name = context_name
@@ -446,7 +446,7 @@ class EndpointCommandHandler:
         raise None
 
     def __repair_path(self, obj, path: str, overridden_path_defaults: Dict[str, Any] = None):
-        overridden_path_defaults = overridden_path_defaults or dict()
+        overridden_path_defaults = overridden_path_defaults or {}
 
         selectors = path.split(r'.')
         visited = []
@@ -498,11 +498,11 @@ class EndpointCommandHandler:
         if hasattr(node, property_name) and getattr(node, property_name) is not None:
             return
         elif str(annotation).startswith('typing.Dict['):
-            setattr(node, property_name, dict())
+            setattr(node, property_name, {})
         elif str(annotation).startswith('typing.List['):
-            setattr(node, property_name, list())
+            setattr(node, property_name, [])
         elif issubclass(annotation, BaseModel):
-            required_properties = annotation.schema().get('required') or []
+            required_properties = annotation.model_json_schema().get('required') or []
             placeholders = {
                 p: self.__get_place_holder(annotation.__annotations__[p])
                 for p in required_properties
@@ -522,30 +522,49 @@ class EndpointCommandHandler:
             raise NotImplementedError(cls)
 
     def __list_all_json_path(self, obj: Dict[str, Any], prefix_path: List[str] = None) -> List[str]:
-        properties = obj.get('properties') or dict()
+        properties = obj.get('properties') or {}
         paths = []
 
-        prefix_path = prefix_path or list()
+        prefix_path = prefix_path or []
 
         if len(prefix_path) == 1 and prefix_path[0] == 'authentication':
             return [
                 f'{prefix_path[0]}.{oauth2_path}'
-                for oauth2_path in self.__list_all_json_path(OAuth2Authentication.schema())
+                for oauth2_path in self.__list_all_json_path(OAuth2Authentication.model_json_schema())
             ]
         else:
             if obj['type'] == 'object':
                 for property_name, obj_property in properties.items():
                     if 'anyOf' in obj_property:
+                        # In Pydantic v2, anyOf is used for Optional types
+                        # Check if there's a non-null type in anyOf
+                        has_ref_or_object = False
                         for property_to_resolve in obj_property['anyOf']:
-                            paths.extend(
-                                self.__list_all_json_path(
-                                    self.__fetch_json_reference(
-                                        property_to_resolve['$ref'],
-                                        self.__schema
-                                    ),
-                                    prefix_path + [property_name]
+                            if '$ref' in property_to_resolve:
+                                has_ref_or_object = True
+                                paths.extend(
+                                    self.__list_all_json_path(
+                                        self.__fetch_json_reference(
+                                            property_to_resolve['$ref'],
+                                            self.__schema
+                                        ),
+                                        prefix_path + [property_name]
+                                    )
                                 )
-                            )
+                            elif property_to_resolve.get('type') == 'object':
+                                has_ref_or_object = True
+                                # Handle inlined object schemas
+                                paths.extend(
+                                    self.__list_all_json_path(
+                                        property_to_resolve,
+                                        prefix_path + [property_name]
+                                    )
+                                )
+
+                        # If anyOf contains simple types (string, int, etc), treat as simple property
+                        if not has_ref_or_object:
+                            prefix_path_string = '.'.join(prefix_path)
+                            paths.append(f'{prefix_path_string}{"." if prefix_path_string else ""}{property_name}')
                     elif obj_property['type'] == 'object':
                         paths.extend(
                             self.__list_all_json_path(
@@ -574,7 +593,7 @@ class EndpointCommandHandler:
 
     def __resolve_json_reference(self, obj: Dict[str, Any], root: Optional[Dict[str, Any]] = None) -> Dict[str, Any]:
         root = root or obj
-        properties = obj.get('properties') or dict()
+        properties = obj.get('properties') or {}
         for property_name, obj_property in properties.items():
             if obj_property.get('$ref'):
                 properties[property_name] = self.__fetch_json_reference(obj_property.get('$ref'), root)

dnastack/cli/commands/config/registries.py

@@ -31,7 +31,7 @@ def registry_command_group():
 def list_registries():
     """ List registered service registries """
     click.echo(to_json([
-        endpoint.dict(exclude_none=True)
+        endpoint.model_dump(exclude_none=True)
         for endpoint in ServiceRegistryCommandHandler().get_registry_endpoint_iterator()
     ]))
 
@@ -126,7 +126,7 @@ def sync(registry_endpoint_id: str):
 def list_endpoints(registry_endpoint_id: str):
     """ List all service endpoints imported from given registry """
     click.echo(to_json([
-        endpoint.dict(exclude_none=True)
+        endpoint.model_dump(exclude_none=True)
         for endpoint in ServiceRegistryCommandHandler().list_endpoints_associated_to(registry_endpoint_id)
     ]))
 

dnastack/cli/commands/dataconnect/tables.py

@@ -70,5 +70,5 @@ def get_table_info(context: Optional[str],
                    no_auth: bool = False,
                    output: Optional[str] = None):
     """ Get info from the given table """
-    obj = _get(context=context, id=endpoint_id).table(table_name, no_auth=no_auth).info.dict()
+    obj = _get(context=context, id=endpoint_id).table(table_name, no_auth=no_auth).info.model_dump()
     click.echo((to_json if output == 'json' else to_yaml)(obj))

dnastack/cli/commands/drs/commands.py

@@ -119,7 +119,7 @@ def init_drs_commands(group: Group):
         drs.events.on('download-ok', display_ok)
         drs.events.on('download-failure', display_failure)
 
-        stats: Dict[str, DownloadProgressEvent] = dict()
+        stats: Dict[str, DownloadProgressEvent] = {}
 
         if not full_output:
             drs._download_files(id_or_urls=download_urls,

dnastack/cli/commands/explorer/questions/commands.py

@@ -43,7 +43,7 @@ def init_questions_commands(group: Group):
         show_iterator(
             output_format=output,
             iterator=questions,
-            transform=lambda q: q.dict()
+            transform=lambda q: q.model_dump()
         )
 
     @formatted_command(
@@ -71,7 +71,7 @@ def init_questions_commands(group: Group):
         show_iterator(
             output_format=output,
             iterator=[question],  # Single item as list
-            transform=lambda q: q.dict()
+            transform=lambda q: q.model_dump()
         )
 
     @formatted_command(
@@ -94,7 +94,8 @@ def init_questions_commands(group: Group):
             ArgumentSpec(
                 name='collections',
                 arg_names=['--collections'],
-                help='Comma-separated list of collection IDs to query (default: all collections for the question)'
+                type=JsonLike,
+                help='Comma-separated list of collection IDs to query, or @filename to read from file (default: all collections for the question)'
             ),
             ArgumentSpec(
                 name='output_file',
@@ -109,7 +110,7 @@ def init_questions_commands(group: Group):
     def ask_question(
         question_name: str,
         args: tuple,
-        collections: Optional[str],
+        collections: Optional[JsonLike],
         output_file: Optional[str],
         output: str,
         context: Optional[str],
@@ -118,9 +119,14 @@ def init_questions_commands(group: Group):
         """Ask a federated question with the provided parameters"""
         trace = Span()
         client = get_explorer_client(context=context, endpoint_id=endpoint_id, trace=trace)
-        
+
         # Parse collections if provided
-        collection_ids = parse_collections_argument(collections)
+        if collections:
+            # Handle JsonLike object - get the actual value (handles @ file reading)
+            collections_str = collections.value()
+            collection_ids = parse_collections_argument(collections_str)
+        else:
+            collection_ids = None
         
         # Parse arguments
         inputs = {}

dnastack/cli/commands/explorer/questions/utils.py

@@ -33,19 +33,28 @@ def get_explorer_client(context: Optional[str] = None,
 
 def parse_collections_argument(collections_str: Optional[str]) -> Optional[List[str]]:
     """
-    Parse a comma-separated collections string into a list.
-    
+    Parse a collections string into a list.
+    Handles both comma-separated and newline-separated formats.
+
     Args:
-        collections_str: Comma-separated collection IDs (e.g., "id1,id2,id3")
-        
+        collections_str: Collection IDs as either:
+                        - Comma-separated (e.g., "id1,id2,id3")
+                        - Newline-separated (one ID per line)
+
     Returns:
         List[str] or None: List of collection IDs or None if input is None/empty
     """
     if not collections_str:
         return None
-    
-    # Split by comma and strip whitespace
-    collections = [col.strip() for col in collections_str.split(',')]
+
+    # Check if it contains newlines (multiline file format)
+    if '\n' in collections_str:
+        # Split by newlines and strip whitespace
+        collections = [col.strip() for col in collections_str.split('\n')]
+    else:
+        # Split by comma and strip whitespace
+        collections = [col.strip() for col in collections_str.split(',')]
+
     # Filter out empty strings
     return [col for col in collections if col]
 

dnastack/cli/commands/publisher/collections/tables.py

@@ -58,4 +58,4 @@ def get_table_info(context: Optional[str],
     """ List all accessible tables """
     client = _switch_to_data_connect(_get_context(context), _get_collection_service_client(context, endpoint_id), collection, no_auth=no_auth)
     obj = client.table(table_name, no_auth=no_auth).info
-    click.echo((to_json if output == 'json' else to_yaml)(obj.dict()))
+    click.echo((to_json if output == 'json' else to_yaml)(obj.model_dump()))

dnastack/cli/commands/publisher/collections/utils.py

@@ -111,7 +111,7 @@ def _abort_with_collection_list(collection_service_client: CollectionServiceClie
 def _transform_to_public_collection(collection: Collection) -> Dict[str, Any]:
     return {
         field_name: value
-        for field_name, value in (collection.dict() if isinstance(collection, Collection) else collection).items()
+        for field_name, value in (collection.model_dump() if isinstance(collection, Collection) else collection).items()
         if field_name not in ['itemsQuery', 'accessTypeLabels']
     }
 

dnastack/cli/commands/publisher/datasources/commands.py

@@ -30,6 +30,6 @@ def init_datasources_commands(group: Group):
 
             show_iterator(output,
                         [
-                            _filter_datasource_fields(datasource.dict())
+                            _filter_datasource_fields(datasource.model_dump())
                             for datasource in response.connections
                         ])

dnastack/cli/commands/workbench/runs/commands.py

@@ -89,6 +89,12 @@ def init_runs_commands(group: Group):
                 arg_names=['--storage-account'],
                 help='Filter runs by the storage account ID. This will return runs that have outputs stored in the specified storage account.',
             ),
+            ArgumentSpec(
+                name='show_hidden',
+                arg_names=['--show-hidden'],
+                help='Include workflow runs with the visibility:hidden tag in the results. By default, hidden runs are excluded.',
+                type=bool,
+            ),
             NAMESPACE_ARG,
             CONTEXT_ARG,
             SINGLE_ENDPOINT_ID_ARG,
@@ -109,6 +115,7 @@ def init_runs_commands(group: Group):
                   tags: JsonLike,
                   samples: Optional[List[str]] = None,
                   storage_account_id: Optional[str] = None,
+                  show_hidden: Optional[bool] = False,
                   states: Optional[List[State]] = None):
         """
         List workflow runs
@@ -141,6 +148,7 @@ def init_runs_commands(group: Group):
             search=search,
             sample_ids=samples,
             storage_account_id=storage_account_id,
+            show_hidden=show_hidden,
             tag=tags
         )
         runs_list = client.list_runs(list_options, max_results)
@@ -608,7 +616,7 @@ def init_runs_commands(group: Group):
             default_workflow_engine_parameters=default_workflow_engine_parameters,
             default_workflow_params=default_workflow_params,
             default_tags=tags.parsed_value() if tags else None,
-            run_requests=list(),
+            run_requests=[],
             samples=parse_samples()
         )
 
@@ -626,12 +634,12 @@ def init_runs_commands(group: Group):
         override_data = parse_and_merge_arguments(input_overrides)
         if override_data:
             if not batch_request.default_workflow_params:
-                batch_request.default_workflow_params = dict()
+                batch_request.default_workflow_params = {}
             merge(batch_request.default_workflow_params, override_data)
 
             for run_request in batch_request.run_requests:
                 if not run_request.workflow_params:
-                    run_request.workflow_params = dict()
+                    run_request.workflow_params = {}
                 merge(run_request.workflow_params, override_data)
 
         if dry_run:

dnastack/cli/commands/workbench/samples/commands.py

@@ -174,7 +174,6 @@ def init_samples_commands(group: Group):
 
         if perspective == PerspectiveType.workflow and not workflow_id:
             raise click.UsageError('When perspective is set to "WORKFLOW", the workflow-id is required.')
-
         client = get_samples_client(context_name=context, endpoint_id=endpoint_id, namespace=namespace)
         list_options: SampleListOptions = SampleListOptions(
             page=page,
@@ -186,7 +185,7 @@ def init_samples_commands(group: Group):
             workflow_version_id=workflow_version_id,
             states=states,
             family_id=family_ids,
-            sample_id=sample_ids,
+            id=sample_ids,
             sexes=sexes,
             perspective=perspective,
             search=search,

dnastack/cli/commands/workbench/workflows/versions/dependencies/commands.py

@@ -151,7 +151,7 @@ def create(context: Optional[str] = None,
         admin_only_action=global_action
     )
 
-    click.echo(json.dumps(dependency.dict(), indent=2))
+    click.echo(json.dumps(dependency.model_dump(), indent=2))
 
 
 @formatted_command(
@@ -249,7 +249,7 @@ def describe(context: Optional[str] = None,
                     workflow_version_id=version_id,
                     dependency_id=dependency_id
                 )
-                dependencies.append(dependency.dict())
+                dependencies.append(dependency.model_dump())
             except Exception as e:
                 logger.error(f"Failed to get dependency {dependency_id}: {e}")
                 raise click.ClickException(f"Failed to get dependency {dependency_id}: {e}")
@@ -318,7 +318,7 @@ def update(context: Optional[str] = None,
             admin_only_action=global_action
         )
 
-        click.echo(json.dumps(dependency.dict(), indent=2))
+        click.echo(json.dumps(dependency.model_dump(), indent=2))
 
     except Exception as e:
         logger.error(f"Failed to update workflow dependency: {e}")

dnastack/cli/commands/workbench/workflows/versions/transformations.py

@@ -4,7 +4,7 @@ import click
 from click import style
 
 from dnastack.cli.commands.workbench.utils import NAMESPACE_ARG
-from dnastack.cli.commands.workbench.workflows.utils import get_workflow_client, JavaScriptFunctionExtractor
+from dnastack.cli.commands.workbench.workflows.utils import get_workflow_client
 from dnastack.cli.core.command import formatted_command
 from dnastack.cli.core.command_spec import ArgumentSpec, ArgumentType, CONTEXT_ARG, SINGLE_ENDPOINT_ID_ARG
 from dnastack.cli.core.group import formatted_group
@@ -12,6 +12,7 @@ from dnastack.cli.helpers.exporter import to_json, normalize
 from dnastack.cli.helpers.iterator_printer import show_iterator, OutputFormat
 from dnastack.client.workbench.workflow.models import WorkflowTransformationListOptions, \
     WorkflowTransformationCreate
+from dnastack.common.json_argument_parser import FileOrValue
 
 
 @formatted_group('transformations')
@@ -173,6 +174,7 @@ def delete_workflow_transformation(context: Optional[str],
                  ' You do not need to return the entire context object, only the parts that you want to modify. '
                  'Results of transformations are merged into the final context object. '
                  'The context object is a JSON object that contains the workflow parameters and other metadata.',
+            type=FileOrValue,
             required=True,
         ),
         ArgumentSpec(
@@ -214,23 +216,17 @@ def add_workflow_transformation(context: Optional[str],
                                 namespace: Optional[str],
                                 workflow_id: str,
                                 version_id: str,
-                                script: str,
+                                script: FileOrValue,
                                 transformation_id: Optional[str],
                                 next_transformation_id: Optional[str],
                                 labels: List[str]):
     """Create a new workflow transformation"""
     client = get_workflow_client(context_name=context, endpoint_id=endpoint_id, namespace=namespace)
 
-    if script.startswith("@"):
-        extractor = JavaScriptFunctionExtractor(script.split("@")[1])
-        script_content = extractor.extract_first_function()
-    else:
-        script_content = script
-
     workflow_transformation = WorkflowTransformationCreate(
         id=transformation_id,
         next_transformation_id=next_transformation_id,
-        script=script_content,
+        script=script.value(),
         labels=labels
     )
 

dnastack/cli/helpers/exporter.py

@@ -24,7 +24,7 @@ def normalize(content: Any, map_decimal: Type = str, sort_keys: bool = True) ->
     if isinstance(content, Decimal):
         return map_decimal(content)
     elif isinstance(content, BaseModel):
-        return normalize(content.dict(), map_decimal=map_decimal)
+        return normalize(content.model_dump(), map_decimal=map_decimal)
     elif isinstance(content, dict):
         # Handle a dictionary
         DEFAULT_WEIGHT = 99999

dnastack/client/base_exceptions.py

@@ -60,7 +60,7 @@ class DataConnectError(RuntimeError):
                  details: Any = None,
                  urls: Optional[List[str]] = None,
                  url: Optional[str] = None):
-        self.__urls = list()
+        self.__urls = []
         self.__status = response_status
         self.__summary = summary or details
         self.__details = details if self.__summary != details else None
@@ -99,4 +99,4 @@ class DataConnectError(RuntimeError):
                 for url in self.__urls:
                     blocks.append(f' → {url}')
 
-        return '\n'.join(blocks)
+        return '\n'.join(blocks)