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Crash when calling query_graph #627

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Crash when calling query_graph#627
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bugSomething isn't workingcypherCypher query language parser/executor bugspriority/highNeeds near-term maintainer attention; high-impact bug, regression, safety issue, or release blocker.stability/performanceServer crashes, OOM, hangs, high CPU/memorywindowsWindows-specific issues
Milestone
0.10.0-rc

Description

@zbynekwinkler
zbynekwinkler
opened on Jun 25, 2026

Version

codebase-memory-mcp 0.8.1

Platform

Windows (x64)

Install channel

GitHub release archive / install.sh / install.ps1

Binary variant

standard

What happened, and what did you expect?

After indexing I tasked my agent to find dead code. It started calling the mcp and it has crashed almost on the first useful query.

Reproduction

It is a private codebase. I had to check the box that it is not. I am doing so in the hopes that it might help anyway.

codebase-memory-mcp cli query_graph '{"project": "YYY", "query": "MATCH (f:Function) WHERE NOT f.file_path CONTAINS ''ext'' AND NOT f.file_path CONTAINS ''Tests'' AND NOT f.file_path CONTAINS ''examples'' AND NOT f.name = ''main'' OPTIONAL MATCH (c)-[:CALLS]->(f) WITH f, c WHERE c IS NULL RETURN f.name, f.qualified_name, f.file_path, f.start_line ORDER BY f.file_path LIMIT 50"}'

no usefull output, just a crash dump appearing in AppData\Local\CrashDumps\

Logs

PS C:\Users\XXX\AppData> codebase-memory-mcp cli query_graph '{"project": "YYY", "query": "MATCH (f:Function) WHERE NOT f.file_path CONTAINS ''ext'' AND NOT f.file_path CONTAINS ''Tests'' AND NOT f.file_path CONTAINS ''examples'' AND NOT f.name = ''main'' OPTIONAL MATCH (c)-[:CALLS]->(f) WITH f, c WHERE c IS NULL RETURN f.name, f.qualified_name, f.file_path, f.start_line ORDER BY f.file_path LIMIT 50"}'
level=info msg=mem.init budget_mb=32596 total_ram_mb=65192
PS C:\Users\XXX\AppData>

Project scale (if relevant)

Nodes: 29,361 Edges: 59,940

Confirmations

  • I searched existing issues and this is not a duplicate.
  • My reproduction uses shareable code (a dummy snippet or a public OSS repository), not proprietary code.

Activity

  1. zbynekwinkler
    added
    bugSomething isn't working
    on Jun 25, 2026

  2. zbynekwinkler commented on Jun 25, 2026

    @zbynekwinkler
    zbynekwinkler
    on Jun 25, 2026
    Author

    I think I have it crashing also under wsl.

    Image

  3. zbynekwinkler commented on Jun 25, 2026

    @zbynekwinkler
    zbynekwinkler
    on Jun 25, 2026
    Author

    That is actually a local build of current main.

  4. zbynekwinkler commented on Jun 25, 2026

    @zbynekwinkler
    zbynekwinkler
    on Jun 25, 2026
    Author

    I asked the agent to try to minimize the crashing query:

    Image

  5. zbynekwinkler commented on Jun 25, 2026

    @zbynekwinkler
    zbynekwinkler
    on Jun 25, 2026
    Author

    btw: It is a really slow to rebuild. Iterating on a fix is not as fast as it could be.

  6. DeusData
    added a commit that references this issue on Jun 25, 2026

    test(repro): crash + trace + gitignore reproductions for #627, #514, #…

    2534f3b

  7. zbynekwinkler commented on Jun 26, 2026

    @zbynekwinkler
    zbynekwinkler
    on Jun 26, 2026
    Author

    I had my agent take a look and it was able to generate some kind of a fix (let me know if you are interested in it). I had the original agent testing it on the private repo and after a couple of iterations, they fixed it. This is the final report:

    Details Here is the complete, comprehensive list of **all four bugs/limitations** we identified and diagnosed in the graph engine during this session:

    1. 🔴 Bare Variable-Binding Corruption (Fixed)

    • What it was: Projecting a node/relationship variable through a WITH clause (e.g., WITH f or WITH f AS func) stripped its property map and bound the variable to a literal string equal to its own identifier name (e.g., "f" or "func"). Any subsequent property lookup (f.qualified_name) evaluated to that string.
    • Status: 🟢 Resolved (Verified fixed in the first patch).

    2. 🔴 Traversal Outer-Join Process Crash (Fixed)

    • What it was: Performing an OPTIONAL MATCH (outer-join/null-padding traversal) over large node/relationship collections crashed the server binary with Connection closed. This was isolated as a crash in the optional matching planner/traversal executor itself, separate from any WITH or WHERE operations.
    • Status: 🟢 Resolved (Verified fixed in the latest patch).

    3. ⚠️ Cypher Parser Nesting Limitations (Constraint)

    • What it is: The Cypher parser throws syntax errors on standard openCypher nested pattern checks inside WHERE clauses (e.g., WHERE NOT (f)<-[:CALLS]-() throws an unexpected operator error).
    • Workaround: Avoid nested pattern checks in WHERE; use explicit MATCH structures or property filtering instead.

    4. ⚠️ Inline Projections Logic Errors (Constraint)

    • What it is: The parser throws parser token errors when evaluating boolean expressions or literal values directly inside WITH projections (e.g., WITH (r IS NULL) AS is_uncalled throws expected token type 85, got 66 or WITH 1 AS x throws expected token type 0, got 13).
    • Workaround: Project node properties directly (e.g., WITH f.qualified_name AS qname, caller.name AS caller_name) which evaluates correctly, and run subsequent operations on those primitives.

    I also have several handoff documents from the session.

    I see that you most likely have a fairly good idea what is going on given the recent 2534f3b, so let me know if you want any more of this.

  8. DeusData commented on Jun 27, 2026

    @DeusData
    DeusData
    on Jun 27, 2026
    Owner

    Hey @zbynekwinkler, yes currently looping through all the issues and trying to find ways to reproduce all the issues and fix them once and for all. Also having some other people on it. Still, would be interested if you could share your reports :) Always helpful to get more information

  9. DeusData commented on Jun 28, 2026

    @DeusData
    DeusData
    on Jun 28, 2026
    Owner

    This issue now has a first-class, durable reproduction in the cumulative bug-reproduction suite landing in #667 — a test that pins the exact failing behaviour, so it's tracked and guarded against silent regression. Where #667 also lands the root-cause fix, that's called out in the PR; otherwise the reproduction makes the eventual fix straightforward and verifiable.

    The reproduction goes live once #667 merges. (Posted from the release branch's QA pass.)

  10. timothybrush
    added 2 commits that reference this issue on Jun 28, 2026

    fix: 17 reproduce-first issue + new-bug fixes (per-case verified)

    3f754cf

    style: clang-format issue-batch additions (cypher/mcp)

    7814568

  11. zbynekwinkler commented on Jun 29, 2026

    @zbynekwinkler
    zbynekwinkler
    on Jun 29, 2026
    Author

    The commits my agent produced are a99a419 and 3fd3543. I'll try to dig up the handoff as well later (they are on a different computer).

  12. zbynekwinkler commented on Jun 29, 2026

    @zbynekwinkler
    zbynekwinkler
    on Jun 29, 2026
    Author

    The reproduction goes live once #667 merges. (Posted from the release branch's QA pass.)

    I see

    got merged. I'll try to verify the fix.

  13. DeusData
    added
    cypherCypher query language parser/executor bugs
    stability/performanceServer crashes, OOM, hangs, high CPU/memory
    windowsWindows-specific issues
    priority/highNeeds near-term maintainer attention; high-impact bug, regression, safety issue, or release blocker.
    on Jun 29, 2026

  14. rudi193-cmd commented on Jul 5, 2026

    @rudi193-cmd
    rudi193-cmd
    on Jul 5, 2026
    Contributor

    Related consumer mitigation + safer dead-code query shape

    Same crash class as #601 — we hit this during a June fleet structural audit on v0.8.1 when an agent issued a whole-graph OPTIONAL MATCH anti-join for dead-code discovery.

    What we do now (willow-2.0 sap/cbm_facade.py):

    1. Block high-risk Cypher before it reaches the server (unbounded count(*), coalesce(), <-, etc.)
    2. Auto-append LIMIT when missing on query_graph
    3. Run the CLI in a subprocess with 30s timeout so a crash/hang does not take down the IDE stdio session

    Safer dead-code pattern (forward-only, bounded — not a full fix for server-side robustness):

    MATCH (f:Function)
WHERE NOT f.is_test
WITH f LIMIT 200
OPTIONAL MATCH (caller)-[:CALLS]->(f)
WITH f, count(caller) AS inbound
WHERE inbound = 0
RETURN f.qualified_name, f.file_path
LIMIT 50

    Still requires grep confirmation for aliased imports (#875) and common-name fan-in (#725), but avoids the whole-graph OPTIONAL MATCH (c)-[:CALLS]->(f) WITH f, c WHERE c IS NULL shape from the original report.

    Public fixture: willow-2.0 (~17.8k nodes). Audit notes: docs/audits/CODEBASE_MEMORY_MCP_TOOL_EVAL_ADDENDUM_2026-07-05.md. Related filing: #873 (DISTINCT ordering, refs #237).

  15. DeusData
    added this to the 0.9.1-rc milestone on Jul 8, 2026
  16. SEPURI-SAI-KRISHNA
    added a commit that references this issue on Jul 19, 2026

    fix(cypher): bound OPTIONAL fallback in expand_pattern_rels to preven…

    a3adfbc
  17. DeusData
    added a commit that references this issue on Aug 18, 2026

    fix(cypher): expansion materializes every matched row — the cap falsi…

    58ef9f1

  18. DeusData commented on Sep 25, 2026

    @DeusData
    DeusData
    on Sep 25, 2026
    Owner

    Thank you, @zbynekwinkler, for the report and the minimization, @rudi193-cmd for the safer query shape, and everyone who shared findings!

    Your query no longer crashes on current main, but it did still return wrong values: a node passed through WITH became a name-only stub, so f.qualified_name came back as "f". That's fixed in a change now in review (#2351); with it, your exact dead-code query returns the right rows.

    While checking, we found one more bug: in a WITH stage, count(c) counts the empty OPTIONAL MATCH row, so WHERE inbound = 0 finds nothing. @zbynekwinkler, you have commits in your fork around this; if you'd like to open a PR for that part, you're very welcome to. Otherwise we'll fix it next. Nested pattern predicates (WHERE NOT (f)<-[:CALLS]-()) and expression or literal projections in WITH aren't supported yet; we'll track them as feature requests.

  19. DeusData commented on Oct 19, 2026

    @DeusData
    DeusData
    on Oct 19, 2026
    Owner

    Thank you again for the minimized query and contribution details. The September update distinguishes the crash, WITH value preservation, optional-row counting, and unsupported syntax; those should not be treated as one completed fix. I have no new verification result for the remaining cases to announce today.

  20. DeusData commented on Oct 25, 2026

    @DeusData
    DeusData
    on Oct 25, 2026
    Owner

    Thank you for your patience. Sorry for the delay. The remaining WITH/counting semantics and unsupported syntax need separate maintainer follow-up rather than a blanket crash-fix claim. I’ll follow up soon.

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