diff --git a/api/tests/unit_tests/core/workflow/nodes/answer/test_answer.py b/api/tests/unit_tests/core/workflow/nodes/answer/test_answer.py
index 85ff4f9c05..1ef024f46b 100644
--- a/api/tests/unit_tests/core/workflow/nodes/answer/test_answer.py
+++ b/api/tests/unit_tests/core/workflow/nodes/answer/test_answer.py
@@ -58,21 +58,26 @@ def test_execute_answer():
     pool.add(["start", "weather"], "sunny")
     pool.add(["llm", "text"], "You are a helpful AI.")
 
+    node_config = {
+        "id": "answer",
+        "data": {
+            "title": "123",
+            "type": "answer",
+            "answer": "Today's weather is {{#start.weather#}}\n{{#llm.text#}}\n{{img}}\nFin.",
+        },
+    }
+
     node = AnswerNode(
         id=str(uuid.uuid4()),
         graph_init_params=init_params,
         graph=graph,
         graph_runtime_state=GraphRuntimeState(variable_pool=pool, start_at=time.perf_counter()),
-        config={
-            "id": "answer",
-            "data": {
-                "title": "123",
-                "type": "answer",
-                "answer": "Today's weather is {{#start.weather#}}\n{{#llm.text#}}\n{{img}}\nFin.",
-            },
-        },
+        config=node_config,
     )
 
+    # Initialize node data
+    node.init_node_data(node_config["data"])
+
     # Mock db.session.close()
     db.session.close = MagicMock()
 
diff --git a/api/tests/unit_tests/core/workflow/nodes/http_request/test_http_request_node.py b/api/tests/unit_tests/core/workflow/nodes/http_request/test_http_request_node.py
index 33f9251a72..71b3a8f7d8 100644
--- a/api/tests/unit_tests/core/workflow/nodes/http_request/test_http_request_node.py
+++ b/api/tests/unit_tests/core/workflow/nodes/http_request/test_http_request_node.py
@@ -57,12 +57,15 @@ def test_http_request_node_binary_file(monkeypatch):
             ),
         ),
     )
+
+    node_config = {
+        "id": "1",
+        "data": data.model_dump(),
+    }
+
     node = HttpRequestNode(
         id="1",
-        config={
-            "id": "1",
-            "data": data.model_dump(),
-        },
+        config=node_config,
         graph_init_params=GraphInitParams(
             tenant_id="1",
             app_id="1",
@@ -90,6 +93,9 @@ def test_http_request_node_binary_file(monkeypatch):
             start_at=0,
         ),
     )
+
+    # Initialize node data
+    node.init_node_data(node_config["data"])
     monkeypatch.setattr(
         "core.workflow.nodes.http_request.executor.file_manager.download",
         lambda *args, **kwargs: b"test",
@@ -145,12 +151,15 @@ def test_http_request_node_form_with_file(monkeypatch):
             ),
         ),
     )
+
+    node_config = {
+        "id": "1",
+        "data": data.model_dump(),
+    }
+
     node = HttpRequestNode(
         id="1",
-        config={
-            "id": "1",
-            "data": data.model_dump(),
-        },
+        config=node_config,
         graph_init_params=GraphInitParams(
             tenant_id="1",
             app_id="1",
@@ -178,6 +187,10 @@ def test_http_request_node_form_with_file(monkeypatch):
             start_at=0,
         ),
     )
+
+    # Initialize node data
+    node.init_node_data(node_config["data"])
+
     monkeypatch.setattr(
         "core.workflow.nodes.http_request.executor.file_manager.download",
         lambda *args, **kwargs: b"test",
@@ -257,12 +270,14 @@ def test_http_request_node_form_with_multiple_files(monkeypatch):
         ),
     )
 
+    node_config = {
+        "id": "1",
+        "data": data.model_dump(),
+    }
+
     node = HttpRequestNode(
         id="1",
-        config={
-            "id": "1",
-            "data": data.model_dump(),
-        },
+        config=node_config,
         graph_init_params=GraphInitParams(
             tenant_id="1",
             app_id="1",
@@ -291,6 +306,9 @@ def test_http_request_node_form_with_multiple_files(monkeypatch):
         ),
     )
 
+    # Initialize node data
+    node.init_node_data(node_config["data"])
+
     monkeypatch.setattr(
         "core.workflow.nodes.http_request.executor.file_manager.download",
         lambda file: b"test_image_data" if file.mime_type == "image/jpeg" else b"test_pdf_data",
diff --git a/api/tests/unit_tests/core/workflow/nodes/iteration/test_iteration.py b/api/tests/unit_tests/core/workflow/nodes/iteration/test_iteration.py
index 17c23b7735..787d4cb3ee 100644
--- a/api/tests/unit_tests/core/workflow/nodes/iteration/test_iteration.py
+++ b/api/tests/unit_tests/core/workflow/nodes/iteration/test_iteration.py
@@ -162,25 +162,30 @@ def test_run():
     )
     pool.add(["pe", "list_output"], ["dify-1", "dify-2"])
 
+    node_config = {
+        "data": {
+            "iterator_selector": ["pe", "list_output"],
+            "output_selector": ["tt", "output"],
+            "output_type": "array[string]",
+            "startNodeType": "template-transform",
+            "start_node_id": "tt",
+            "title": "迭代",
+            "type": "iteration",
+        },
+        "id": "iteration-1",
+    }
+
     iteration_node = IterationNode(
         id=str(uuid.uuid4()),
         graph_init_params=init_params,
         graph=graph,
         graph_runtime_state=GraphRuntimeState(variable_pool=pool, start_at=time.perf_counter()),
-        config={
-            "data": {
-                "iterator_selector": ["pe", "list_output"],
-                "output_selector": ["tt", "output"],
-                "output_type": "array[string]",
-                "startNodeType": "template-transform",
-                "start_node_id": "tt",
-                "title": "迭代",
-                "type": "iteration",
-            },
-            "id": "iteration-1",
-        },
+        config=node_config,
     )
 
+    # Initialize node data
+    iteration_node.init_node_data(node_config["data"])
+
     def tt_generator(self):
         return NodeRunResult(
             status=WorkflowNodeExecutionStatus.SUCCEEDED,
@@ -379,25 +384,30 @@ def test_run_parallel():
     )
     pool.add(["pe", "list_output"], ["dify-1", "dify-2"])
 
+    node_config = {
+        "data": {
+            "iterator_selector": ["pe", "list_output"],
+            "output_selector": ["tt", "output"],
+            "output_type": "array[string]",
+            "startNodeType": "template-transform",
+            "start_node_id": "iteration-start",
+            "title": "迭代",
+            "type": "iteration",
+        },
+        "id": "iteration-1",
+    }
+
     iteration_node = IterationNode(
         id=str(uuid.uuid4()),
         graph_init_params=init_params,
         graph=graph,
         graph_runtime_state=GraphRuntimeState(variable_pool=pool, start_at=time.perf_counter()),
-        config={
-            "data": {
-                "iterator_selector": ["pe", "list_output"],
-                "output_selector": ["tt", "output"],
-                "output_type": "array[string]",
-                "startNodeType": "template-transform",
-                "start_node_id": "iteration-start",
-                "title": "迭代",
-                "type": "iteration",
-            },
-            "id": "iteration-1",
-        },
+        config=node_config,
     )
 
+    # Initialize node data
+    iteration_node.init_node_data(node_config["data"])
+
     def tt_generator(self):
         return NodeRunResult(
             status=WorkflowNodeExecutionStatus.SUCCEEDED,
@@ -595,45 +605,55 @@ def test_iteration_run_in_parallel_mode():
     )
     pool.add(["pe", "list_output"], ["dify-1", "dify-2"])
 
+    parallel_node_config = {
+        "data": {
+            "iterator_selector": ["pe", "list_output"],
+            "output_selector": ["tt", "output"],
+            "output_type": "array[string]",
+            "startNodeType": "template-transform",
+            "start_node_id": "iteration-start",
+            "title": "迭代",
+            "type": "iteration",
+            "is_parallel": True,
+        },
+        "id": "iteration-1",
+    }
+
     parallel_iteration_node = IterationNode(
         id=str(uuid.uuid4()),
         graph_init_params=init_params,
         graph=graph,
         graph_runtime_state=GraphRuntimeState(variable_pool=pool, start_at=time.perf_counter()),
-        config={
-            "data": {
-                "iterator_selector": ["pe", "list_output"],
-                "output_selector": ["tt", "output"],
-                "output_type": "array[string]",
-                "startNodeType": "template-transform",
-                "start_node_id": "iteration-start",
-                "title": "迭代",
-                "type": "iteration",
-                "is_parallel": True,
-            },
-            "id": "iteration-1",
-        },
+        config=parallel_node_config,
     )
+
+    # Initialize node data
+    parallel_iteration_node.init_node_data(parallel_node_config["data"])
+    sequential_node_config = {
+        "data": {
+            "iterator_selector": ["pe", "list_output"],
+            "output_selector": ["tt", "output"],
+            "output_type": "array[string]",
+            "startNodeType": "template-transform",
+            "start_node_id": "iteration-start",
+            "title": "迭代",
+            "type": "iteration",
+            "is_parallel": True,
+        },
+        "id": "iteration-1",
+    }
+
     sequential_iteration_node = IterationNode(
         id=str(uuid.uuid4()),
         graph_init_params=init_params,
         graph=graph,
         graph_runtime_state=GraphRuntimeState(variable_pool=pool, start_at=time.perf_counter()),
-        config={
-            "data": {
-                "iterator_selector": ["pe", "list_output"],
-                "output_selector": ["tt", "output"],
-                "output_type": "array[string]",
-                "startNodeType": "template-transform",
-                "start_node_id": "iteration-start",
-                "title": "迭代",
-                "type": "iteration",
-                "is_parallel": True,
-            },
-            "id": "iteration-1",
-        },
+        config=sequential_node_config,
     )
 
+    # Initialize node data
+    sequential_iteration_node.init_node_data(sequential_node_config["data"])
+
     def tt_generator(self):
         return NodeRunResult(
             status=WorkflowNodeExecutionStatus.SUCCEEDED,
@@ -818,26 +838,31 @@ def test_iteration_run_error_handle():
         environment_variables=[],
     )
     pool.add(["pe", "list_output"], ["1", "1"])
+    error_node_config = {
+        "data": {
+            "iterator_selector": ["pe", "list_output"],
+            "output_selector": ["tt", "output"],
+            "output_type": "array[string]",
+            "startNodeType": "template-transform",
+            "start_node_id": "iteration-start",
+            "title": "iteration",
+            "type": "iteration",
+            "is_parallel": True,
+            "error_handle_mode": ErrorHandleMode.CONTINUE_ON_ERROR,
+        },
+        "id": "iteration-1",
+    }
+
     iteration_node = IterationNode(
         id=str(uuid.uuid4()),
         graph_init_params=init_params,
         graph=graph,
         graph_runtime_state=GraphRuntimeState(variable_pool=pool, start_at=time.perf_counter()),
-        config={
-            "data": {
-                "iterator_selector": ["pe", "list_output"],
-                "output_selector": ["tt", "output"],
-                "output_type": "array[string]",
-                "startNodeType": "template-transform",
-                "start_node_id": "iteration-start",
-                "title": "iteration",
-                "type": "iteration",
-                "is_parallel": True,
-                "error_handle_mode": ErrorHandleMode.CONTINUE_ON_ERROR,
-            },
-            "id": "iteration-1",
-        },
+        config=error_node_config,
     )
+
+    # Initialize node data
+    iteration_node.init_node_data(error_node_config["data"])
     # execute continue on error node
     result = iteration_node._run()
     result_arr = []
diff --git a/api/tests/unit_tests/core/workflow/nodes/llm/test_node.py b/api/tests/unit_tests/core/workflow/nodes/llm/test_node.py
index 42f3bffab1..23a7fab7cf 100644
--- a/api/tests/unit_tests/core/workflow/nodes/llm/test_node.py
+++ b/api/tests/unit_tests/core/workflow/nodes/llm/test_node.py
@@ -119,17 +119,20 @@ def llm_node(
     llm_node_data: LLMNodeData, graph_init_params: GraphInitParams, graph: Graph, graph_runtime_state: GraphRuntimeState
 ) -> LLMNode:
     mock_file_saver = mock.MagicMock(spec=LLMFileSaver)
+    node_config = {
+        "id": "1",
+        "data": llm_node_data.model_dump(),
+    }
     node = LLMNode(
         id="1",
-        config={
-            "id": "1",
-            "data": llm_node_data.model_dump(),
-        },
+        config=node_config,
         graph_init_params=graph_init_params,
         graph=graph,
         graph_runtime_state=graph_runtime_state,
         llm_file_saver=mock_file_saver,
     )
+    # Initialize node data
+    node.init_node_data(node_config["data"])
     return node
 
 
@@ -488,7 +491,7 @@ def test_handle_list_messages_basic(llm_node):
     variable_pool = llm_node.graph_runtime_state.variable_pool
     vision_detail_config = ImagePromptMessageContent.DETAIL.HIGH
 
-    result = llm_node._handle_list_messages(
+    result = llm_node.handle_list_messages(
         messages=messages,
         context=context,
         jinja2_variables=jinja2_variables,
@@ -506,17 +509,20 @@ def llm_node_for_multimodal(
     llm_node_data, graph_init_params, graph, graph_runtime_state
 ) -> tuple[LLMNode, LLMFileSaver]:
     mock_file_saver: LLMFileSaver = mock.MagicMock(spec=LLMFileSaver)
+    node_config = {
+        "id": "1",
+        "data": llm_node_data.model_dump(),
+    }
     node = LLMNode(
         id="1",
-        config={
-            "id": "1",
-            "data": llm_node_data.model_dump(),
-        },
+        config=node_config,
         graph_init_params=graph_init_params,
         graph=graph,
         graph_runtime_state=graph_runtime_state,
         llm_file_saver=mock_file_saver,
     )
+    # Initialize node data
+    node.init_node_data(node_config["data"])
     return node, mock_file_saver
 
 
@@ -544,6 +550,8 @@ class TestLLMNodeSaveMultiModalImageOutput:
             content=content,
             file_saver=mock_file_saver,
         )
+        # Manually append to _file_outputs since the static method doesn't do it
+        llm_node._file_outputs.append(file)
         assert llm_node._file_outputs == [mock_file]
         assert file == mock_file
         mock_file_saver.save_binary_string.assert_called_once_with(
@@ -573,6 +581,8 @@ class TestLLMNodeSaveMultiModalImageOutput:
             content=content,
             file_saver=mock_file_saver,
         )
+        # Manually append to _file_outputs since the static method doesn't do it
+        llm_node._file_outputs.append(file)
         assert llm_node._file_outputs == [mock_file]
         assert file == mock_file
         mock_file_saver.save_remote_url.assert_called_once_with(content.url, FileType.IMAGE)
@@ -588,7 +598,9 @@ def test_llm_node_image_file_to_markdown(llm_node: LLMNode):
 class TestSaveMultimodalOutputAndConvertResultToMarkdown:
     def test_str_content(self, llm_node_for_multimodal):
         llm_node, mock_file_saver = llm_node_for_multimodal
-        gen = llm_node._save_multimodal_output_and_convert_result_to_markdown("hello world")
+        gen = llm_node._save_multimodal_output_and_convert_result_to_markdown(
+            contents="hello world", file_saver=mock_file_saver, file_outputs=[]
+        )
         assert list(gen) == ["hello world"]
         mock_file_saver.save_binary_string.assert_not_called()
         mock_file_saver.save_remote_url.assert_not_called()
@@ -596,7 +608,7 @@ class TestSaveMultimodalOutputAndConvertResultToMarkdown:
     def test_text_prompt_message_content(self, llm_node_for_multimodal):
         llm_node, mock_file_saver = llm_node_for_multimodal
         gen = llm_node._save_multimodal_output_and_convert_result_to_markdown(
-            [TextPromptMessageContent(data="hello world")]
+            contents=[TextPromptMessageContent(data="hello world")], file_saver=mock_file_saver, file_outputs=[]
         )
         assert list(gen) == ["hello world"]
         mock_file_saver.save_binary_string.assert_not_called()
@@ -622,13 +634,15 @@ class TestSaveMultimodalOutputAndConvertResultToMarkdown:
         )
         mock_file_saver.save_binary_string.return_value = mock_saved_file
         gen = llm_node._save_multimodal_output_and_convert_result_to_markdown(
-            [
+            contents=[
                 ImagePromptMessageContent(
                     format="png",
                     base64_data=image_b64_data,
                     mime_type="image/png",
                 )
-            ]
+            ],
+            file_saver=mock_file_saver,
+            file_outputs=llm_node._file_outputs,
         )
         yielded_strs = list(gen)
         assert len(yielded_strs) == 1
@@ -651,21 +665,27 @@ class TestSaveMultimodalOutputAndConvertResultToMarkdown:
 
     def test_unknown_content_type(self, llm_node_for_multimodal):
         llm_node, mock_file_saver = llm_node_for_multimodal
-        gen = llm_node._save_multimodal_output_and_convert_result_to_markdown(frozenset(["hello world"]))
+        gen = llm_node._save_multimodal_output_and_convert_result_to_markdown(
+            contents=frozenset(["hello world"]), file_saver=mock_file_saver, file_outputs=[]
+        )
         assert list(gen) == ["frozenset({'hello world'})"]
         mock_file_saver.save_binary_string.assert_not_called()
         mock_file_saver.save_remote_url.assert_not_called()
 
     def test_unknown_item_type(self, llm_node_for_multimodal):
         llm_node, mock_file_saver = llm_node_for_multimodal
-        gen = llm_node._save_multimodal_output_and_convert_result_to_markdown([frozenset(["hello world"])])
+        gen = llm_node._save_multimodal_output_and_convert_result_to_markdown(
+            contents=[frozenset(["hello world"])], file_saver=mock_file_saver, file_outputs=[]
+        )
         assert list(gen) == ["frozenset({'hello world'})"]
         mock_file_saver.save_binary_string.assert_not_called()
         mock_file_saver.save_remote_url.assert_not_called()
 
     def test_none_content(self, llm_node_for_multimodal):
         llm_node, mock_file_saver = llm_node_for_multimodal
-        gen = llm_node._save_multimodal_output_and_convert_result_to_markdown(None)
+        gen = llm_node._save_multimodal_output_and_convert_result_to_markdown(
+            contents=None, file_saver=mock_file_saver, file_outputs=[]
+        )
         assert list(gen) == []
         mock_file_saver.save_binary_string.assert_not_called()
         mock_file_saver.save_remote_url.assert_not_called()
diff --git a/api/tests/unit_tests/core/workflow/nodes/test_answer.py b/api/tests/unit_tests/core/workflow/nodes/test_answer.py
index 44c31b212e..466d7bad06 100644
--- a/api/tests/unit_tests/core/workflow/nodes/test_answer.py
+++ b/api/tests/unit_tests/core/workflow/nodes/test_answer.py
@@ -61,21 +61,26 @@ def test_execute_answer():
     variable_pool.add(["start", "weather"], "sunny")
     variable_pool.add(["llm", "text"], "You are a helpful AI.")
 
+    node_config = {
+        "id": "answer",
+        "data": {
+            "title": "123",
+            "type": "answer",
+            "answer": "Today's weather is {{#start.weather#}}\n{{#llm.text#}}\n{{img}}\nFin.",
+        },
+    }
+
     node = AnswerNode(
         id=str(uuid.uuid4()),
         graph_init_params=init_params,
         graph=graph,
         graph_runtime_state=GraphRuntimeState(variable_pool=variable_pool, start_at=time.perf_counter()),
-        config={
-            "id": "answer",
-            "data": {
-                "title": "123",
-                "type": "answer",
-                "answer": "Today's weather is {{#start.weather#}}\n{{#llm.text#}}\n{{img}}\nFin.",
-            },
-        },
+        config=node_config,
     )
 
+    # Initialize node data
+    node.init_node_data(node_config["data"])
+
     # Mock db.session.close()
     db.session.close = MagicMock()
 
diff --git a/api/tests/unit_tests/core/workflow/nodes/test_document_extractor_node.py b/api/tests/unit_tests/core/workflow/nodes/test_document_extractor_node.py
index 66c7818adf..486ae51e5f 100644
--- a/api/tests/unit_tests/core/workflow/nodes/test_document_extractor_node.py
+++ b/api/tests/unit_tests/core/workflow/nodes/test_document_extractor_node.py
@@ -27,13 +27,17 @@ def document_extractor_node():
         title="Test Document Extractor",
         variable_selector=["node_id", "variable_name"],
     )
-    return DocumentExtractorNode(
+    node_config = {"id": "test_node_id", "data": node_data.model_dump()}
+    node = DocumentExtractorNode(
         id="test_node_id",
-        config={"id": "test_node_id", "data": node_data.model_dump()},
+        config=node_config,
         graph_init_params=Mock(),
         graph=Mock(),
         graph_runtime_state=Mock(),
     )
+    # Initialize node data
+    node.init_node_data(node_config["data"])
+    return node
 
 
 @pytest.fixture
diff --git a/api/tests/unit_tests/core/workflow/nodes/test_if_else.py b/api/tests/unit_tests/core/workflow/nodes/test_if_else.py
index 167a92484d..8383aee0e4 100644
--- a/api/tests/unit_tests/core/workflow/nodes/test_if_else.py
+++ b/api/tests/unit_tests/core/workflow/nodes/test_if_else.py
@@ -57,57 +57,62 @@ def test_execute_if_else_result_true():
     pool.add(["start", "null"], None)
     pool.add(["start", "not_null"], "1212")
 
+    node_config = {
+        "id": "if-else",
+        "data": {
+            "title": "123",
+            "type": "if-else",
+            "logical_operator": "and",
+            "conditions": [
+                {
+                    "comparison_operator": "contains",
+                    "variable_selector": ["start", "array_contains"],
+                    "value": "ab",
+                },
+                {
+                    "comparison_operator": "not contains",
+                    "variable_selector": ["start", "array_not_contains"],
+                    "value": "ab",
+                },
+                {"comparison_operator": "contains", "variable_selector": ["start", "contains"], "value": "ab"},
+                {
+                    "comparison_operator": "not contains",
+                    "variable_selector": ["start", "not_contains"],
+                    "value": "ab",
+                },
+                {"comparison_operator": "start with", "variable_selector": ["start", "start_with"], "value": "ab"},
+                {"comparison_operator": "end with", "variable_selector": ["start", "end_with"], "value": "ab"},
+                {"comparison_operator": "is", "variable_selector": ["start", "is"], "value": "ab"},
+                {"comparison_operator": "is not", "variable_selector": ["start", "is_not"], "value": "ab"},
+                {"comparison_operator": "empty", "variable_selector": ["start", "empty"], "value": "ab"},
+                {"comparison_operator": "not empty", "variable_selector": ["start", "not_empty"], "value": "ab"},
+                {"comparison_operator": "=", "variable_selector": ["start", "equals"], "value": "22"},
+                {"comparison_operator": "≠", "variable_selector": ["start", "not_equals"], "value": "22"},
+                {"comparison_operator": ">", "variable_selector": ["start", "greater_than"], "value": "22"},
+                {"comparison_operator": "<", "variable_selector": ["start", "less_than"], "value": "22"},
+                {
+                    "comparison_operator": "≥",
+                    "variable_selector": ["start", "greater_than_or_equal"],
+                    "value": "22",
+                },
+                {"comparison_operator": "≤", "variable_selector": ["start", "less_than_or_equal"], "value": "22"},
+                {"comparison_operator": "null", "variable_selector": ["start", "null"]},
+                {"comparison_operator": "not null", "variable_selector": ["start", "not_null"]},
+            ],
+        },
+    }
+
     node = IfElseNode(
         id=str(uuid.uuid4()),
         graph_init_params=init_params,
         graph=graph,
         graph_runtime_state=GraphRuntimeState(variable_pool=pool, start_at=time.perf_counter()),
-        config={
-            "id": "if-else",
-            "data": {
-                "title": "123",
-                "type": "if-else",
-                "logical_operator": "and",
-                "conditions": [
-                    {
-                        "comparison_operator": "contains",
-                        "variable_selector": ["start", "array_contains"],
-                        "value": "ab",
-                    },
-                    {
-                        "comparison_operator": "not contains",
-                        "variable_selector": ["start", "array_not_contains"],
-                        "value": "ab",
-                    },
-                    {"comparison_operator": "contains", "variable_selector": ["start", "contains"], "value": "ab"},
-                    {
-                        "comparison_operator": "not contains",
-                        "variable_selector": ["start", "not_contains"],
-                        "value": "ab",
-                    },
-                    {"comparison_operator": "start with", "variable_selector": ["start", "start_with"], "value": "ab"},
-                    {"comparison_operator": "end with", "variable_selector": ["start", "end_with"], "value": "ab"},
-                    {"comparison_operator": "is", "variable_selector": ["start", "is"], "value": "ab"},
-                    {"comparison_operator": "is not", "variable_selector": ["start", "is_not"], "value": "ab"},
-                    {"comparison_operator": "empty", "variable_selector": ["start", "empty"], "value": "ab"},
-                    {"comparison_operator": "not empty", "variable_selector": ["start", "not_empty"], "value": "ab"},
-                    {"comparison_operator": "=", "variable_selector": ["start", "equals"], "value": "22"},
-                    {"comparison_operator": "≠", "variable_selector": ["start", "not_equals"], "value": "22"},
-                    {"comparison_operator": ">", "variable_selector": ["start", "greater_than"], "value": "22"},
-                    {"comparison_operator": "<", "variable_selector": ["start", "less_than"], "value": "22"},
-                    {
-                        "comparison_operator": "≥",
-                        "variable_selector": ["start", "greater_than_or_equal"],
-                        "value": "22",
-                    },
-                    {"comparison_operator": "≤", "variable_selector": ["start", "less_than_or_equal"], "value": "22"},
-                    {"comparison_operator": "null", "variable_selector": ["start", "null"]},
-                    {"comparison_operator": "not null", "variable_selector": ["start", "not_null"]},
-                ],
-            },
-        },
+        config=node_config,
     )
 
+    # Initialize node data
+    node.init_node_data(node_config["data"])
+
     # Mock db.session.close()
     db.session.close = MagicMock()
 
@@ -162,33 +167,38 @@ def test_execute_if_else_result_false():
     pool.add(["start", "array_contains"], ["1ab", "def"])
     pool.add(["start", "array_not_contains"], ["ab", "def"])
 
+    node_config = {
+        "id": "if-else",
+        "data": {
+            "title": "123",
+            "type": "if-else",
+            "logical_operator": "or",
+            "conditions": [
+                {
+                    "comparison_operator": "contains",
+                    "variable_selector": ["start", "array_contains"],
+                    "value": "ab",
+                },
+                {
+                    "comparison_operator": "not contains",
+                    "variable_selector": ["start", "array_not_contains"],
+                    "value": "ab",
+                },
+            ],
+        },
+    }
+
     node = IfElseNode(
         id=str(uuid.uuid4()),
         graph_init_params=init_params,
         graph=graph,
         graph_runtime_state=GraphRuntimeState(variable_pool=pool, start_at=time.perf_counter()),
-        config={
-            "id": "if-else",
-            "data": {
-                "title": "123",
-                "type": "if-else",
-                "logical_operator": "or",
-                "conditions": [
-                    {
-                        "comparison_operator": "contains",
-                        "variable_selector": ["start", "array_contains"],
-                        "value": "ab",
-                    },
-                    {
-                        "comparison_operator": "not contains",
-                        "variable_selector": ["start", "array_not_contains"],
-                        "value": "ab",
-                    },
-                ],
-            },
-        },
+        config=node_config,
     )
 
+    # Initialize node data
+    node.init_node_data(node_config["data"])
+
     # Mock db.session.close()
     db.session.close = MagicMock()
 
@@ -228,17 +238,22 @@ def test_array_file_contains_file_name():
         ],
     )
 
+    node_config = {
+        "id": "if-else",
+        "data": node_data.model_dump(),
+    }
+
     node = IfElseNode(
         id=str(uuid.uuid4()),
         graph_init_params=Mock(),
         graph=Mock(),
         graph_runtime_state=Mock(),
-        config={
-            "id": "if-else",
-            "data": node_data.model_dump(),
-        },
+        config=node_config,
     )
 
+    # Initialize node data
+    node.init_node_data(node_config["data"])
+
     node.graph_runtime_state.variable_pool.get.return_value = ArrayFileSegment(
         value=[
             File(
diff --git a/api/tests/unit_tests/core/workflow/nodes/test_list_operator.py b/api/tests/unit_tests/core/workflow/nodes/test_list_operator.py
index 7d3a1d6a2d..5fc9eab2df 100644
--- a/api/tests/unit_tests/core/workflow/nodes/test_list_operator.py
+++ b/api/tests/unit_tests/core/workflow/nodes/test_list_operator.py
@@ -33,16 +33,19 @@ def list_operator_node():
         "title": "Test Title",
     }
     node_data = ListOperatorNodeData(**config)
+    node_config = {
+        "id": "test_node_id",
+        "data": node_data.model_dump(),
+    }
     node = ListOperatorNode(
         id="test_node_id",
-        config={
-            "id": "test_node_id",
-            "data": node_data.model_dump(),
-        },
+        config=node_config,
         graph_init_params=MagicMock(),
         graph=MagicMock(),
         graph_runtime_state=MagicMock(),
     )
+    # Initialize node data
+    node.init_node_data(node_config["data"])
     node.graph_runtime_state = MagicMock()
     node.graph_runtime_state.variable_pool = MagicMock()
     return node
diff --git a/api/tests/unit_tests/core/workflow/nodes/tool/test_tool_node.py b/api/tests/unit_tests/core/workflow/nodes/tool/test_tool_node.py
index 2776e57777..0eaabd0c40 100644
--- a/api/tests/unit_tests/core/workflow/nodes/tool/test_tool_node.py
+++ b/api/tests/unit_tests/core/workflow/nodes/tool/test_tool_node.py
@@ -38,12 +38,13 @@ def _create_tool_node():
         system_variables=SystemVariable.empty(),
         user_inputs={},
     )
+    node_config = {
+        "id": "1",
+        "data": data.model_dump(),
+    }
     node = ToolNode(
         id="1",
-        config={
-            "id": "1",
-            "data": data.model_dump(),
-        },
+        config=node_config,
         graph_init_params=GraphInitParams(
             tenant_id="1",
             app_id="1",
@@ -71,6 +72,8 @@ def _create_tool_node():
             start_at=0,
         ),
     )
+    # Initialize node data
+    node.init_node_data(node_config["data"])
     return node
 
 
diff --git a/api/tests/unit_tests/core/workflow/nodes/variable_assigner/v1/test_variable_assigner_v1.py b/api/tests/unit_tests/core/workflow/nodes/variable_assigner/v1/test_variable_assigner_v1.py
index 62e3e37104..ee51339427 100644
--- a/api/tests/unit_tests/core/workflow/nodes/variable_assigner/v1/test_variable_assigner_v1.py
+++ b/api/tests/unit_tests/core/workflow/nodes/variable_assigner/v1/test_variable_assigner_v1.py
@@ -82,23 +82,28 @@ def test_overwrite_string_variable():
     mock_conv_var_updater = mock.Mock(spec=ConversationVariableUpdater)
     mock_conv_var_updater_factory = mock.Mock(return_value=mock_conv_var_updater)
 
+    node_config = {
+        "id": "node_id",
+        "data": {
+            "title": "test",
+            "assigned_variable_selector": ["conversation", conversation_variable.name],
+            "write_mode": WriteMode.OVER_WRITE.value,
+            "input_variable_selector": [DEFAULT_NODE_ID, input_variable.name],
+        },
+    }
+
     node = VariableAssignerNode(
         id=str(uuid.uuid4()),
         graph_init_params=init_params,
         graph=graph,
         graph_runtime_state=GraphRuntimeState(variable_pool=variable_pool, start_at=time.perf_counter()),
-        config={
-            "id": "node_id",
-            "data": {
-                "title": "test",
-                "assigned_variable_selector": ["conversation", conversation_variable.name],
-                "write_mode": WriteMode.OVER_WRITE.value,
-                "input_variable_selector": [DEFAULT_NODE_ID, input_variable.name],
-            },
-        },
+        config=node_config,
         conv_var_updater_factory=mock_conv_var_updater_factory,
     )
 
+    # Initialize node data
+    node.init_node_data(node_config["data"])
+
     list(node.run())
     expected_var = StringVariable(
         id=conversation_variable.id,
@@ -178,23 +183,28 @@ def test_append_variable_to_array():
     mock_conv_var_updater = mock.Mock(spec=ConversationVariableUpdater)
     mock_conv_var_updater_factory = mock.Mock(return_value=mock_conv_var_updater)
 
+    node_config = {
+        "id": "node_id",
+        "data": {
+            "title": "test",
+            "assigned_variable_selector": ["conversation", conversation_variable.name],
+            "write_mode": WriteMode.APPEND.value,
+            "input_variable_selector": [DEFAULT_NODE_ID, input_variable.name],
+        },
+    }
+
     node = VariableAssignerNode(
         id=str(uuid.uuid4()),
         graph_init_params=init_params,
         graph=graph,
         graph_runtime_state=GraphRuntimeState(variable_pool=variable_pool, start_at=time.perf_counter()),
-        config={
-            "id": "node_id",
-            "data": {
-                "title": "test",
-                "assigned_variable_selector": ["conversation", conversation_variable.name],
-                "write_mode": WriteMode.APPEND.value,
-                "input_variable_selector": [DEFAULT_NODE_ID, input_variable.name],
-            },
-        },
+        config=node_config,
         conv_var_updater_factory=mock_conv_var_updater_factory,
     )
 
+    # Initialize node data
+    node.init_node_data(node_config["data"])
+
     list(node.run())
     expected_value = list(conversation_variable.value)
     expected_value.append(input_variable.value)
@@ -265,23 +275,28 @@ def test_clear_array():
     mock_conv_var_updater = mock.Mock(spec=ConversationVariableUpdater)
     mock_conv_var_updater_factory = mock.Mock(return_value=mock_conv_var_updater)
 
+    node_config = {
+        "id": "node_id",
+        "data": {
+            "title": "test",
+            "assigned_variable_selector": ["conversation", conversation_variable.name],
+            "write_mode": WriteMode.CLEAR.value,
+            "input_variable_selector": [],
+        },
+    }
+
     node = VariableAssignerNode(
         id=str(uuid.uuid4()),
         graph_init_params=init_params,
         graph=graph,
         graph_runtime_state=GraphRuntimeState(variable_pool=variable_pool, start_at=time.perf_counter()),
-        config={
-            "id": "node_id",
-            "data": {
-                "title": "test",
-                "assigned_variable_selector": ["conversation", conversation_variable.name],
-                "write_mode": WriteMode.CLEAR.value,
-                "input_variable_selector": [],
-            },
-        },
+        config=node_config,
         conv_var_updater_factory=mock_conv_var_updater_factory,
     )
 
+    # Initialize node data
+    node.init_node_data(node_config["data"])
+
     list(node.run())
     expected_var = ArrayStringVariable(
         id=conversation_variable.id,
diff --git a/api/tests/unit_tests/core/workflow/nodes/variable_assigner/v2/test_variable_assigner_v2.py b/api/tests/unit_tests/core/workflow/nodes/variable_assigner/v2/test_variable_assigner_v2.py
index a3a90b0599..987eaf7534 100644
--- a/api/tests/unit_tests/core/workflow/nodes/variable_assigner/v2/test_variable_assigner_v2.py
+++ b/api/tests/unit_tests/core/workflow/nodes/variable_assigner/v2/test_variable_assigner_v2.py
@@ -115,28 +115,33 @@ def test_remove_first_from_array():
         conversation_variables=[conversation_variable],
     )
 
+    node_config = {
+        "id": "node_id",
+        "data": {
+            "title": "test",
+            "version": "2",
+            "items": [
+                {
+                    "variable_selector": ["conversation", conversation_variable.name],
+                    "input_type": InputType.VARIABLE,
+                    "operation": Operation.REMOVE_FIRST,
+                    "value": None,
+                }
+            ],
+        },
+    }
+
     node = VariableAssignerNode(
         id=str(uuid.uuid4()),
         graph_init_params=init_params,
         graph=graph,
         graph_runtime_state=GraphRuntimeState(variable_pool=variable_pool, start_at=time.perf_counter()),
-        config={
-            "id": "node_id",
-            "data": {
-                "title": "test",
-                "version": "2",
-                "items": [
-                    {
-                        "variable_selector": ["conversation", conversation_variable.name],
-                        "input_type": InputType.VARIABLE,
-                        "operation": Operation.REMOVE_FIRST,
-                        "value": None,
-                    }
-                ],
-            },
-        },
+        config=node_config,
     )
 
+    # Initialize node data
+    node.init_node_data(node_config["data"])
+
     # Skip the mock assertion since we're in a test environment
     # Print the variable before running
     print(f"Before: {variable_pool.get(['conversation', conversation_variable.name]).to_object()}")
@@ -202,28 +207,33 @@ def test_remove_last_from_array():
         conversation_variables=[conversation_variable],
     )
 
+    node_config = {
+        "id": "node_id",
+        "data": {
+            "title": "test",
+            "version": "2",
+            "items": [
+                {
+                    "variable_selector": ["conversation", conversation_variable.name],
+                    "input_type": InputType.VARIABLE,
+                    "operation": Operation.REMOVE_LAST,
+                    "value": None,
+                }
+            ],
+        },
+    }
+
     node = VariableAssignerNode(
         id=str(uuid.uuid4()),
         graph_init_params=init_params,
         graph=graph,
         graph_runtime_state=GraphRuntimeState(variable_pool=variable_pool, start_at=time.perf_counter()),
-        config={
-            "id": "node_id",
-            "data": {
-                "title": "test",
-                "version": "2",
-                "items": [
-                    {
-                        "variable_selector": ["conversation", conversation_variable.name],
-                        "input_type": InputType.VARIABLE,
-                        "operation": Operation.REMOVE_LAST,
-                        "value": None,
-                    }
-                ],
-            },
-        },
+        config=node_config,
     )
 
+    # Initialize node data
+    node.init_node_data(node_config["data"])
+
     # Skip the mock assertion since we're in a test environment
     list(node.run())
 
@@ -281,28 +291,33 @@ def test_remove_first_from_empty_array():
         conversation_variables=[conversation_variable],
     )
 
+    node_config = {
+        "id": "node_id",
+        "data": {
+            "title": "test",
+            "version": "2",
+            "items": [
+                {
+                    "variable_selector": ["conversation", conversation_variable.name],
+                    "input_type": InputType.VARIABLE,
+                    "operation": Operation.REMOVE_FIRST,
+                    "value": None,
+                }
+            ],
+        },
+    }
+
     node = VariableAssignerNode(
         id=str(uuid.uuid4()),
         graph_init_params=init_params,
         graph=graph,
         graph_runtime_state=GraphRuntimeState(variable_pool=variable_pool, start_at=time.perf_counter()),
-        config={
-            "id": "node_id",
-            "data": {
-                "title": "test",
-                "version": "2",
-                "items": [
-                    {
-                        "variable_selector": ["conversation", conversation_variable.name],
-                        "input_type": InputType.VARIABLE,
-                        "operation": Operation.REMOVE_FIRST,
-                        "value": None,
-                    }
-                ],
-            },
-        },
+        config=node_config,
     )
 
+    # Initialize node data
+    node.init_node_data(node_config["data"])
+
     # Skip the mock assertion since we're in a test environment
     list(node.run())
 
@@ -360,28 +375,33 @@ def test_remove_last_from_empty_array():
         conversation_variables=[conversation_variable],
     )
 
+    node_config = {
+        "id": "node_id",
+        "data": {
+            "title": "test",
+            "version": "2",
+            "items": [
+                {
+                    "variable_selector": ["conversation", conversation_variable.name],
+                    "input_type": InputType.VARIABLE,
+                    "operation": Operation.REMOVE_LAST,
+                    "value": None,
+                }
+            ],
+        },
+    }
+
     node = VariableAssignerNode(
         id=str(uuid.uuid4()),
         graph_init_params=init_params,
         graph=graph,
         graph_runtime_state=GraphRuntimeState(variable_pool=variable_pool, start_at=time.perf_counter()),
-        config={
-            "id": "node_id",
-            "data": {
-                "title": "test",
-                "version": "2",
-                "items": [
-                    {
-                        "variable_selector": ["conversation", conversation_variable.name],
-                        "input_type": InputType.VARIABLE,
-                        "operation": Operation.REMOVE_LAST,
-                        "value": None,
-                    }
-                ],
-            },
-        },
+        config=node_config,
     )
 
+    # Initialize node data
+    node.init_node_data(node_config["data"])
+
     # Skip the mock assertion since we're in a test environment
     list(node.run())