[Bug] KuzuDB 0.11.3 backend: systemic query incompatibilities break call-graph, deps, and resolution phase

Summary

The KuzuDB backend in CGC 0.3.1 has three distinct query compatibility failures with KuzuDB 0.11.3 that collectively break call-graph edges, dependency analysis, and the resolution phase of indexing. These appear to be the root cause behind several existing open issues (#727, #756, #757, #683, #684).

Environment

CGC: 0.3.1
KuzuDB: 0.11.3 (kuzu Python package)
Python: 3.13.5
OS: Windows 11
Config: INDEX_SOURCE=false, INDEX_VARIABLES=false, DEFAULT_DATABASE=kuzudb

Three Distinct Failures

1. Resolution phase: "Casting between NODE and NODE is not implemented"

During the resolution phase (after parsing completes at 100%), every single call-graph edge insertion fails:

ERROR - Kuzu Query failed:
    OPTIONAL MATCH (caller:Function {name: $caller_name, path: $caller_file_path})
    ... Error: Runtime exception: Casting between NODE and NODE is not implemented.

Impact: Zero call-graph edges are stored. The resolution phase burns CPU for ~45+ minutes on a 1312-file repo producing no useful output. analyze callers and analyze calls return empty or near-empty results.

Related issues: #756, #683

2. Dependency queries: "Variable file is not in scope"

analyze deps (module dependencies) fails with a Binder exception:

MATCH (file:File)-[imp:IMPORTS]->(module:Module {name: $module_name})
WHERE 1=1 {repo_filter}
OPTIONAL MATCH (repo:Repository)-[:CONTAINS]->(file)
... Error: Binder exception: Variable file is not in scope.

The file variable from the first MATCH clause is not visible in the subsequent OPTIONAL MATCH in KuzuDB's query planner.

Related issues: #757, #684

3. Fulltext index creation: Parser exception on `CALL db.idx.fulltext.createNodeIndex`

On every cgc command (list, find, etc.), two errors appear:

ERROR - Kuzu Query failed: CALL db.idx.fulltext.createNodeIndex('Function', 'name', 'source', 'docstring')
... Error: Parser exception: Invalid input <CALL db.>: expected rule oC_Statement

Impact: Full-text search (find content) is broken. Node lookup (find name) still works because it uses exact match, not fulltext.

What Works vs What's Broken

Feature	Status	Notes
`find name` (exact node lookup)	✅ Works	Simple node query
`find pattern` (substring)	✅ Works	Simple node query
`analyze tree` (inheritance)	✅ Works	INHERITS edges stored during parse phase
`analyze callers` (call graph)	❌ Broken	"Casting NODE/NODE" kills edge creation
`analyze calls` (callees)	❌ Broken	Same casting error
`analyze chain` (call chain)	❌ Broken	Depends on call edges
`analyze deps` (imports)	❌ Broken	"Variable not in scope"
`find content` (fulltext)	❌ Broken	Fulltext index creation fails

Reproduction

# 1. Install CGC with KuzuDB
pip install codegraphcontext kuzu

# 2. Configure
cgc config set DEFAULT_DATABASE kuzudb
cgc config set INDEX_SOURCE false
cgc config set INDEX_VARIABLES false

# 3. Index any Python repo with >50 files
cgc index /path/to/repo --force
# Observe: progress bar reaches 100%, then resolution phase spews
# "Casting between NODE and NODE" errors for 30-60+ minutes

# 4. Test queries
cgc analyze callers "any_function"  # empty or near-empty
cgc analyze deps "any_module"       # crashes with "Variable not in scope"
cgc find content "any_string"       # fails silently (no fulltext index)

Root Cause Hypothesis

CGC's Cypher queries were likely developed/tested against an older KuzuDB version (possibly 0.8.x-0.10.x). KuzuDB 0.11.x appears to have introduced:

Stricter type casting rules for node variables across OPTIONAL MATCH chains
Changes to variable scoping in multi-clause queries
Different syntax for fulltext index creation (CALL db.idx... vs whatever the new API is)

Suggested Fix

The database_kuzu.py translation layer needs to be updated for KuzuDB 0.11.x query semantics. The three failures are in different query patterns but share a common cause: the Neo4j-to-Kuzu query translator produces queries that 0.11.x rejects.

Additionally, the resolution phase should fail fast rather than retrying the same broken query pattern thousands of times. A single failed OPTIONAL MATCH pattern should disable that query type for the rest of the run, not repeat the error for every call in every file.

Workaround

For users who only need symbol lookup (find name, find pattern, analyze tree), CGC with KuzuDB still works. The parsing phase correctly stores nodes and inheritance edges. Call-graph and dependency features require either:

Downgrading kuzu to a compatible version (untested — which version works?)
Using Neo4j or FalkorDB backend instead

Hi! 👋 Join our CodeGraphContext Discord channel to collaborate: https://discord.gg/dR4QY32uYQ

@tucaman

Hey @tucaman I am working on the exact same bug, there's a bug in kuzudb indexing logic and hence I need some time figuring this out

@tucaman

Hey @tucaman can you check if the kuzudb indexing works now??

Hey @tucaman can you check if the kuzudb indexing works now??

Did you make any progress already? Or do you want me to create a fix?

https://pypi.org/project/codegraphcontext/0.3.5/

https://pypi.org/project/codegraphcontext/0.3.5/

Will test now

Hey @tucaman can you check if the kuzudb indexing works now??

Did you make any progress already? Or do you want me to create a fix?

Fixed it in the latest PR, need some testing

@Shashankss1205

@Shashankss1205 Thanks for the quick response!

We upgraded from 0.3.1 → 0.3.4 (via uv pip install --upgrade codegraphcontext) and re-tested. Same three failures persist on 0.3.4:

Fulltext index: CALL db.idx.fulltext.createNodeIndex still fails with parser exception on every command
Deps query: analyze deps still crashes with "Variable file is not in scope"
Call-graph edges: analyze callers "transform" returns only 1 caller (should be dozens) — resolution phase still logs "Casting between NODE and NODE" for every edge

We also tried installing 0.3.5 but it can't resolve — it depends on inquirerpy>=0.3.5 which doesn't exist on PyPI yet:

Because only inquirerpy<=0.3.4 is available and codegraphcontext==0.3.5
depends on inquirerpy>=0.3.5, we can conclude that codegraphcontext==0.3.5
cannot be used.

Happy to test a fix if you point us to a branch or pre-release. Our setup:

KuzuDB 0.11.3, Python 3.13.5, Windows 11
~1312 Python files indexed
Config: INDEX_SOURCE=false, INDEX_VARIABLES=false

Hey, please test 0.3.5 and beyond versions.

https://pypi.org/project/codegraphcontext/0.3.5/

Hi, would love to, but cannot sync:

x No solution found when resolving dependencies for split (python_full_version >= '3.14' and sys_platform != 'win32'):
`-> Because only inquirerpy<=0.3.4 is available and codegraphcontext==0.3.5 depends on inquirerpy>=0.3.5, we can conclude that codegraphcontext==0.3.5 cannot be used.
And because only codegraphcontext<=0.3.5 is available and your project depends on codegraphcontext>=0.3.5, we can conclude that your project's requirements are unsatisfiable.
  hint: While the active Python version is 3.13, the resolution failed for other Python versions supported by your project. Consider limiting your project's supported Python
  versions using `requires-python`.

fixing #769

Umm, Another version-
https://pypi.org/project/codegraphcontext/0.3.7/

Let me know if this works, or I will have to recheck each dependency again with 100% perfect way out

CGC 0.3.9 Upgrade Report — adAPPter_uv (Windows 11)

Environment

OS: Windows 11 (10.0.26100)
Python: 3.13.5 (uv venv)
KuzuDB: 0.11.3
CGC: 0.3.7 → 0.3.9
Repo: ~1,312 Python files, 11 workspace packages

Indexing Results

Metric	0.3.7 (old)	0.3.9 (new)
CALLS edges	0 (hung 30-60 min)	42,298 in 11.7s
Inheritance links	58	58 in 0.2s
Total index time	hung/Ctrl+C	482 seconds
Post-processing	broken	11.9 seconds total

PR #796 is a massive improvement. The UNWIND batching fix completely resolves the CALLS edge creation failure. Breakdown: fn→fn=34,178, fn→cls=905, cls→fn=6,006, file→fn=1,182, file→cls=27.

Feature Test Results

Feature	Status	Notes
`find name`	✅ PASS	Found symbols at correct file:line
`analyze callers`	✅ PASS	4 callers for `transform` — works!
`analyze tree`	✅ PASS	Inheritance hierarchy + 47 methods
`analyze deps`	❌ FAIL	Same `Binder exception: Variable file is not in scope` (#757)
`find content`	❌ FAIL	Fulltext index creation still fails (`CALL db.idx.fulltext.createNodeIndex` parser error)

Summary

3/5 features now working (up from 2/5 on 0.3.7). The CALLS engine rewrite is the key fix — call graph analysis is now functional and fast.

Still broken:

analyze deps — [Bug] module_deps query fails with KeyError 'imported_by_files' #757 scoping bug in OPTIONAL MATCH query
find content — KuzuDB 0.11.x fulltext index limitation

Minor issues:

.ruff_cache and .pentagon directories generate thousands of "No parser found" warnings — should be added to IGNORE_DIRS or .cgcignore
Fulltext index errors fire on every CGC startup (cosmetic but noisy)

@sonxy-cn

Hey @sonxy-cn thanks for bringing this to notice. I will try to shift from kuzudb to ladybug db, because of better maintainability.

fixing CodeGraphContext#769

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[Bug] KuzuDB 0.11.3 backend: systemic query incompatibilities break call-graph, deps, and resolution phase #769

Summary

Environment

Three Distinct Failures

1. Resolution phase: "Casting between NODE and NODE is not implemented"

2. Dependency queries: "Variable file is not in scope"

3. Fulltext index creation: Parser exception on `CALL db.idx.fulltext.createNodeIndex`

What Works vs What's Broken

Reproduction

Root Cause Hypothesis

Suggested Fix

Workaround

CGC 0.3.9 Upgrade Report — adAPPter_uv (Windows 11)

Environment

Indexing Results

Feature Test Results

Summary

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[Bug] KuzuDB 0.11.3 backend: systemic query incompatibilities break call-graph, deps, and resolution phase #769

Description

Summary

Environment

Three Distinct Failures

1. Resolution phase: "Casting between NODE and NODE is not implemented"

2. Dependency queries: "Variable file is not in scope"

3. Fulltext index creation: Parser exception on CALL db.idx.fulltext.createNodeIndex

What Works vs What's Broken

Reproduction

Root Cause Hypothesis

Suggested Fix

Workaround

Activity

github-actions commented on Mar 29, 2026

Shashankss1205 commented on Mar 29, 2026

Shashankss1205 commented on Mar 29, 2026

tucaman commented on Mar 29, 2026

Shashankss1205 commented on Mar 29, 2026

tucaman commented on Mar 29, 2026

Shashankss1205 commented on Mar 29, 2026

tucaman commented on Mar 29, 2026

Shashankss1205 commented on Mar 29, 2026

tucaman commented on Mar 29, 2026

Shashankss1205 commented on Mar 29, 2026

tucaman commented on Apr 6, 2026

CGC 0.3.9 Upgrade Report — adAPPter_uv (Windows 11)

Environment

Indexing Results

Feature Test Results

Summary

Shashankss1205 commented on Apr 30, 2026

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3. Fulltext index creation: Parser exception on `CALL db.idx.fulltext.createNodeIndex`