feat(core): port the indexer to backend-neutral write helpers#19
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Third step of the Kuzu -> DuckDB migration. The indexer no longer emits raw Cypher — every read and write goes through GraphDB helper methods that each backend implements in its own dialect. End result: `CGH_DB=duckdb cgh index` works end-to-end. What lands: - codegraph/core/protocol.py: GraphDB grew six write/read helpers. upsert_node, ensure_edge, purge_file_data, delete_file_completely, find_node_keys, query_node_field, list_node_fields. Each one matches a specific pattern the indexer used to write in Cypher. - codegraph/core/graph_model.py: single source of truth for the graph model — NODES (label -> table + key_field) and EDGES (relationship -> table + columns + props). Both adapters consume this to know what tables to write to and how to validate labels. - codegraph/core/db_kuzu.py + db_duckdb.py: the six new helpers implemented on both adapters. Kuzu uses Cypher with parameterised queries; DuckDB uses parameterised SQL with INSERT ... ON CONFLICT for the upsert semantics. Edge tables use INSERT ... ON CONFLICT DO NOTHING to match Kuzu's MERGE-without-set semantics. Both backends validate the label / edge_type argument against the graph_model registry so callers can't sneak arbitrary identifiers into the query string. - codegraph/indexer.py: every MERGE / MATCH / DETACH DELETE call replaced with a helper call. The Cypher dialect is gone from indexer.py entirely — `grep -nE "conn\.execute" indexer.py` is empty. Stops importing kuzu. _resolve_calls and _resolve_inherits stay name-based: find_node_keys returns every matching id, ensure_edge writes one edge per. Same best-effort semantics as before, both backends. Endpoint -> handler IMPLEMENTED_BY linking now filters by file id prefix in Python since neither backend has a "MATCH WHERE name = ? AND file_path = ?" helper yet (good candidate for the next PR). Markdown DEFINES_SECTION + CONTAINS_SECTION + MD_LINKS_TO + MD_REFS_SYMBOL + MD_REFS_CLASS all ported. The ENDS WITH match in MD_LINKS_TO downgrades to exact path match for now — a suffix-match helper can come later if it turns out to matter. - tests/test_core/test_graph_helpers.py: 22 parametrized tests running every helper against both backends. upsert_node, ensure_edge, purge_file_data, find_node_keys all covered. The same fixture runs twice via pytest.fixture(params=...) so any divergence between Kuzu and DuckDB shows up as a test failure rather than at runtime. End-to-end verification on a 2-file Python repo: Kuzu: 2 files, 3 functions, 1 CALLS edge, 3 DEFINES_FN edges DuckDB: 2 files, 3 functions, 1 CALLS edge, 3 DEFINES_FN edges Test count: 252 -> 274 (+22 parity tests, all existing still green). What's NOT in this PR (future migration work): - MCP tools (server/tools_*.py) still emit Cypher. They use raw conn.execute and need their own port pass. - federation.py still uses Kuzu APIs directly via .raw — that's the next dedicated PR in the chain. - cli/commands_monitor.py stats queries are Cypher; minor port to add to the queries PR.
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Summary
Third PR in the Kuzu → DuckDB migration. The indexer no longer emits raw Cypher — every read and write goes through `GraphDB` helper methods. End result: `CGH_DB=duckdb cgh index` works end-to-end.
What lands
End-to-end verification
```bash
Kuzu (default)
cgh index --root /tmp/sample
Files: 2, Functions: 3, CALLS: 1, DEFINES_FN: 3
DuckDB
CGH_DB=duckdb cgh index --root /tmp/sample
Files: 2, Functions: 3, CALLS: 1, DEFINES_FN: 3 (identical)
```
Test count
252 → 274 (+22 parity tests, all existing still green).
Not in this PR (follow-ups)