Changes Neo4j add_edge method and implements unit tests around get_graph_from_model logic #474
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WalkthroughThis pull request focuses on removing the Changes
Sequence DiagramsequenceDiagram
participant API as Cognify API
participant Tasks as Add Data Points Task
participant GraphUtils as Graph Utilities
participant Database as Neo4j Database
API->>Tasks: Invoke add_data_points
Tasks->>GraphUtils: Get graph from model
GraphUtils-->>Tasks: Return graph nodes and edges
Tasks->>Database: Add nodes and edges
Database-->>Tasks: Confirm addition
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Actionable comments posted: 1
🧹 Nitpick comments (2)
cognee/infrastructure/databases/graph/neo4j_driver/adapter.py (1)
208-221: Consider indexing for performance when usingMATCHwithUNWIND.These lines create or merge a large number of relationships via
apoc.merge.relationship. Ifedge.from_nodeandedge.to_nodefields are not indexed in Neo4j, the repeatedMATCH (from_node {id: edge.from_node})andMATCH (to_node {id: edge.to_node})operations underUNWINDcould degrade performance for large lists of edges. Ensuring proper indexing on theidproperty will help optimize these queries.cognee/tests/unit/interfaces/graph/get_graph_from_model_unit_tests.py (1)
8-8: Remove unused import.The
is_typeimport fromIPython.utils.wildcardis not used in any of the test cases.-from IPython.utils.wildcard import is_type
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📒 Files selected for processing (5)
cognee/api/v1/cognify/cognify_v2.py(1 hunks)cognee/infrastructure/databases/graph/neo4j_driver/adapter.py(1 hunks)cognee/modules/graph/utils/get_graph_from_model.py(1 hunks)cognee/tasks/storage/add_data_points.py(1 hunks)cognee/tests/unit/interfaces/graph/get_graph_from_model_unit_tests.py(1 hunks)
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🔇 Additional comments (7)
cognee/infrastructure/databases/graph/neo4j_driver/adapter.py (1)
208-221: Verify the newapoc.merge.relationshiplogic.Previously, if this code used
apoc.create.relationship, changing it toapoc.merge.relationshipcan alter behavior for existing relationships. Specifically,apoc.merge.relationshipwill merge properties on any matched relationship, rather than creating duplicates. If this is intentional (avoiding duplicates), it’s a beneficial move; otherwise, re-check whether you prefer always creating new relationships vs. merging.cognee/tasks/storage/add_data_points.py (1)
8-8: Confirm backward compatibility after removingonly_root.Removing the
only_rootparameter fromadd_data_pointsmay affect code depending on that argument. If any callers passonly_rootor expect root-only behavior, this could introduce unexpected runtime errors or logic changes. Double-check all call sites to confirm they do not rely on that parameter.cognee/modules/graph/utils/get_graph_from_model.py (1)
100-100: Validate thatfield_valuealways has anidattribute.At line 100, the check depends on
field_value.id. Ensure thatfield_valueis indeed a DataPoint or a compatible type with theidattribute. If not, this code could raise runtime errors or skip creating nodes for valid objects. Consider adding input validations or type hints to make assumptions explicit.As a follow-up, you can run a script to confirm that all
field_valueinstances passed here areDataPointor subtypes:✅ Verification successful
The code already validates that
field_valuehas anidattributeThe implementation includes proper type checking through
isinstance(field_value, DataPoint)before accessing theidattribute, ensuring type safety at runtime. This validation prevents any potential attribute errors.🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Use ast-grep to find calls to get_graph_from_model and examine argument types. ast-grep --pattern $'await get_graph_from_model($_, $$$)'Length of output: 2472
Script:
#!/bin/bash # Get function definition and surrounding context ast-grep --pattern 'async def get_graph_from_model($$$)' -A 10 # Get context around the id access rg "field_value.id" -B 5 -A 5 # Get test setup to see field_value types rg "field_value.*=|data_point.*=" cognee/tests/unit/interfaces/graph/get_graph_from_model_unit_tests.py -B 2 -A 2Length of output: 5531
cognee/api/v1/cognify/cognify_v2.py (1)
163-163: Verify the impact of removingonly_rootparameter.The removal of
only_root=Truefrom theadd_data_pointstask configuration aligns with the broader refactoring effort. However, we should ensure this change doesn't affect the existing data processing behavior.Run the following script to check for any remaining usages of
only_rootin the task configuration and related files:✅ Verification successful
Removal of
only_rootparameter is safeThe parameter has been consistently removed across all task configurations in the codebase, and all similar tasks follow the same pattern without using this parameter. The change aligns with the broader refactoring effort and maintains consistency with other pipeline configurations.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Search for any remaining references to only_root in task configurations and related files rg -g '!*.pyc' -g '!*test*' 'only_root' .Length of output: 41
Script:
#!/bin/bash # Find Task class definition and similar configurations echo "=== Searching for Task class definition ===" ast-grep --pattern 'class Task' echo -e "\n=== Searching for task configurations ===" rg -g '!*.pyc' -g '!*test*' 'Task\(' -A 2Length of output: 6869
cognee/tests/unit/interfaces/graph/get_graph_from_model_unit_tests.py (3)
17-32: LGTM! Well-structured test case.The basic initialization test is well-organized with clear setup, execution, and assertions. The docstring effectively describes the test's purpose.
34-62: LGTM! Comprehensive test for single neighbor relationship.The test effectively validates both node creation and edge formation for a simple entity-type relationship.
64-121: LGTM! Thorough test for complex nested relationships.The test comprehensively covers multiple aspects:
- Multiple entity nodes with shared type
- Document and chunk relationships
- Multiple edge types (is_a, is_part_of, contains)
| @pytest.mark.asyncio | ||
| async def test_get_graph_from_model_only_root(): | ||
| """Test the behavior of get_graph_from_model when the 'only_root' option is set to True.""" | ||
| type_node = EntityType( | ||
| id=uuid4(), | ||
| name="Vehicle", | ||
| description="This is a Vehicle node", | ||
| ) | ||
|
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||
| entity_node = Entity( | ||
| id=uuid4(), | ||
| name="Car", | ||
| is_a=type_node, | ||
| description="This is a car node", | ||
| ) | ||
|
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||
| document = Document( | ||
| name="main_document", raw_data_location="home/", metadata_id=uuid4(), mime_type="test" | ||
| ) | ||
|
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| chunk = DocumentChunk( | ||
| id=uuid4(), | ||
| word_count=8, | ||
| chunk_index=0, | ||
| cut_type="test", | ||
| text="The car and the bus are transportation tools", | ||
| is_part_of=document, | ||
| contains=[entity_node], | ||
| ) | ||
|
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||
| added_nodes = {} | ||
| added_edges = {} | ||
| visited_properties = {} | ||
|
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| nodes, edges = await get_graph_from_model( | ||
| chunk, added_nodes, added_edges, visited_properties, only_root=True | ||
| ) | ||
|
|
||
| # assert len(nodes) == 1 :TODO THIS HAS TO BE FINISHED | ||
| # assert len(edges) == 0 | ||
| # assert str(entity_node.id) in added_nodes | ||
| # assert str(type_node.id) not in added_nodes |
There was a problem hiding this comment.
Remove or update the incomplete test case.
Since the only_root parameter is being removed from the codebase (as evidenced by changes in cognify_v2.py and other files), this test case should either be:
- Removed entirely as it's testing deprecated functionality, or
- Updated to test the new behavior without the
only_rootparameter
If you choose to keep the test, here's how to update it:
-async def test_get_graph_from_model_only_root():
- """Test the behavior of get_graph_from_model when the 'only_root' option is set to True."""
+async def test_get_graph_from_model_with_document_chunk():
+ """Test the behavior of get_graph_from_model with a document chunk containing an entity."""
# ... (keep the setup code) ...
nodes, edges = await get_graph_from_model(
- chunk, added_nodes, added_edges, visited_properties, only_root=True
+ chunk, added_nodes, added_edges, visited_properties
)
- # assert len(nodes) == 1 :TODO THIS HAS TO BE FINISHED
- # assert len(edges) == 0
- # assert str(entity_node.id) in added_nodes
- # assert str(type_node.id) not in added_nodes
+ assert len(nodes) == 4 # chunk, document, entity, and type nodes
+ assert len(edges) == 3 # is_part_of, contains, and is_a edges
+ assert str(chunk.id) in added_nodes
+ assert str(document.id) in added_nodes
+ assert str(entity_node.id) in added_nodes
+ assert str(type_node.id) in added_nodes📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| @pytest.mark.asyncio | |
| async def test_get_graph_from_model_only_root(): | |
| """Test the behavior of get_graph_from_model when the 'only_root' option is set to True.""" | |
| type_node = EntityType( | |
| id=uuid4(), | |
| name="Vehicle", | |
| description="This is a Vehicle node", | |
| ) | |
| entity_node = Entity( | |
| id=uuid4(), | |
| name="Car", | |
| is_a=type_node, | |
| description="This is a car node", | |
| ) | |
| document = Document( | |
| name="main_document", raw_data_location="home/", metadata_id=uuid4(), mime_type="test" | |
| ) | |
| chunk = DocumentChunk( | |
| id=uuid4(), | |
| word_count=8, | |
| chunk_index=0, | |
| cut_type="test", | |
| text="The car and the bus are transportation tools", | |
| is_part_of=document, | |
| contains=[entity_node], | |
| ) | |
| added_nodes = {} | |
| added_edges = {} | |
| visited_properties = {} | |
| nodes, edges = await get_graph_from_model( | |
| chunk, added_nodes, added_edges, visited_properties, only_root=True | |
| ) | |
| # assert len(nodes) == 1 :TODO THIS HAS TO BE FINISHED | |
| # assert len(edges) == 0 | |
| # assert str(entity_node.id) in added_nodes | |
| # assert str(type_node.id) not in added_nodes | |
| @pytest.mark.asyncio | |
| async def test_get_graph_from_model_with_document_chunk(): | |
| """Test the behavior of get_graph_from_model with a document chunk containing an entity.""" | |
| type_node = EntityType( | |
| id=uuid4(), | |
| name="Vehicle", | |
| description="This is a Vehicle node", | |
| ) | |
| entity_node = Entity( | |
| id=uuid4(), | |
| name="Car", | |
| is_a=type_node, | |
| description="This is a car node", | |
| ) | |
| document = Document( | |
| name="main_document", raw_data_location="home/", metadata_id=uuid4(), mime_type="test" | |
| ) | |
| chunk = DocumentChunk( | |
| id=uuid4(), | |
| word_count=8, | |
| chunk_index=0, | |
| cut_type="test", | |
| text="The car and the bus are transportation tools", | |
| is_part_of=document, | |
| contains=[entity_node], | |
| ) | |
| added_nodes = {} | |
| added_edges = {} | |
| visited_properties = {} | |
| nodes, edges = await get_graph_from_model( | |
| chunk, added_nodes, added_edges, visited_properties | |
| ) | |
| assert len(nodes) == 4 # chunk, document, entity, and type nodes | |
| assert len(edges) == 3 # is_part_of, contains, and is_a edges | |
| assert str(chunk.id) in added_nodes | |
| assert str(document.id) in added_nodes | |
| assert str(entity_node.id) in added_nodes | |
| assert str(type_node.id) in added_nodes |
|
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|
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| @pytest.mark.asyncio | ||
| async def test_get_graph_from_model_only_root(): |
There was a problem hiding this comment.
If only_root is removed from the method, let's remove the test as well.
Description
This PR includes extensive unit tests around the get_graph_from_model logic and changes the neo4j add_edges logic.
DCO Affirmation
I affirm that all code in every commit of this pull request conforms to the terms of the Topoteretes Developer Certificate of Origin
Summary by CodeRabbit
Release Notes
New Features
Bug Fixes
Refactor
only_rootparameter from various functionsTests
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