fix: skip upserting edges when nodes don't exist

[ChenZiHong-Gavin]

No description provided.

[gemini-code-assist]

Summary of Changes

Hello @ChenZiHong-Gavin, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request enhances the robustness of edge creation across different graph storage implementations by enforcing stricter validation. It ensures that edges are only established between pre-existing nodes, preventing the creation of orphaned edges or unintended implicit node generation. This change leads to more predictable graph states and improved data integrity within the graph generation process.

Highlights

• Kuzu Storage Edge Upsertion: Modified the upsert_edge method in kuzu_storage.py to explicitly check for the existence of both source and target nodes. If either node is missing, the edge upsertion is skipped, and a warning message is printed, preventing the previous behavior of implicitly creating missing nodes.
• NetworkX Storage Edge Upsertion: Introduced a new check in the upsert_edge method of networkx_storage.py to ensure that both the source and target nodes exist in the graph before attempting to add an edge. If any node is not found, the edge creation is aborted, and a warning is logged.

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[gemini-code-assist]

Code Review

This pull request changes the behavior of upsert_edge in both KuzuStorage and NetworkXStorage. Instead of creating nodes if they don't exist when an edge is being upserted, the new implementation skips the edge upsert operation if either the source or target node is missing. This change is consistent with the pull request's title and is applied uniformly across both storage backends.

My main feedback is regarding the use of print() to report that the edge upsert is being skipped. While this is consistent with other parts of the codebase, using the logging module would be a better practice for library code, as it provides more flexibility for consumers to handle log messages. I've left specific comments on this.

[gemini-code-assist]

Using print() for logging is generally discouraged in library code because it's not configurable by the application using the library. It's better to use the logging module. This allows consumers to control log levels, format, and output destinations.

I suggest using logging.warning here. This also uses the recommended practice of passing arguments to logging methods to defer string formatting.

Note: You will need to add import logging at the top of the file.

Suggested change

	print(
	f"Cannot upsert edge {source_node_id}->{target_node_id} as one or both nodes do not exist."
	)
	logging.warning(
	"Cannot upsert edge %s->%s as one or both nodes do not exist.",
	source_node_id,
	target_node_id,
	)

[gemini-code-assist]

As with the other storage implementation, using print() for logging is not ideal. Using the logging module provides better control for consumers of this library.

I suggest using logging.warning here. This also uses the recommended practice of passing arguments to logging methods to defer string formatting.

Note: You will need to add import logging at the top of the file.

Suggested change

	print(
	f"Cannot upsert edge {source_node_id} -> {target_node_id} because one or both nodes do not exist."
	)
	logging.warning(
	"Cannot upsert edge %s -> %s because one or both nodes do not exist.",
	source_node_id,
	target_node_id,
	)