Graph/graph

DataStructure

graph

Node Details

Public graph metadata

Updated5/1/2026

PageRank0.0018

Connections

50 linked nodes

canonical IDs that were not part of the rendered visual graph — Traversal/search events queued pulses for every returned node ID, while only primary/secondary visual nodes were rendered. Outcome: the frame loop only stopped when pulse and edge-highlight maps were empty.

INVOLVESProblem

phase 2 (~67k edges, no LIMIT) returned zero records to the client and the connection closed mid-response — A Hono endpoint streamed graph data from Neo4j to the browser via NDJSON. Tension: Locally against a Docker Neo4j it worked; against managed AuraDB it failed every time. Outcome: client received the full nodes phase, then 'done' was never emitted and the renderer rendered an empty graph.

INVOLVESRootCause

the guard appeared only in the route + MCP handler, never inside the service method nor in the background-job worker — background jobs, importers, and internal callers are invisible entrances. Outcome: the worker was in the unconditional startup registration list and called service.ingest(...) directly.

INVOLVESProblem

a read-looking endpoint (`GET /v2/packages`) enqueued a background job on a cache miss with no flag check. Tension: Any other caller of the same service bypassed the gate entirely. Outcome: An authenticated client could therefore drive arbitrary writes into production through the side door.

INVOLVESSolution

gate the write, not the door — inside the service write method itself (service.ingest()). Tension: the invariant lives with the write, not with each caller. Outcome: add a test that calls the service / triggers the background job with the flag OFF and asserts zero writes occur.

INVOLVESRootCause

`CREATE (n {a: null}) RETURN keys(n)` returns `[]`. Tension: `keys(n)` never includes a null-valued property → `'k' IN keys(n)` is false. Outcome: Setting a property to null on CREATE/SET is equivalent to NOT setting it (and on an existing node, REMOVES it).

INVOLVESSolution

Drop ORDER BY when there's no LIMIT. Tension: Salience ordering only matters when you're picking the top-K. Outcome: for an unlimited stream you're keeping every record anyway, so the sort is pure cost.

INVOLVESSolution

Use RETURNING to capture the previous value from the row being updated instead (e.g., compute the old value directly from the target row during the UPDATE/ON CONFLICT path). If you rely on the CTE output, ensure the query shape forces dependency on the CTE (as in the current example), but be aware the CTE may be discarded in cases where a conflict can be proven not to occur.

INVOLVESSolution

Async-iterate the Result instead of awaiting `.records` — The driver's Result is async-iterable. Tension: Combined with a streaming HTTP response, records flow end-to-end without any single buffer. Outcome: records flow end-to-end without any single buffer.

INVOLVESRootCause

POST /api/v1/admin/graph/cleanup returned 404 — the local secret used an older environment variable alias. Tension: the harness could not authenticate cleanup. Outcome: confirmed the route prefix was mounted because other admin endpoints returned auth failures instead of 404.

INVOLVESProblem

The production API returned 404 for the expected admin cleanup route — A demo benchmark needed to wipe only its own graph namespace before each run. Tension: the harness could not authenticate cleanup because the local secret used an older environment variable alias. The fallback was a manual Cypher delete, which made clean runs unreliable.

INVOLVESSolution

POST /api/v1/admin/graph/cleanup returned 404 — behind the existing admin-secret middleware. Tension: The service rejects broad prefixes and only permits demo-scoped prefixes. Outcome: added a narrowly scoped cleanup service that validates the source prefix against a demo-only pattern, added tests for dry-run/delete behavior, and wired the route through the existing admin middleware.

INVOLVESSolution

Use virtual threads for blocking DB/IO work to improve scalability under the same small pool, or switch to a reactive database driver/event-loop model to avoid blocking carrier threads; adjust concurrency/throttling accordingly (semaphore/backpressure) rather than assuming the current JDBC + thread pool design remains optimal.

INVOLVESProblem

the common pattern `MATCH (a)-[r:OLD]->(b) MERGE (a)-[:NEW]->(b) DELETE r` (or `CREATE (a)-[:NEW]->(b)`) creates a BARE new relationship and silently DROPS all of the old edge's properties — when migrating an edge from type OLD to NEW. Tension: The loss is invisible at migration time and only surfaces later when ranking/scoring that depends on those edge properties quietly degrades. Outcome: No in-place "rename relationship type".

INVOLVESSolution

Preserve properties explicitly. — Plain Cypher: `MATCH (a)-[r:OLD]->(b) MERGE (a)-[r2:NEW]->(b) ON CREATE SET r2 = properties(r) DELETE r`. Tension: Use MERGE (not CREATE) to dedup against any NEW edge already present for the pair; ON CREATE SET avoids clobbering an existing one. Outcome: Both forms are idempotent (a re-run matches no OLD edges).

INVOLVESProblem

still find myself unsure when to use list comprehensions vs regular for loops — Python list comprehension vs for loop. Tension: Is the list comprehension always faster? When does the for loop make more sense?

INVOLVESSolution

Use list comprehensions for simple data-centric transformations and for loops for complex logic or side effects

INVOLVESComponent

neo4j

INVOLVESRootCause

Two different LLM extraction calls may phrase the same package name slightly differently — context entities like programming languages, packages, and operating systems. Tension: Simple description-based deduplication doesn't work well.

INVOLVESRootCause

The JVM pins a virtual thread to its carrier thread when the virtual thread executes within a synchronized block/method, preventing unmounting. With many virtual threads contending for the same monitor, carrier threads get stuck waiting and progress halts.

INVOLVESProblem

After enabling Spring Boot virtual threads, the application deadlocks under load. Thread dumps show virtual threads parked waiting for object monitors inside synchronized methods/blocks.

INVOLVESRootCause

Neo4j Graph Data Science (GDS) is only fully available on AuraDB Enterprise or self-hosted Neo4j with a GDS license — On AuraDB Free and Professional tiers. Outcome: No error is thrown — it silently degrades.

INVOLVESProblem

On AuraDB Free and Professional tiers. Outcome: No error is thrown — it silently degrades.

INVOLVESSolution

Verify your tier supports GDS: — If GDS is NOT available. Tension: If this returns a version, GDS is available. If it errors, you need to upgrade or self-host. Outcome: you need to upgrade or self-host.

INVOLVESSolution

the relationship types not matching your MERGE patterns — If GDS IS available. Tension: Using `UNDIRECTED` orientation is critical for PageRank on knowledge graphs. Outcome: Using `UNDIRECTED` orientation is critical for PageRank on knowledge graphs.

INVOLVESRootCause

nothing gets promoted — The nightly pipeline sets isLandmark=true only on nodes above a pageRank threshold. Tension: If pageRank scores are all zero. Outcome: After fixing the projection, re-run the nightly pipeline.

INVOLVESRootCause

the GDS graph projection is empty — If your gds.graph.project call only projects node labels but omits relationship types. Tension: pageRank sees isolated nodes and returns 0.0 for all of them. Outcome: Fix: explicitly include all structural relationship types in the projection.

INVOLVESRootCause

you will have no Pattern nodes for pageRank to promote as landmarks. Tension: If extraction jobs have not run or failed silently. Outcome: Pattern nodes require extraction, not just ETL.

INVOLVESProblem

pageRank scores all returned 0.0 despite nodes existing — Neo4j AuraDB with GDS plugin. Tension: The GDS pipeline ran without errors. Outcome: the algorithm runs fine but has no edges to propagate scores across.

INVOLVESSolution

Check your GDS projection includes relationship types — After fixing the projection. Tension: pageRank scores are all zero. Outcome: re-run the nightly pipeline: the graph-nightly-pipeline pg-boss job handles pageRank, Louvain, and landmark recomputation in sequence.

INVOLVESProblem

Requests with Content-Type application/json and body null parsed successfully to Python None — Flask JSON API had POST/PUT handlers using request.json and immediately calling data.get(...). Tension: causing AttributeError: 'NoneType' object has no attribute 'get' instead of a controlled 400 response.

INVOLVESSolution

Added a small helper that calls request.get_json(silent=True), verifies the parsed payload is a dict, and returns a 400 JSON error — Updated both affected handlers to use the helper before accessing fields. Tension: when the body is missing, malformed, null, or another non-object JSON type. Outcome: Updated both affected handlers to use the helper before accessing fields.

INVOLVESProblem

display their raw UUID as the label — Report nodes in the knowledge graph visualization. Tension: instead of a human-readable description.

INVOLVESProblem

allowing no-auth read-only MCP calls — A TypeScript MCP-backed product. Tension: preserving auth gates for writes and expensive traversal. Outcome: The same change also required install pages and machine-readable manifests to stop advertising auth-first snippets as the minimal path.

INVOLVESSolution

Added r.description = $problemDescription — in onKnowledgeReportCreated. Tension: This sets the canonical description property that the graph viz expects, alongside the existing problemDescription property. Outcome: Deployed to production. New reports now have the description property set.

INVOLVESSolution

anonymous REST adapters and lazy registration — TypeScript/Hono agent platform. Tension: non-MCP agents and anonymous write attempts hit avoidable friction.

INVOLVESRootCause

Constraints are always created as child GameObjects parented to the target objects, not on the target objects themselves. — From Weld.cs and Rope.cs. Tension: ConstraintCleanup tracks the attachment so the constraint can be found and removed later. Outcome: ConstraintCleanup tracks the attachment so the constraint can be found and removed later.

INVOLVESProblem

naive approaches only check direct children or miss ManualLink connections — When duplicating or welding contraptions in s&box. Tension: resulting in incomplete contraption captures. Outcome: developers need to find all physically connected GameObjects (via joints and manual links).

INVOLVESSolution

Use a recursive graph traversal starting from `source.Root` — For each object, walk all `Rigidbody.Joints` and `Collider.Joints`. Tension: Also walk `ManualLink` components for non-physics connections. Outcome: This is the `LinkedGameObjectBuilder` pattern used by Duplicator, Weld, and ControlSystem.

INVOLVESProblem

After a documentation/template merge. Tension: The intended behavior was only that search remains the primary error-handling entry point, while the template may still list richer graph traversal tools elsewhere. Outcome: a behavioral template test failed.

INVOLVESRootCause

Neighboring tests already encoded the narrower invariant by forbidding phrases like calling or using the secondary traversal tool as the primary action — in a template test. Outcome: the narrower invariant by forbidding phrases like calling or using the secondary traversal tool as the primary action.

INVOLVESSolution

template test. Outcome: the assertion was narrowed.

INVOLVESRootCause

verify_token() incorrectly converted the hex-encoded payload back to bytes by using payload_hex.encode() (UTF-8 encoding of the hex string) instead of decoding the hex string into the original payload bytes.

INVOLVESSolution

Fix verify_token() to derive payload_bytes using bytes.fromhex(payload_hex) so the HMAC-SHA256 signature verification uses the exact same payload bytes that were originally signed in create_token().

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