query_graph: WHERE NOT <predicate> on the target node or relationship of a MATCH pattern silently returns 0 rows — same predicate with <>, inside OR, or after WITH returns the right rows #2250

Summary

In query_graph, a WHERE NOT <predicate> that references the target node or the relationship of a MATCH pattern returns 0 rows with no error — even when the predicate is a tautology (NOT b.name = 'zzz' against a graph where no b is named zzz), and even when the query is an aggregate (RETURN count(*) returns zero rows, not one row with 0). The same predicate spelled with <> returns the correct rows, NOT on the source node works, and moving the NOT behind a WITH also works. So this is not "negation unsupported": it is a silent wrong answer for one shape of query.

I checked #1293 first — that one is about inbound anti-joins (NOT EXISTS { (f)<-[:CALLS]-() }); this is plain property negation and I could not find it reported.

Reproduction (public, 3 files, 25 nodes)

pkg/__init__.py      (empty)
pkg/core.py
main.py

pkg/core.py:

def alpha():
    return 1


def beta():
    return alpha() + 1


def gamma():
    return alpha() + beta()


def delta_helper():
    return gamma()

main.py:

from pkg.core import alpha, beta, gamma, delta_helper


def run():
    return alpha() + beta() + gamma() + delta_helper()

codebase-memory-mcp cli index_repository --repo-path <dir> --name cbmnot --mode fast
codebase-memory-mcp cli query_graph --project cbmnot --format json --query "<query>"

Baseline, so the expected numbers are on the record:

MATCH (a)-[:CALLS]->(b) RETURN a.name, b.name
-> 8 rows: run→alpha, run→beta, run→gamma, run→delta_helper, beta→alpha, gamma→alpha, gamma→beta, delta_helper→gamma

Results

NOT on a single-node pattern is correct in every form:

NOT on the source node of a relationship pattern is correct:

NOT on the target node or the relationship returns nothing, silently:

Two results that narrow where it lives:

The --json envelope carries no warning or diagnostic field for the failing cases; the only thing that comes back is the generic "hint": "Query returned no results. Use get_graph_schema() to see available labels and edge types.", which points the user at the schema rather than at the query.

Also on a large graph, and on the previous release

Same shape on an indexed project of 108,825 nodes / 558,430 edges (v0.11.0, freshly built):

MATCH (a:Function)-[:CALLS]->(b) WHERE b.name <> 'str'            RETURN count(*)  -> 116905
MATCH (a:Function)-[:CALLS]->(b) WHERE NOT b.name = 'str'         RETURN count(*)  -> 0 rows
MATCH (a:Function)-[:CALLS]->(b) WHERE NOT b.name = 'zzz_no_such' RETURN count(*)  -> 0 rows

I had the same result on v0.10.8 against the same repositories before upgrading (that is how I noticed it), so it is not a v0.11.0 regression — it predates the Cypher fail-closed work (#1875, #1918, #1922, #1998) and is not covered by it.

Reading of the mechanism (a guess, offered to be shot down)

The pattern fits a predicate pushdown: a top-level NOT … that references only the target node (or the relationship) is pushed to the expansion stage, where b/r is not bound yet, and NOT <null> evaluates to false for every candidate — so a tautology filters everything out. The evidence for that reading is that (a) the identical term is evaluated correctly once it sits inside an OR, or after a WITH, i.e. once it can no longer be pushed as a standalone conjunct; (b) NOT on the source node, which is bound at expansion time, is correct; (c) <> is never affected, so it presumably is not pushed the same way. I have not read the planner, so treat the paragraph as a hypothesis, not a finding.

Expected

Either of these would be fine; the current behaviour is the one thing that should not happen:

1. NOT <predicate> on the target node / relationship evaluates the same as <> / after WITH (the correct rows).
2. If the shape is genuinely unsupported, the query is refused with an error, the way the v0.11.0 Cypher work refuses a WITH wider than its binding — not answered with an empty result set that is indistinguishable from "no such edges". An empty result for NOT b.name = 'zzz' on a graph with 8 edges is a wrong answer, not a limitation.

Environment

• codebase-memory-mcp 0.11.0, release binary codebase-memory-mcp-windows-amd64.zip (SHA-256 verified against checksums.txt), run through cli; also reproduced on 0.10.8.
• Windows 11 Pro 10.0.26200, x64, 32 GB RAM.
• Store built fresh by 0.11.0 (--mode fast for the 3-file repo, --mode moderate for the large one).

Happy to re-run the table against a candidate build; the small fixture makes it a 10-second check.