diff --git a/AGENTS.md b/AGENTS.md index 35fb55ab..89f6d824 100644 --- a/AGENTS.md +++ b/AGENTS.md @@ -154,15 +154,6 @@ The repo has a strong "propose then implement" culture (`propose/`, Skip this for clearly-bounded fixes (one-file bugs, doc edits, test loosening). Use judgement. -When brainstorming produces a spec/design, write it as a proposal in -`propose/active/-PROPOSE.md` using the format established in -`propose/completed/` (open a completed proposal there and match its -section structure, headings, and level of detail — specific headings vary -by proposal but always include: TL;DR, design principles, proposed -surface/solution, risks and mitigations, decisions taken, tests, out of -scope, migration plan). Do NOT use a brainstorming skill's default -`docs/superpowers/specs/` location. - ## Per-PR agent task contract When you're given a per-PR task prompt from `plans/AGENT-PROMPTS-*.md` diff --git a/README.md b/README.md index 60363857..fe565d8f 100644 --- a/README.md +++ b/README.md @@ -84,8 +84,6 @@ If vector hits come back and graph expansion adds neighbor symbols, the install ## Wire into an MCP host -The server discovers your project automatically: it walks up from cwd looking for `.java-codebase-rag.yml` (or `.yaml`), like git finds `.git`. No env vars required if you have a YAML config in your project tree. For full precedence details, see [`docs/CONFIGURATION.md`](./docs/CONFIGURATION.md). - ### Claude Code With the package installed, the console script `java-codebase-rag-mcp` is on your `PATH`. Register it project-scoped: @@ -94,7 +92,7 @@ With the package installed, the console script `java-codebase-rag-mcp` is on you claude mcp add --transport stdio java-codebase-rag -- java-codebase-rag-mcp ``` -No env vars needed — the server walks up from cwd to find `.java-codebase-rag.yml`. For a minimal `.mcp.json` template, see [`mcp.json.example`](./mcp.json.example). Official docs: [Claude Code settings](https://docs.anthropic.com/en/docs/claude-code/settings). +Then set env vars (`JAVA_CODEBASE_RAG_INDEX_DIR`, `JAVA_CODEBASE_RAG_SOURCE_ROOT`, `SBERT_MODEL`, …) in `.mcp.json` or your shell profile. For a project-scoped `.mcp.json` template, see [`mcp.json.example`](./mcp.json.example). Official docs: [Claude Code settings](https://docs.anthropic.com/en/docs/claude-code/settings). ### Claude Desktop @@ -104,14 +102,16 @@ Edit `claude_desktop_config.json` (macOS: `~/Library/Application Support/Claude/ { "mcpServers": { "java-codebase-rag": { - "command": "java-codebase-rag-mcp" + "command": "java-codebase-rag-mcp", + "env": { + "JAVA_CODEBASE_RAG_INDEX_DIR": "/ABSOLUTE/PATH/TO/.java-codebase-rag", + "JAVA_CODEBASE_RAG_SOURCE_ROOT": "/ABSOLUTE/PATH/TO/your-java-project" + } } } } ``` -The server discovers the project via walk-up from the cwd of the MCP host process. If your Java project is not the cwd, either set `JAVA_CODEBASE_RAG_SOURCE_ROOT` in the `env` block or add a `source_root` field to `.java-codebase-rag.yml` (see [`docs/CONFIGURATION.md`](./docs/CONFIGURATION.md)). - See [`mcp.json.example`](./mcp.json.example) for the same shape in `.mcp.json` (Claude Code project-scoped) form. ### Driving the MCP from an agent diff --git a/build_ast_graph.py b/build_ast_graph.py index 040ca25b..0d11db80 100644 --- a/build_ast_graph.py +++ b/build_ast_graph.py @@ -401,24 +401,6 @@ class GraphTables: type_role_by_node_id: dict[str, str] = field(default_factory=dict) -# ---------- per-file dependency tracking (sidecar .deps.json) ---------- - - -@dataclass -class FileDeps: - """Per-file dependency metadata for incremental rebuild closure expansion.""" - - ext_hash: str = "" - declares: list[str] = field(default_factory=list) - injects: list[str] = field(default_factory=list) - extends: list[str] = field(default_factory=list) - calls: list[str] = field(default_factory=list) - uses_anno: list[str] = field(default_factory=list) - overrides: list[str] = field(default_factory=list) - declares_clients: list[str] = field(default_factory=list) - declares_producers: list[str] = field(default_factory=list) - - # ---------- file walk (see `path_filtering.iter_java_source_files`) ---------- @@ -2395,8 +2377,7 @@ def _micro_factor(member: MemberEntry | None) -> float: "pass3_unresolved_phantom_receiver INT64, " "pass3_unresolved_chained INT64, " "pass4_exposes_suppressed_feign INT64, " - "cross_service_resolution STRING, " - "last_rebuild_mode STRING" + "cross_service_resolution STRING" ")" ) @@ -2510,1703 +2491,118 @@ def _drop_all(conn: kuzu.Connection) -> None: pass -# --------------------------------------------------------------------------- -# Symmetric delete helpers (PR-T2) -# --------------------------------------------------------------------------- - -def _del_count( - conn: kuzu.Connection, count_q: str, del_q: str, fp: str -) -> int: - r = conn.execute(count_q, {"fp": fp}) - n = int(r.get_next()[0]) if r.has_next() else 0 - if n > 0: - conn.execute(del_q, {"fp": fp}) - return n - - -def delete_symbols_for_file(conn: kuzu.Connection, file_path: str) -> int: - for edge in ( - "DECLARES", "EXTENDS", "IMPLEMENTS", "INJECTS", "CALLS", "OVERRIDES", +def _create_schema(conn: kuzu.Connection) -> None: + for stmt in ( + _SCHEMA_NODE, + _SCHEMA_UNRESOLVED_CALL_SITE, + _SCHEMA_ROUTE, + _SCHEMA_CLIENT, + _SCHEMA_PRODUCER, + _SCHEMA_META, + _SCHEMA_EXTENDS, + _SCHEMA_IMPLEMENTS, + _SCHEMA_INJECTS, + _SCHEMA_DECLARES, + _SCHEMA_OVERRIDES, + _SCHEMA_CALLS, + _SCHEMA_UNRESOLVED_AT, + _SCHEMA_EXPOSES, + _SCHEMA_DECLARES_CLIENT, + _SCHEMA_DECLARES_PRODUCER, + _SCHEMA_HTTP_CALLS, + _SCHEMA_ASYNC_CALLS, ): - conn.execute( - f"MATCH (a:Symbol)-[e:{edge}]->(b:Symbol) " - "WHERE a.filename = $fp OR b.filename = $fp DELETE e", - {"fp": file_path}, - ) - conn.execute( - "MATCH (s:Symbol)-[e:UNRESOLVED_AT]->(u:UnresolvedCallSite) " - "WHERE s.filename = $fp DELETE e", - {"fp": file_path}, - ) - conn.execute( - "MATCH (s:Symbol), (u:UnresolvedCallSite) " - "WHERE s.filename = $fp AND u.caller_id = s.id DELETE u", - {"fp": file_path}, - ) - conn.execute( - "MATCH (s:Symbol)-[e:EXPOSES]->(r:Route) " - "WHERE s.filename = $fp DELETE e", - {"fp": file_path}, - ) - conn.execute( - "MATCH (s:Symbol)-[e:DECLARES_CLIENT]->(c:Client) " - "WHERE s.filename = $fp DELETE e", - {"fp": file_path}, - ) - conn.execute( - "MATCH (s:Symbol)-[e:DECLARES_PRODUCER]->(p:Producer) " - "WHERE s.filename = $fp DELETE e", - {"fp": file_path}, - ) - return _del_count( - conn, - "MATCH (s:Symbol) WHERE s.filename = $fp RETURN count(s) AS n", - "MATCH (s:Symbol) WHERE s.filename = $fp DELETE s", - file_path, - ) - - -def delete_extends_for_file(conn: kuzu.Connection, file_path: str) -> int: - return _del_count( - conn, - "MATCH (a:Symbol)-[e:EXTENDS]->(b:Symbol) " - "WHERE a.filename = $fp RETURN count(e) AS n", - "MATCH (a:Symbol)-[e:EXTENDS]->(b:Symbol) " - "WHERE a.filename = $fp DELETE e", - file_path, - ) - - -def delete_implements_for_file(conn: kuzu.Connection, file_path: str) -> int: - return _del_count( - conn, - "MATCH (a:Symbol)-[e:IMPLEMENTS]->(b:Symbol) " - "WHERE a.filename = $fp RETURN count(e) AS n", - "MATCH (a:Symbol)-[e:IMPLEMENTS]->(b:Symbol) " - "WHERE a.filename = $fp DELETE e", - file_path, - ) - - -def delete_injects_for_file(conn: kuzu.Connection, file_path: str) -> int: - return _del_count( - conn, - "MATCH (a:Symbol)-[e:INJECTS]->(b:Symbol) " - "WHERE a.filename = $fp RETURN count(e) AS n", - "MATCH (a:Symbol)-[e:INJECTS]->(b:Symbol) " - "WHERE a.filename = $fp DELETE e", - file_path, - ) - - -def delete_calls_for_file(conn: kuzu.Connection, file_path: str) -> int: - conn.execute( - "MATCH (s:Symbol)-[e:UNRESOLVED_AT]->(u:UnresolvedCallSite) " - "WHERE s.filename = $fp DELETE e", - {"fp": file_path}, - ) - conn.execute( - "MATCH (s:Symbol), (u:UnresolvedCallSite) " - "WHERE s.filename = $fp AND u.caller_id = s.id DELETE u", - {"fp": file_path}, - ) - return _del_count( - conn, - "MATCH (a:Symbol)-[e:CALLS]->(b:Symbol) " - "WHERE a.filename = $fp RETURN count(e) AS n", - "MATCH (a:Symbol)-[e:CALLS]->(b:Symbol) " - "WHERE a.filename = $fp DELETE e", - file_path, - ) - - -def delete_routes_for_file(conn: kuzu.Connection, file_path: str) -> int: - conn.execute( - "MATCH (s:Symbol)-[e:EXPOSES]->(r:Route) " - "WHERE r.filename = $fp DELETE e", - {"fp": file_path}, - ) - conn.execute( - "MATCH (c:Client)-[e:HTTP_CALLS]->(r:Route) " - "WHERE r.filename = $fp DELETE e", - {"fp": file_path}, - ) - conn.execute( - "MATCH (p:Producer)-[e:ASYNC_CALLS]->(r:Route) " - "WHERE r.filename = $fp DELETE e", - {"fp": file_path}, - ) - return _del_count( - conn, - "MATCH (r:Route) WHERE r.filename = $fp RETURN count(r) AS n", - "MATCH (r:Route) WHERE r.filename = $fp DELETE r", - file_path, - ) - - -def delete_clients_for_file(conn: kuzu.Connection, file_path: str) -> int: - conn.execute( - "MATCH (s:Symbol)-[e:DECLARES_CLIENT]->(c:Client) " - "WHERE c.filename = $fp DELETE e", - {"fp": file_path}, - ) - conn.execute( - "MATCH (c:Client)-[e:HTTP_CALLS]->(r:Route) " - "WHERE c.filename = $fp DELETE e", - {"fp": file_path}, - ) - return _del_count( - conn, - "MATCH (c:Client) WHERE c.filename = $fp RETURN count(c) AS n", - "MATCH (c:Client) WHERE c.filename = $fp DELETE c", - file_path, - ) - - -def delete_producers_for_file(conn: kuzu.Connection, file_path: str) -> int: - conn.execute( - "MATCH (s:Symbol)-[e:DECLARES_PRODUCER]->(p:Producer) " - "WHERE p.filename = $fp DELETE e", - {"fp": file_path}, - ) - conn.execute( - "MATCH (p:Producer)-[e:ASYNC_CALLS]->(r:Route) " - "WHERE p.filename = $fp DELETE e", - {"fp": file_path}, - ) - return _del_count( - conn, - "MATCH (p:Producer) WHERE p.filename = $fp RETURN count(p) AS n", - "MATCH (p:Producer) WHERE p.filename = $fp DELETE p", - file_path, - ) - - -def delete_http_calls_for_file(conn: kuzu.Connection, file_path: str) -> int: - return _del_count( - conn, - "MATCH (c:Client)-[e:HTTP_CALLS]->(r:Route) " - "WHERE c.filename = $fp RETURN count(e) AS n", - "MATCH (c:Client)-[e:HTTP_CALLS]->(r:Route) " - "WHERE c.filename = $fp DELETE e", - file_path, - ) - - -def delete_async_calls_for_file(conn: kuzu.Connection, file_path: str) -> int: - return _del_count( - conn, - "MATCH (p:Producer)-[e:ASYNC_CALLS]->(r:Route) " - "WHERE p.filename = $fp RETURN count(e) AS n", - "MATCH (p:Producer)-[e:ASYNC_CALLS]->(r:Route) " - "WHERE p.filename = $fp DELETE e", - file_path, - ) - - -def delete_overrides_for_file(conn: kuzu.Connection, file_path: str) -> int: - return _del_count( - conn, - "MATCH (a:Symbol)-[e:OVERRIDES]->(b:Symbol) " - "WHERE a.filename = $fp RETURN count(e) AS n", - "MATCH (a:Symbol)-[e:OVERRIDES]->(b:Symbol) " - "WHERE a.filename = $fp DELETE e", - file_path, - ) + conn.execute(stmt) -def delete_all_for_file( - conn: kuzu.Connection, file_path: str -) -> dict[str, int]: - return { - "http_calls": delete_http_calls_for_file(conn, file_path), - "async_calls": delete_async_calls_for_file(conn, file_path), - "routes": delete_routes_for_file(conn, file_path), - "clients": delete_clients_for_file(conn, file_path), - "producers": delete_producers_for_file(conn, file_path), - "calls": delete_calls_for_file(conn, file_path), - "extends": delete_extends_for_file(conn, file_path), - "implements": delete_implements_for_file(conn, file_path), - "injects": delete_injects_for_file(conn, file_path), - "overrides": delete_overrides_for_file(conn, file_path), - "symbols": delete_symbols_for_file(conn, file_path), +def _node_row(**kwargs) -> dict: + base = { + "kind": "", "name": "", "fqn": "", "package": "", + "module": "", "microservice": "", + "filename": "", "start_line": 0, "end_line": 0, + "start_byte": 0, "end_byte": 0, + "modifiers": [], "annotations": [], "capabilities": [], + "role": "OTHER", "signature": "", "parent_id": "", "resolved": True, } + base.update(kwargs) + return base -# --------------------------------------------------------------------------- -# Incremental rebuild (PR-T3) -# --------------------------------------------------------------------------- - - -def expand_to_closure( - changed_paths: set[str], - deps_index: DepsIndex, -) -> set[str]: - """Expand changed_paths to include all transitively affected files. - - Implements the 8 closure rules from proposal §2.3 using inverted .deps.json - maps. Rule 5 (brownfield-override) forces full rebuild at the caller level, - not here. - """ - if not changed_paths: - return set() - - files = deps_index.files - - # --- build inverse maps --- - # type FQN → file that declares it - declared_by: dict[str, str] = {} - for fp, deps in files.items(): - for fqn in deps.declares: - declared_by[fqn] = fp - - # annotation simple name → set of files using it - anno_users: dict[str, set[str]] = defaultdict(set) - for fp, deps in files.items(): - for anno in deps.uses_anno: - anno_users[anno].add(fp) - - # method/type FQN → set of files calling it (strip method part for type lookup) - callers_of: dict[str, set[str]] = defaultdict(set) - for fp, deps in files.items(): - for callee in deps.calls: - callers_of[callee].add(fp) - # also index the declaring type so type-level changes reach callers - type_fqn = callee.split("#")[0] - if type_fqn: - callers_of[type_fqn].add(fp) - - # type FQN → set of files extending it - extenders_of: dict[str, set[str]] = defaultdict(set) - for fp, deps in files.items(): - for ext in deps.extends: - extenders_of[ext].add(fp) - - # type FQN → set of files injecting it - injectors_of: dict[str, set[str]] = defaultdict(set) - for fp, deps in files.items(): - for inj in deps.injects: - injectors_of[inj].add(fp) - - # method FQN → set of files overriding it - overriders_of: dict[str, set[str]] = defaultdict(set) - for fp, deps in files.items(): - for ov in deps.overrides: - overriders_of[ov].add(fp) - type_fqn = ov.split("#")[0] - if type_fqn: - overriders_of[type_fqn].add(fp) - - # member FQN → file declaring client/producer (inverse of declares_clients/producers) - client_producer_declaring_files: dict[str, str] = {} - for fp, deps in files.items(): - for mfqn in deps.declares_clients + deps.declares_producers: - client_producer_declaring_files[mfqn] = fp - - # --- fixed-point expansion --- - dirty: set[str] = {p for p in changed_paths if p in files} - frontier = set(dirty) - while frontier: - new_frontier: set[str] = set() - for fp in frontier: - deps = files.get(fp) - if deps is None: - continue - - # Rule 1: Inverse-INJECTS — files that inject symbols declared in fp - for fqn in deps.declares: - for other in injectors_of.get(fqn, ()): - if other not in dirty: - new_frontier.add(other) - - # Rule 2: Inverse-EXTENDS / Inverse-IMPLEMENTS — files that extend/implement from fp - for fqn in deps.declares: - for other in extenders_of.get(fqn, ()): - if other not in dirty: - new_frontier.add(other) - - # Rule 3: Inverse-CALLS — files that call symbols declared in fp - for fqn in deps.declares: - for other in callers_of.get(fqn, ()): - if other not in dirty: - new_frontier.add(other) - - # Rule 4: Meta-annotation closure — if fp declares an @interface, dirty its users - for fqn in deps.declares: - simple = fqn.rsplit(".", 1)[-1] - for other in anno_users.get(simple, ()): - if other not in dirty: - new_frontier.add(other) - - # Rule 6: Route resolution — files that extend types from fp (already covered - # by rule 2) plus files whose calls reference methods from fp (already covered - # by rule 3). No additional expansion needed. - - # Rule 7: Inverse-OVERRIDES — files that override methods declared in fp - for fqn in deps.declares: - for other in overriders_of.get(fqn, ()): - if other not in dirty: - new_frontier.add(other) - - # Rule 8: Inverse-DECLARES_CLIENT/PRODUCER — already covered by rule 3 - # (callers of methods in fp). The client/producer nodes are re-emitted - # when their declaring method's file is re-processed. - - # Also: forward deps — if fp injects/extends/calls something, and that - # thing is in another file, that file may need re-processing for resolution. - for fqn in deps.injects + deps.extends + deps.calls: - type_fqn = fqn.split("#")[0] - declaring_file = declared_by.get(type_fqn) - if declaring_file and declaring_file not in dirty: - new_frontier.add(declaring_file) - - # Forward overrides: if fp overrides something in another file - for ov in deps.overrides: - type_fqn = ov.split("#")[0] - declaring_file = declared_by.get(type_fqn) - if declaring_file and declaring_file not in dirty: - new_frontier.add(declaring_file) - - dirty |= new_frontier - frontier = new_frontier - - return dirty - - -def pass1_parse_subset( - root: Path, - dirty: set[str], - *, - verbose: bool, -) -> dict[str, JavaFileAst]: - """Re-parse only dirty files. Returns path -> AST.""" - asts: dict[str, JavaFileAst] = {} - t0 = time.time() - n_files = 0 - if verbose: - _verbose_stderr_line(f"[graph] incremental pass 1 · parsing {len(dirty)} dirty files") - for rel_path in sorted(dirty): - p = root / rel_path - if not p.is_file(): - continue - n_files += 1 - try: - content = p.read_bytes() - except OSError: - continue - if not content.strip(): - continue - try: - ast = parse_java(content, filename=rel_path, verbose=verbose) - except Exception: - continue - asts[rel_path] = ast - if verbose: - elapsed = time.time() - t0 - _verbose_stderr_line( - f"[graph] incremental pass 1 · parsed {n_files} files in {elapsed:.2f}s", - ) - return asts - - -def pass2_edges_subset( - tables: GraphTables, - asts: dict[str, JavaFileAst], - dirty: set[str], - *, - verbose: bool, -) -> None: - """Re-emit EXTENDS/IMPLEMENTS/INJECTS edges for types in dirty files.""" - if verbose: - _verbose_stderr_line("[graph] incremental pass 2 · emitting edges for dirty files") - seen_ext: set[tuple[str, str]] = set() - seen_impl: set[tuple[str, str]] = set() - seen_inj: set[tuple[str, str, str, str]] = set() - for fqn, entry in tables.types.items(): - if entry.file_path not in dirty: - continue - ast = asts.get(entry.file_path) - if ast is None: - continue - _emit_extends_implements(entry, ast, tables, seen_ext=seen_ext, seen_impl=seen_impl) - _emit_injects(entry, ast, tables, seen=seen_inj) - - -def pass3_calls_subset( - tables: GraphTables, - asts: dict[str, JavaFileAst], - dirty: set[str], - *, - verbose: bool, -) -> None: - """Re-emit CALLS + UnresolvedCallSite for dirty caller files.""" - if verbose: - _verbose_stderr_line("[graph] incremental pass 3 · resolving calls for dirty files") - _build_member_indexes(tables) - stats = CallResolutionStats() - for rel_path, file_ast in asts.items(): - if rel_path not in dirty: - continue - try: - _process_file_calls(file_ast, rel_path, tables, stats) - except Exception as e: - log.error("Call extraction failed for %s: %s", rel_path, e) +_CREATE_SYMBOL = ( + "CREATE (:Symbol {id: $id, kind: $kind, name: $name, fqn: $fqn, " + "package: $package, module: $module, microservice: $microservice, " + "filename: $filename, " + "start_line: $start_line, end_line: $end_line, " + "start_byte: $start_byte, end_byte: $end_byte, " + "modifiers: $modifiers, annotations: $annotations, capabilities: $capabilities, " + "role: $role, signature: $signature, parent_id: $parent_id, resolved: $resolved})" +) -def pass4_routes_subset( +def _write_nodes( + conn: kuzu.Connection, tables: GraphTables, - asts: dict[str, JavaFileAst], - dirty: set[str], *, - source_root: Path, - verbose: bool, + project_root: Path, + meta_chain: dict[str, frozenset[str]] | None, ) -> None: - """Re-emit Route/EXPOSES for methods in dirty files.""" - if verbose: - _verbose_stderr_line("[graph] incremental pass 4 · extracting routes for dirty files") - stats = tables.route_stats - overrides = load_brownfield_overrides(source_root) + overrides = load_brownfield_overrides(project_root) try: - prs = str(source_root.resolve()) + prs = str(project_root.resolve()) except OSError: - prs = str(source_root) + prs = str(project_root) tables.cross_service_resolution = _load_config_cross_service_resolution(prs) - meta_chain = collect_annotation_meta_chain(prs) - - routes_by_id: dict[str, RouteRow] = {} - exposes_seen: set[tuple[str, str]] = set() - http_kinds = frozenset({"http_endpoint", "http_consumer"}) - - for member in sorted(tables.members, key=lambda m: m.node_id): - if member.file_path not in dirty: - continue - if member.decl.is_constructor: - continue - ast = asts.get(member.file_path) - if ast is None: - continue - type_decl = tables.types[member.parent_fqn].decl - final_routes = resolve_routes_for_method( - method_decl=member.decl, - enclosing_type=type_decl, + mch = meta_chain + # packages + for pkg, pid in tables.packages.items(): + conn.execute(_CREATE_SYMBOL, _node_row( + id=pid, kind="package", name=pkg.rsplit(".", 1)[-1], fqn=pkg, package=pkg, + )) + # files + for path, fid in tables.files.items(): + conn.execute(_CREATE_SYMBOL, _node_row( + id=fid, kind="file", name=Path(path).name, fqn=path, filename=path, + )) + # types + for entry in tables.types.values(): + d = entry.decl + role, capabilities = resolve_role_and_capabilities( + d, overrides=overrides, - meta_chain=meta_chain, - builtin_routes=member.decl.routes, + meta_chain=mch, ) - if not final_routes: - continue - for decl in final_routes: - path_template, path_regex = ("", "") - if decl.kind in http_kinds: - if decl.resolved and decl.resolution_strategy in ( - "annotation", - "codebase_route", - ): - path_template, path_regex = _normalize_path(decl.path) - rid = _route_id( - decl.framework, decl.kind, decl.http_method, - path_template, decl.path, decl.topic, decl.broker, - member.microservice, - ) - layer = decl.route_source_layer - if rid not in routes_by_id: - routes_by_id[rid] = RouteRow( - id=rid, kind=decl.kind, framework=decl.framework, - method=decl.http_method, path=decl.path, - path_template=path_template, path_regex=path_regex, - topic=decl.topic, broker=decl.broker, - feign_name=decl.feign_name, feign_url=decl.feign_url, - microservice=member.microservice, module=member.module, - filename=decl.filename, - start_line=decl.start_line, end_line=decl.end_line, - resolved=decl.resolved, source_layer=layer, - ) - else: - prev = routes_by_id[rid] - if _ROUTE_LAYER_RANK.get(layer, 0) > _ROUTE_LAYER_RANK.get( - prev.source_layer, 0, - ): - routes_by_id[rid] = replace(prev, source_layer=layer) - ek = (member.node_id, rid) - if ek not in exposes_seen: - route_kind = routes_by_id[rid].kind - if route_kind == "http_consumer": - stats.exposes_suppressed_feign += 1 - continue - exposes_seen.add(ek) - tables.exposes_rows.append( - ExposesRow( - symbol_id=member.node_id, route_id=rid, - confidence=decl.confidence, - strategy=decl.resolution_strategy, - ), - ) - - tables.routes_rows = sorted(routes_by_id.values(), key=lambda r: r.id) - for row in tables.routes_rows: - stats.by_framework[row.framework] += 1 - stats.by_kind[row.kind] += 1 - n_routes = len(tables.routes_rows) - if n_routes: - stats.routes_resolved_pct = 100.0 * sum( - 1 for r in tables.routes_rows if r.resolved - ) / n_routes - else: - stats.routes_resolved_pct = 100.0 - stats.routes_from_brownfield_pct = 0.0 - by_layer: dict[str, int] = defaultdict(int) - for row in tables.routes_rows: - by_layer[row.source_layer] += 1 - stats.routes_by_layer = dict(sorted(by_layer.items())) - - -def pass5_imperative_edges_subset( - tables: GraphTables, - dirty: set[str], - *, - source_root: Path, - verbose: bool, -) -> None: - """Re-emit Client/Producer/HTTP_CALLS/ASYNC_CALLS for members in dirty files.""" - if verbose: - _verbose_stderr_line("[graph] incremental pass 5 · extracting callers for dirty files") - overrides = load_brownfield_overrides(source_root) - try: - prs = str(source_root.resolve()) - except OSError: - prs = str(source_root) - tables.cross_service_resolution = _load_config_cross_service_resolution(prs) - meta_chain = collect_annotation_meta_chain(prs) - routes_by_id = {r.id: r for r in tables.routes_rows} - existing_route_ids = set(routes_by_id) - http_seen: set[tuple[str, str]] = set() - async_seen: set[tuple[str, str]] = set() - client_seen: set[str] = set() - producer_seen: set[str] = set() - declares_client_seen: set[tuple[str, str]] = set() - declares_producer_seen: set[tuple[str, str]] = set() - route_rows = list(tables.routes_rows) - - def _micro_factor(member: MemberEntry) -> float: - ms = microservice_for_path(member.file_path, source_root) - return 1.0 if ms else 0.85 - - def _append_route(row: RouteRow) -> None: - if row.id in existing_route_ids: - return - existing_route_ids.add(row.id) - routes_by_id[row.id] = row - route_rows.append(row) - - def _phantom_http_route_id(call: OutgoingCallDecl) -> str: - if call.path_template_call and call.method_call: - return _route_id("", "http_endpoint", call.method_call, call.path_template_call, call.path_template_call, "", "", "") - uniq = hashlib.sha1(f"{call.filename}:{call.start_line}:{call.raw_uri}".encode()).hexdigest()[:12] - return f"r:phantom:{uniq}" - - def _phantom_async_route_id(call: OutgoingCallDecl) -> str: - if call.topic_call: - return _route_id("", "kafka_topic", "", "", "", call.topic_call, call.broker_call, "") - uniq = hashlib.sha1(f"{call.filename}:{call.start_line}:{call.raw_topic}".encode()).hexdigest()[:12] - return f"r:phantom:{uniq}" - - for member in sorted(tables.members, key=lambda x: x.node_id): - if member.file_path not in dirty: - continue - if member.decl.is_constructor: - continue - type_decl = tables.types[member.parent_fqn].decl - final_http_calls = resolve_http_client_for_method( - method_decl=member.decl, - enclosing_type=type_decl, - overrides=overrides, - meta_chain=meta_chain, - builtin_calls=member.decl.outgoing_calls, - ) - final_async_calls = resolve_async_producer_for_method( - method_decl=member.decl, - enclosing_type=type_decl, - overrides=overrides, - meta_chain=meta_chain, - builtin_calls=member.decl.outgoing_calls, - ) - micro_factor = _micro_factor(member) - for call in final_http_calls + final_async_calls: - if call.channel == "http": - client_path = (call.path_template_call or "").strip() - client_method = (call.method_call or "").strip().upper() - client_path_template = "" - client_path_regex = "" - if client_path: - client_path_template, client_path_regex = _normalize_path(client_path) - cid = _client_id( - microservice=member.microservice, - member_fqn=call.method_fqn, - client_kind=call.client_kind, - path=client_path, - method=client_method, - ) - if cid not in client_seen: - client_seen.add(cid) - tables.client_rows.append( - ClientRow( - id=cid, client_kind=call.client_kind, - target_service=call.feign_target_name, - path=client_path, - path_template=client_path_template, - path_regex=client_path_regex, - method=client_method, - member_fqn=call.method_fqn, - member_id=member.node_id, - microservice=member.microservice, - module=member.module, - filename=call.filename, - start_line=call.start_line, - end_line=call.end_line, - resolved=call.resolved, - source_layer=_client_source_layer(call.resolution_strategy), - ), - ) - dkey = (member.node_id, cid) - if dkey not in declares_client_seen: - declares_client_seen.add(dkey) - tables.declares_client_rows.append( - DeclaresClientRow( - symbol_id=member.node_id, - client_id=cid, - confidence=call.confidence_base, - strategy=call.resolution_strategy, - ), - ) - rid = "" - strategy = call.resolution_strategy - if call.client_kind == "feign_method": - exposing = next( - (e for e in tables.exposes_rows if e.symbol_id == member.node_id), - None, - ) - if exposing is not None: - rid = exposing.route_id - if not rid: - rid = _phantom_http_route_id(call) - _append_route( - RouteRow( - id=rid, kind="http_endpoint", framework="", - method=call.method_call, path=call.path_template_call, - path_template=call.path_template_call, path_regex="", - topic="", broker="", - feign_name=call.feign_target_name, - feign_url=call.feign_target_url, - microservice="", module="", - filename=call.filename, - start_line=call.start_line, end_line=call.end_line, - resolved=False, source_layer="builtin", - ), - ) - key = (cid, rid) - if key in http_seen: - continue - http_seen.add(key) - conf = call.confidence_base * 0.3 * micro_factor - tables.http_call_rows.append( - HttpCallRow( - client_id=cid, route_id=rid, - confidence=conf, strategy=strategy, - method_call=call.method_call, raw_uri=call.raw_uri, - match="unresolved", - ), - ) - tables.call_edge_stats.http_calls_total += 1 - tables.call_edge_stats.http_calls_by_client_kind[call.client_kind] += 1 - tables.call_edge_stats.http_calls_by_strategy[strategy] += 1 - elif call.channel == "async": - topic_atom = (call.topic_call or "").strip() - pid = _producer_id( - microservice=member.microservice, - member_fqn=call.method_fqn, - producer_kind=call.client_kind, - topic=topic_atom, - ) - if pid not in producer_seen: - producer_seen.add(pid) - tables.producer_rows.append( - ProducerRow( - id=pid, producer_kind=call.client_kind, - topic=topic_atom, broker=call.broker_call, - direction="producer", - member_fqn=call.method_fqn, - member_id=member.node_id, - microservice=member.microservice, - module=member.module, - filename=call.filename, - start_line=call.start_line, - end_line=call.end_line, - resolved=call.resolved, - source_layer=_producer_source_layer(call.resolution_strategy), - ), - ) - dpkey = (member.node_id, pid) - if dpkey not in declares_producer_seen: - declares_producer_seen.add(dpkey) - tables.declares_producer_rows.append( - DeclaresProducerRow( - symbol_id=member.node_id, - producer_id=pid, - confidence=call.confidence_base, - strategy=call.resolution_strategy, - ), - ) - rid = _phantom_async_route_id(call) - _append_route( - RouteRow( - id=rid, kind="kafka_topic", framework="", - method="", path="", path_template="", path_regex="", - topic=call.topic_call, broker=call.broker_call, - feign_name="", feign_url="", - microservice="", module="", - filename=call.filename, - start_line=call.start_line, end_line=call.end_line, - resolved=False, source_layer="builtin", - ), - ) - key = (pid, rid) - if key in async_seen: - continue - async_seen.add(key) - conf = call.confidence_base * 0.3 * micro_factor - strategy = call.resolution_strategy - tables.async_call_rows.append( - AsyncCallRow( - producer_id=pid, route_id=rid, - confidence=conf, strategy=strategy, - direction="producer", raw_topic=call.raw_topic, - match="unresolved", - ), - ) - tables.call_edge_stats.async_calls_total += 1 - tables.call_edge_stats.async_calls_by_client_kind[call.client_kind] += 1 - tables.call_edge_stats.async_calls_by_strategy[strategy] += 1 - - tables.routes_rows = sorted(route_rows, key=lambda r: r.id) - tables.client_rows = sorted(tables.client_rows, key=lambda c: c.id) - tables.declares_client_rows = sorted( - tables.declares_client_rows, - key=lambda e: (e.symbol_id, e.client_id), - ) - tables.client_stats.clients_total = len(tables.client_rows) - tables.client_stats.declares_client_total = len(tables.declares_client_rows) - tables.client_stats.clients_by_kind = defaultdict(int) - for row in tables.client_rows: - tables.client_stats.clients_by_kind[row.client_kind] += 1 - tables.producer_rows = sorted(tables.producer_rows, key=lambda p: p.id) - tables.declares_producer_rows = sorted( - tables.declares_producer_rows, - key=lambda e: (e.symbol_id, e.producer_id), - ) - tables.producer_stats.producers_total = len(tables.producer_rows) - tables.producer_stats.declares_producer_total = len(tables.declares_producer_rows) - tables.producer_stats.producers_by_kind = defaultdict(int) - for row in tables.producer_rows: - tables.producer_stats.producers_by_kind[row.producer_kind] += 1 - - -def _load_remaining_from_db( - conn: kuzu.Connection, - dirty: set[str], -) -> GraphTables: - """Load all remaining (non-dirty) data from DB into a fresh GraphTables.""" - tables = GraphTables() - - # Routes - try: - r = conn.execute( - "MATCH (r:Route) RETURN r.id, r.kind, r.framework, r.method, " - "r.path, r.path_template, r.path_regex, r.topic, r.broker, " - "r.feign_name, r.feign_url, r.microservice, r.module, " - "r.filename, r.start_line, r.end_line, r.resolved" - ) - while r.has_next(): - row = r.get_next() - tables.routes_rows.append(RouteRow( - id=row[0], kind=row[1], framework=row[2], method=row[3], - path=row[4], path_template=row[5], path_regex=row[6], - topic=row[7], broker=row[8], feign_name=row[9], feign_url=row[10], - microservice=row[11], module=row[12], filename=row[13], - start_line=row[14], end_line=row[15], resolved=row[16], - )) - except Exception: - pass - - # Clients - try: - r = conn.execute( - "MATCH (c:Client) RETURN c.id, c.client_kind, c.target_service, " - "c.path, c.path_template, c.path_regex, c.method, " - "c.member_fqn, c.member_id, c.microservice, c.module, " - "c.filename, c.start_line, c.end_line, c.resolved, c.source_layer" - ) - while r.has_next(): - row = r.get_next() - tables.client_rows.append(ClientRow( - id=row[0], client_kind=row[1], target_service=row[2], - path=row[3], path_template=row[4], path_regex=row[5], - method=row[6], member_fqn=row[7], member_id=row[8], - microservice=row[9], module=row[10], filename=row[11], - start_line=row[12], end_line=row[13], resolved=row[14], - source_layer=row[15], - )) - except Exception: - pass - - # Producers - try: - r = conn.execute( - "MATCH (p:Producer) RETURN p.id, p.producer_kind, p.topic, p.broker, " - "p.direction, p.member_fqn, p.member_id, p.microservice, p.module, " - "p.filename, p.start_line, p.end_line, p.resolved, p.source_layer" - ) - while r.has_next(): - row = r.get_next() - tables.producer_rows.append(ProducerRow( - id=row[0], producer_kind=row[1], topic=row[2], broker=row[3], - direction=row[4], member_fqn=row[5], member_id=row[6], - microservice=row[7], module=row[8], filename=row[9], - start_line=row[10], end_line=row[11], resolved=row[12], - source_layer=row[13], - )) - except Exception: - pass - - # HTTP_CALLS - try: - r = conn.execute( - "MATCH (c:Client)-[e:HTTP_CALLS]->(r:Route) " - "RETURN c.id, r.id, e.confidence, e.strategy, " - "e.method_call, e.raw_uri, e.match" - ) - while r.has_next(): - row = r.get_next() - tables.http_call_rows.append(HttpCallRow( - client_id=row[0], route_id=row[1], - confidence=row[2], strategy=row[3], - method_call=row[4], raw_uri=row[5], match=row[6], - )) - except Exception: - pass - - # ASYNC_CALLS - try: - r = conn.execute( - "MATCH (p:Producer)-[e:ASYNC_CALLS]->(r:Route) " - "RETURN p.id, r.id, e.confidence, e.strategy, " - "e.direction, e.raw_topic, e.match" - ) - while r.has_next(): - row = r.get_next() - tables.async_call_rows.append(AsyncCallRow( - producer_id=row[0], route_id=row[1], - confidence=row[2], strategy=row[3], - direction=row[4], raw_topic=row[5], match=row[6], - )) - except Exception: - pass - - # Members (needed for pass6 member_by_id) - try: - r = conn.execute( - "MATCH (s:Symbol) WHERE s.kind = 'method' OR s.kind = 'constructor' " - "RETURN s.id, s.kind, s.name, s.fqn, s.package, " - "s.module, s.microservice, s.filename, " - "s.start_line, s.end_line, s.start_byte, s.end_byte, " - "s.modifiers, s.annotations, s.signature, s.parent_id, s.resolved" - ) - while r.has_next(): - row = r.get_next() - member = MemberEntry( - kind=row[1], - decl=MethodDecl( - name=row[2], - signature=row[14], - start_line=row[8], - end_line=row[9], - start_byte=row[10], - end_byte=row[11], - is_constructor=(row[1] == "constructor"), - modifiers=list(row[12]) if row[12] else [], - annotations=[], - parameters=[], - call_sites=[], - routes=[], - outgoing_calls=[], - local_vars=[], - ), - parent_id=row[15], - parent_fqn=row[3].split("#")[0] if "#" in row[3] else "", - file_path=row[7], - module=row[5], - microservice=row[6], - node_id=row[0], - ) - tables.members.append(member) - except Exception: - pass - - # EXPOSES - try: - r = conn.execute( - "MATCH (s:Symbol)-[e:EXPOSES]->(r:Route) " - "RETURN s.id, r.id, e.confidence, e.strategy" - ) - while r.has_next(): - row = r.get_next() - tables.exposes_rows.append(ExposesRow( - symbol_id=row[0], route_id=row[1], - confidence=row[2], strategy=row[3], - )) - except Exception: - pass - - # DECLARES_CLIENT (for client_hints_by_member in pass6) - try: - r = conn.execute( - "MATCH (s:Symbol)-[e:DECLARES_CLIENT]->(c:Client) " - "RETURN s.id, c.id, e.confidence, e.strategy" - ) - while r.has_next(): - row = r.get_next() - tables.declares_client_rows.append(DeclaresClientRow( - symbol_id=row[0], client_id=row[1], - confidence=row[2], strategy=row[3], - )) - except Exception: - pass - - # DECLARES_PRODUCER (for producer_hints_by_member in pass6) - try: - r = conn.execute( - "MATCH (s:Symbol)-[e:DECLARES_PRODUCER]->(p:Producer) " - "RETURN s.id, p.id, e.confidence, e.strategy" - ) - while r.has_next(): - row = r.get_next() - tables.declares_producer_rows.append(DeclaresProducerRow( - symbol_id=row[0], producer_id=row[1], - confidence=row[2], strategy=row[3], - )) - except Exception: - pass - - return tables - - -def _merge_tables(base: GraphTables, partial: GraphTables) -> GraphTables: - """Merge partial (dirty-file) data into base (remaining from DB). - - Returns a new GraphTables with combined data. Pass6 requires the full set. - """ - merged = GraphTables() - merged.routes_rows = sorted( - base.routes_rows + partial.routes_rows, key=lambda r: r.id, - ) - merged.client_rows = sorted( - base.client_rows + partial.client_rows, key=lambda c: c.id, - ) - merged.producer_rows = sorted( - base.producer_rows + partial.producer_rows, key=lambda p: p.id, - ) - merged.http_call_rows = base.http_call_rows + partial.http_call_rows - merged.async_call_rows = base.async_call_rows + partial.async_call_rows - merged.members = base.members + partial.members - merged.exposes_rows = base.exposes_rows + partial.exposes_rows - merged.declares_client_rows = base.declares_client_rows + partial.declares_client_rows - merged.declares_producer_rows = base.declares_producer_rows + partial.declares_producer_rows - merged.cross_service_resolution = partial.cross_service_resolution or base.cross_service_resolution - return merged - - -def _delete_all_http_async_calls(conn: kuzu.Connection) -> None: - """Delete ALL HTTP_CALLS and ASYNC_CALLS from DB (pre-pass6 rewrite).""" - try: - conn.execute("MATCH (c:Client)-[e:HTTP_CALLS]->(r:Route) DELETE e") - except Exception: - pass - try: - conn.execute("MATCH (p:Producer)-[e:ASYNC_CALLS]->(r:Route) DELETE e") - except Exception: - pass - - -def _write_call_edges_fresh(conn: kuzu.Connection, tables: GraphTables) -> None: - """Write ALL HTTP_CALLS and ASYNC_CALLS from tables (after pass6).""" - for row in tables.http_call_rows: - conn.execute(_CREATE_HTTP_CALL, { - "cid": row.client_id, "rid": row.route_id, - "confidence": row.confidence, "strategy": row.strategy, - "method_call": row.method_call, "raw_uri": row.raw_uri, - "match": row.match, - }) - for row in tables.async_call_rows: - conn.execute(_CREATE_ASYNC_CALL, { - "pid": row.producer_id, "rid": row.route_id, - "confidence": row.confidence, "strategy": row.strategy, - "direction": row.direction, "raw_topic": row.raw_topic, - "match": row.match, - }) - - -def _prune_phantom_routes(conn: kuzu.Connection, tables: GraphTables) -> None: - """Delete phantom routes that pass6 removed from tables.routes_rows.""" - inbound_ids = {r.route_id for r in tables.http_call_rows} | {r.route_id for r in tables.async_call_rows} - surviving = { - r.id for r in tables.routes_rows - if not ( - r.microservice == "" - and r.framework == "" - and not r.resolved - and r.id not in inbound_ids - ) - } - try: - r = conn.execute("MATCH (r:Route) RETURN r.id") - db_ids: set[str] = set() - while r.has_next(): - db_ids.add(r.get_next()[0]) - except Exception: - return - for rid in db_ids - surviving: - # Delete edges first - try: - conn.execute( - "MATCH (s:Symbol)-[e:EXPOSES]->(r:Route {id: $rid}) DELETE e", - {"rid": rid}, - ) - except Exception: - pass - try: - conn.execute( - "MATCH (c:Client)-[e:HTTP_CALLS]->(r:Route {id: $rid}) DELETE e", - {"rid": rid}, - ) - except Exception: - pass - try: - conn.execute( - "MATCH (p:Producer)-[e:ASYNC_CALLS]->(r:Route {id: $rid}) DELETE e", - {"rid": rid}, - ) - except Exception: - pass - try: - conn.execute("MATCH (r:Route {id: $rid}) DELETE r", {"rid": rid}) - except Exception: - pass - - -def _write_meta_incremental( - conn: kuzu.Connection, - source_root: Path, - *, - verbose: bool, -) -> None: - """Write GraphMeta by querying live DB for global stats (incremental mode).""" - - def _count(q: str) -> int: - try: - r = conn.execute(q) - return int(r.get_next()[0]) if r.has_next() else 0 - except Exception: - return 0 - - def _count_json(q: str) -> str: - try: - r = conn.execute(q) - d: dict[str, int] = {} - while r.has_next(): - k, v = r.get_next() - if k: - d[str(k)] = int(v) - return json.dumps(dict(sorted(d.items()))) - except Exception: - return "{}" - - routes_total = _count("MATCH (r:Route) RETURN count(r)") - exposes_total = _count("MATCH ()-[e:EXPOSES]->() RETURN count(e)") - clients_total = _count("MATCH (c:Client) RETURN count(c)") - declares_client_total = _count("MATCH ()-[e:DECLARES_CLIENT]->() RETURN count(e)") - producers_total = _count("MATCH (p:Producer) RETURN count(p)") - declares_producer_total = _count("MATCH ()-[e:DECLARES_PRODUCER]->() RETURN count(e)") - http_calls_total = _count("MATCH ()-[e:HTTP_CALLS]->() RETURN count(e)") - async_calls_total = _count("MATCH ()-[e:ASYNC_CALLS]->() RETURN count(e)") - packages_total = _count("MATCH (s:Symbol) WHERE s.kind = 'package' RETURN count(s)") - files_total = _count("MATCH (s:Symbol) WHERE s.kind = 'file' RETURN count(s)") - types_total = _count( - "MATCH (s:Symbol) WHERE s.kind IN ['class','interface','enum','record','annotation'] RETURN count(s)" - ) - members_total = _count( - "MATCH (s:Symbol) WHERE s.kind IN ['method','constructor'] RETURN count(s)" - ) - phantoms_total = _count("MATCH (s:Symbol) WHERE s.resolved = false RETURN count(s)") - extends_total = _count("MATCH ()-[e:EXTENDS]->() RETURN count(e)") - implements_total = _count("MATCH ()-[e:IMPLEMENTS]->() RETURN count(e)") - injects_total = _count("MATCH ()-[e:INJECTS]->() RETURN count(e)") - declares_total = _count("MATCH ()-[e:DECLARES]->() RETURN count(e)") - overrides_total = _count("MATCH ()-[e:OVERRIDES]->() RETURN count(e)") - calls_total = _count("MATCH ()-[e:CALLS]->() RETURN count(e)") - - routes_fw = _count_json( - "MATCH (r:Route) RETURN r.framework AS k, count(r) AS v" - ) - routes_by_layer = _count_json( - "MATCH (r:Route) WHERE r.source_layer IS NOT NULL RETURN r.source_layer AS k, count(r) AS v" - ) - clients_by_kind = _count_json( - "MATCH (c:Client) RETURN c.client_kind AS k, count(c) AS v" - ) - producers_by_kind = _count_json( - "MATCH (p:Producer) RETURN p.producer_kind AS k, count(p) AS v" - ) - http_by_strategy = _count_json( - "MATCH ()-[e:HTTP_CALLS]->() RETURN e.strategy AS k, count(e) AS v" - ) - async_by_strategy = _count_json( - "MATCH ()-[e:ASYNC_CALLS]->() RETURN e.strategy AS k, count(e) AS v" - ) - http_match_breakdown = _count_json( - "MATCH ()-[e:HTTP_CALLS]->() RETURN e.match AS k, count(e) AS v" - ) - async_match_breakdown = _count_json( - "MATCH ()-[e:ASYNC_CALLS]->() RETURN e.match AS k, count(e) AS v" - ) - - routes_resolved = _count("MATCH (r:Route) WHERE r.resolved = true RETURN count(r)") - routes_resolved_pct = (100.0 * routes_resolved / routes_total) if routes_total else 100.0 - brownfield_routes = _count( - "MATCH (r:Route) WHERE r.source_layer IS NOT NULL AND r.source_layer != 'builtin' RETURN count(r)" - ) - routes_from_brownfield_pct = (100.0 * brownfield_routes / routes_total) if routes_total else 0.0 - - cross_service_total = _count( - "MATCH ()-[e:HTTP_CALLS]->() WHERE e.match = 'cross_service' RETURN count(e)" - ) + _count( - "MATCH ()-[e:ASYNC_CALLS]->() WHERE e.match = 'cross_service' RETURN count(e)" - ) - - http_resolved = _count( - "MATCH ()-[e:HTTP_CALLS]->() WHERE e.strategy != 'unresolved' RETURN count(e)" - ) - http_resolved_pct = float(http_resolved) / float(http_calls_total) if http_calls_total else 0.0 - async_resolved = _count( - "MATCH ()-[e:ASYNC_CALLS]->() WHERE e.strategy != 'unresolved' RETURN count(e)" - ) - async_resolved_pct = float(async_resolved) / float(async_calls_total) if async_calls_total else 0.0 - - http_brownfield = _count( - "MATCH ()-[e:HTTP_CALLS]->() WHERE e.strategy IN " - "['layer_b_ann','layer_a_meta','layer_c_source','layer_b_fqn','codebase_client'] " - "RETURN count(e)" - ) - http_brownfield_pct = (100.0 * http_brownfield / http_calls_total) if http_calls_total else 0.0 - async_brownfield = _count( - "MATCH ()-[e:ASYNC_CALLS]->() WHERE e.strategy IN " - "['layer_b_ann','layer_a_meta','layer_c_source','layer_b_fqn','codebase_producer'] " - "RETURN count(e)" - ) - async_brownfield_pct = (100.0 * async_brownfield / async_calls_total) if async_calls_total else 0.0 - - counts = { - "packages": packages_total, - "files": files_total, - "types": types_total, - "members": members_total, - "phantoms": phantoms_total, - "extends": extends_total, - "implements": implements_total, - "injects": injects_total, - "declares": declares_total, - "overrides": overrides_total, - "calls": calls_total, - "routes": routes_total, - "exposes": exposes_total, - "clients": clients_total, - "declares_client": declares_client_total, - "producers": producers_total, - "declares_producer": declares_producer_total, - "http_calls": http_calls_total, - "async_calls": async_calls_total, - } - - cross_service_resolution = "auto" - try: - r = conn.execute( - "MATCH (m:GraphMeta {key: 'graph'}) RETURN m.cross_service_resolution" - ) - if r.has_next(): - cross_service_resolution = r.get_next()[0] or "auto" - except Exception: - pass - - # Delete old meta before writing new - conn.execute("MATCH (m:GraphMeta {key: 'graph'}) DELETE m") - - conn.execute( - "CREATE (:GraphMeta {key: $k, ontology_version: $ov, built_at: $t, " - "source_root: $sr, counts_json: $cj, parse_errors: $pe, " - "routes_total: $routes_total, exposes_total: $exposes_total, " - "routes_by_framework: $routes_by_framework, routes_resolved_pct: $routes_resolved_pct, " - "routes_from_brownfield_pct: $routes_from_brownfield_pct, routes_by_layer: $routes_by_layer, " - "clients_total: $clients_total, declares_client_total: $declares_client_total, " - "clients_by_kind: $clients_by_kind, " - "producers_total: $producers_total, declares_producer_total: $declares_producer_total, " - "producers_by_kind: $producers_by_kind, " - "http_calls_total: $http_calls_total, async_calls_total: $async_calls_total, " - "http_calls_by_strategy: $http_calls_by_strategy, async_calls_by_strategy: $async_calls_by_strategy, " - "http_calls_resolved_pct: $http_calls_resolved_pct, async_calls_resolved_pct: $async_calls_resolved_pct, " - "http_clients_from_brownfield_pct: $http_clients_from_brownfield_pct, " - "async_producers_from_brownfield_pct: $async_producers_from_brownfield_pct, " - "http_calls_match_breakdown: $http_calls_match_breakdown, " - "async_calls_match_breakdown: $async_calls_match_breakdown, " - "cross_service_calls_total: $cross_service_calls_total, " - "pass3_skipped_cross_service: $pass3_skipped_cross_service, " - "pass3_unresolved_phantom_receiver: $pass3_unresolved_phantom_receiver, " - "pass3_unresolved_chained: $pass3_unresolved_chained, " - "pass4_exposes_suppressed_feign: $pass4_exposes_suppressed_feign, " - "cross_service_resolution: $cross_service_resolution, " - "last_rebuild_mode: $last_rebuild_mode})", - { - "k": "graph", - "ov": ONTOLOGY_VERSION, - "t": int(time.time()), - "sr": str(source_root.resolve()), - "cj": json.dumps(counts), - "pe": 0, - "routes_total": routes_total, - "exposes_total": exposes_total, - "routes_by_framework": routes_fw, - "routes_resolved_pct": routes_resolved_pct, - "routes_from_brownfield_pct": routes_from_brownfield_pct, - "routes_by_layer": routes_by_layer, - "clients_total": clients_total, - "declares_client_total": declares_client_total, - "clients_by_kind": clients_by_kind, - "producers_total": producers_total, - "declares_producer_total": declares_producer_total, - "producers_by_kind": producers_by_kind, - "http_calls_total": http_calls_total, - "async_calls_total": async_calls_total, - "http_calls_by_strategy": http_by_strategy, - "async_calls_by_strategy": async_by_strategy, - "http_calls_resolved_pct": http_resolved_pct, - "async_calls_resolved_pct": async_resolved_pct, - "http_clients_from_brownfield_pct": http_brownfield_pct, - "async_producers_from_brownfield_pct": async_brownfield_pct, - "http_calls_match_breakdown": http_match_breakdown, - "async_calls_match_breakdown": async_match_breakdown, - "cross_service_calls_total": cross_service_total, - "pass3_skipped_cross_service": 0, - "pass3_unresolved_phantom_receiver": 0, - "pass3_unresolved_chained": 0, - "pass4_exposes_suppressed_feign": 0, - "cross_service_resolution": cross_service_resolution, - "last_rebuild_mode": "incremental", - }, - ) - - -def _node_exists(conn: kuzu.Connection, kind: str, node_id: str) -> bool: - try: - r = conn.execute( - f"MATCH (n:{kind} {{id: $id}}) RETURN count(n)", {"id": node_id} - ) - return r.has_next() and int(r.get_next()[0]) > 0 - except Exception: - return False - - -def _write_nodes_incremental( - conn: kuzu.Connection, - tables: GraphTables, - *, - project_root: Path, - meta_chain: dict[str, frozenset[str]] | None, -) -> None: - """Like _write_nodes but skips nodes whose primary key already exists in DB.""" - overrides = load_brownfield_overrides(project_root) - try: - prs = str(project_root.resolve()) - except OSError: - prs = str(project_root) - tables.cross_service_resolution = _load_config_cross_service_resolution(prs) - - # Pre-collect existing IDs to avoid per-query overhead - existing_ids: set[str] = set() - for kind in ("Symbol", "Route", "Client", "Producer", "UnresolvedCallSite"): - try: - r = conn.execute(f"MATCH (n:{kind}) RETURN n.id") - while r.has_next(): - existing_ids.add(r.get_next()[0]) - except Exception: - pass - - mch = meta_chain - for pkg, pid in tables.packages.items(): - if pid not in existing_ids: - conn.execute(_CREATE_SYMBOL, _node_row( - id=pid, kind="package", name=pkg.rsplit(".", 1)[-1], fqn=pkg, package=pkg, - )) - existing_ids.add(pid) - for path, fid in tables.files.items(): - if fid not in existing_ids: - conn.execute(_CREATE_SYMBOL, _node_row( - id=fid, kind="file", name=Path(path).name, fqn=path, filename=path, - )) - existing_ids.add(fid) - for entry in tables.types.values(): - if entry.node_id in existing_ids: - continue - d = entry.decl - role, capabilities = resolve_role_and_capabilities( - d, overrides=overrides, meta_chain=mch, - ) - tables.type_role_by_node_id[entry.node_id] = role - conn.execute(_CREATE_SYMBOL, _node_row( - id=entry.node_id, kind=d.kind, name=d.name, fqn=d.fqn, - package=entry.package, module=entry.module, microservice=entry.microservice, - filename=entry.file_path, - start_line=d.start_line, end_line=d.end_line, - start_byte=d.start_byte, end_byte=d.end_byte, - modifiers=list(d.modifiers), - annotations=[a.name for a in d.annotations], - capabilities=capabilities, - role=role, - signature="", - parent_id=tables.types[entry.outer_fqn].node_id if entry.outer_fqn and entry.outer_fqn in tables.types else "", - )) - existing_ids.add(entry.node_id) - for m in tables.members: - if m.node_id in existing_ids: - continue - conn.execute(_CREATE_SYMBOL, _node_row( - id=m.node_id, kind=m.kind, name=m.decl.name, - fqn=f"{m.parent_fqn}#{m.decl.signature}", - package=tables.types[m.parent_fqn].package if m.parent_fqn in tables.types else "", - module=m.module, microservice=m.microservice, - filename=m.file_path, - start_line=m.decl.start_line, end_line=m.decl.end_line, - start_byte=m.decl.start_byte, end_byte=m.decl.end_byte, - modifiers=list(m.decl.modifiers), - annotations=[a.name for a in m.decl.annotations], - signature=m.decl.signature, parent_id=m.parent_id, - )) - existing_ids.add(m.node_id) - for pid, row in tables.phantoms.items(): - if pid not in existing_ids: - conn.execute(_CREATE_SYMBOL, row) - existing_ids.add(pid) - - -def _write_routes_and_exposes_incremental( - conn: kuzu.Connection, tables: GraphTables, -) -> None: - """Like _write_routes_and_exposes but skips nodes whose PK already exists.""" - existing_route_ids: set[str] = set() - try: - r = conn.execute("MATCH (r:Route) RETURN r.id") - while r.has_next(): - existing_route_ids.add(r.get_next()[0]) - except Exception: - pass - existing_client_ids: set[str] = set() - try: - r = conn.execute("MATCH (c:Client) RETURN c.id") - while r.has_next(): - existing_client_ids.add(r.get_next()[0]) - except Exception: - pass - existing_producer_ids: set[str] = set() - try: - r = conn.execute("MATCH (p:Producer) RETURN p.id") - while r.has_next(): - existing_producer_ids.add(r.get_next()[0]) - except Exception: - pass - - for row in tables.routes_rows: - if row.id not in existing_route_ids: - conn.execute(_CREATE_ROUTE, { - "id": row.id, "kind": row.kind, "framework": row.framework, - "method": row.method, "path": row.path, - "path_template": row.path_template, "path_regex": row.path_regex, - "topic": row.topic, "broker": row.broker, - "feign_name": row.feign_name, "feign_url": row.feign_url, - "microservice": row.microservice, "module": row.module, - "filename": row.filename, - "start_line": row.start_line, "end_line": row.end_line, - "resolved": row.resolved, - }) - for row in tables.exposes_rows: - conn.execute(_CREATE_EXPOSES, { - "sid": row.symbol_id, "rid": row.route_id, - "confidence": row.confidence, "strategy": row.strategy, - }) - for row in tables.client_rows: - if row.id not in existing_client_ids: - conn.execute(_CREATE_CLIENT, asdict(row)) - for row in tables.declares_client_rows: - conn.execute(_CREATE_DECLARES_CLIENT, { - "sid": row.symbol_id, "cid": row.client_id, - "confidence": row.confidence, "strategy": row.strategy, - }) - for row in tables.producer_rows: - if row.id not in existing_producer_ids: - conn.execute(_CREATE_PRODUCER, asdict(row)) - for row in tables.declares_producer_rows: - conn.execute(_CREATE_DECLARES_PRODUCER, { - "sid": row.symbol_id, "pid": row.producer_id, - "confidence": row.confidence, "strategy": row.strategy, - }) - - -def build_ast_graph_incremental( - source_root: Path, - kuzu_path: Path, - changed_paths: set[str], - *, - verbose: bool = False, -) -> str | None: - """Incremental Kuzu rebuild. Returns None on fallback-needed, "incremental" on success.""" - deps_path = kuzu_path.parent / ".deps.json" - deps_index = _read_dependency_index(deps_path) - if deps_index is None: - if verbose: - _verbose_stderr_line("[graph] incremental · .deps.json missing or stale, falling back to full") - return None - - # Heuristic: skip incremental if >50% files are dirty - dirty = expand_to_closure(changed_paths, deps_index) - total = len(deps_index.files) - if total and len(dirty) > 0.5 * total: - if verbose: - _verbose_stderr_line( - f"[graph] incremental · dirty set {len(dirty)}/{total} > 50%, falling back to full" - ) - return None - - if verbose: - _verbose_stderr_line( - f"[graph] incremental · {len(changed_paths)} changed, " - f"{len(dirty)} after closure expansion" - ) - - db = kuzu.Database(str(kuzu_path)) - conn = kuzu.Connection(db) - try: - conn.execute("BEGIN TRANSACTION") - except Exception: - # Kuzu may not support explicit transactions; continue without - pass - - try: - # Delete dirty-file data from DB - if verbose: - _verbose_stderr_line("[graph] incremental · deleting dirty-file data from DB") - for fp in sorted(dirty): - counts = delete_all_for_file(conn, fp) - if verbose: - dirty_counts = {k: v for k, v in counts.items() if v > 0} - if dirty_counts: - _verbose_stderr_line(f" {fp}: {dirty_counts}") - - # Run pass1-5 subset - partial = GraphTables() - asts = pass1_parse_subset(source_root, dirty, verbose=verbose) - - # Register types (pass1 equivalent) - for rel_path, ast in asts.items(): - module = module_for_path(str(source_root / rel_path), source_root) - microservice = microservice_for_path(str(source_root / rel_path), source_root) - file_id = symbol_id("file", rel_path, rel_path, 0) - partial.files[rel_path] = file_id - if ast.package and ast.package not in partial.packages: - partial.packages[ast.package] = symbol_id("package", ast.package, "", 0) - for t in ast.top_level_types: - _register_type( - partial, t, file_path=rel_path, - module=module, microservice=microservice, outer_fqn=None, - ) - - pass2_edges_subset(partial, asts, dirty, verbose=verbose) - pass3_calls_subset(partial, asts, dirty, verbose=verbose) - pass4_routes_subset(partial, asts, dirty, source_root=source_root, verbose=verbose) - pass5_imperative_edges_subset(partial, dirty, source_root=source_root, verbose=verbose) - - # Load remaining non-dirty data from DB for pass6 - remaining = _load_remaining_from_db(conn, dirty) - full = _merge_tables(remaining, partial) - - # Run pass6 globally on full data - pass6_match_edges(full, verbose=verbose) - - # Write partial (dirty-file) data to DB - meta_chain = collect_annotation_meta_chain(str(source_root.resolve())) - _write_nodes_incremental(conn, partial, project_root=source_root, meta_chain=meta_chain) - _populate_declares_rows(partial) - _populate_overrides_rows(partial) - _write_edges(conn, partial) - _write_routes_and_exposes_incremental(conn, partial) - - # Rewrite ALL HTTP_CALLS/ASYNC_CALLS with pass6 outcomes - _delete_all_http_async_calls(conn) - _write_call_edges_fresh(conn, full) - _prune_phantom_routes(conn, full) - - # Write meta (queries live DB for global stats) - _write_meta_incremental(conn, source_root, verbose=verbose) - - # Merge deps: update dirty entries, preserve unchanged - new_deps = _build_file_deps(partial, source_root) - merged_files = dict(deps_index.files) - for fp, deps in new_deps.items(): - merged_files[fp] = deps - merged_index = DepsIndex( - version=_DEPS_VERSION, - ontology_version=ONTOLOGY_VERSION, - files=merged_files, - ) - _write_dependency_index_data(kuzu_path, merged_index) - - try: - conn.execute("COMMIT") - except Exception: - pass - conn.close() - - if verbose: - _verbose_stderr_line("[graph] incremental · done") - return "incremental" - - except Exception: - try: - conn.execute("ROLLBACK") - except Exception: - pass - conn.close() - if verbose: - _verbose_stderr_line("[graph] incremental · failed, falling back to full rebuild") - raise - - -def _create_schema(conn: kuzu.Connection) -> None: - for stmt in ( - _SCHEMA_NODE, - _SCHEMA_UNRESOLVED_CALL_SITE, - _SCHEMA_ROUTE, - _SCHEMA_CLIENT, - _SCHEMA_PRODUCER, - _SCHEMA_META, - _SCHEMA_EXTENDS, - _SCHEMA_IMPLEMENTS, - _SCHEMA_INJECTS, - _SCHEMA_DECLARES, - _SCHEMA_OVERRIDES, - _SCHEMA_CALLS, - _SCHEMA_UNRESOLVED_AT, - _SCHEMA_EXPOSES, - _SCHEMA_DECLARES_CLIENT, - _SCHEMA_DECLARES_PRODUCER, - _SCHEMA_HTTP_CALLS, - _SCHEMA_ASYNC_CALLS, - ): - conn.execute(stmt) - - -def _node_row(**kwargs) -> dict: - base = { - "kind": "", "name": "", "fqn": "", "package": "", - "module": "", "microservice": "", - "filename": "", "start_line": 0, "end_line": 0, - "start_byte": 0, "end_byte": 0, - "modifiers": [], "annotations": [], "capabilities": [], - "role": "OTHER", "signature": "", "parent_id": "", "resolved": True, - } - base.update(kwargs) - return base - - -_CREATE_SYMBOL = ( - "CREATE (:Symbol {id: $id, kind: $kind, name: $name, fqn: $fqn, " - "package: $package, module: $module, microservice: $microservice, " - "filename: $filename, " - "start_line: $start_line, end_line: $end_line, " - "start_byte: $start_byte, end_byte: $end_byte, " - "modifiers: $modifiers, annotations: $annotations, capabilities: $capabilities, " - "role: $role, signature: $signature, parent_id: $parent_id, resolved: $resolved})" -) - - -def _write_nodes( - conn: kuzu.Connection, - tables: GraphTables, - *, - project_root: Path, - meta_chain: dict[str, frozenset[str]] | None, -) -> None: - overrides = load_brownfield_overrides(project_root) - try: - prs = str(project_root.resolve()) - except OSError: - prs = str(project_root) - tables.cross_service_resolution = _load_config_cross_service_resolution(prs) - mch = meta_chain - # packages - for pkg, pid in tables.packages.items(): - conn.execute(_CREATE_SYMBOL, _node_row( - id=pid, kind="package", name=pkg.rsplit(".", 1)[-1], fqn=pkg, package=pkg, - )) - # files - for path, fid in tables.files.items(): - conn.execute(_CREATE_SYMBOL, _node_row( - id=fid, kind="file", name=Path(path).name, fqn=path, filename=path, - )) - # types - for entry in tables.types.values(): - d = entry.decl - role, capabilities = resolve_role_and_capabilities( - d, - overrides=overrides, - meta_chain=mch, - ) - tables.type_role_by_node_id[entry.node_id] = role - conn.execute(_CREATE_SYMBOL, _node_row( - id=entry.node_id, kind=d.kind, name=d.name, fqn=d.fqn, - package=entry.package, - module=entry.module, microservice=entry.microservice, - filename=entry.file_path, - start_line=d.start_line, end_line=d.end_line, - start_byte=d.start_byte, end_byte=d.end_byte, - modifiers=list(d.modifiers), - annotations=[a.name for a in d.annotations], - capabilities=capabilities, - role=role, - signature="", - parent_id=tables.types[entry.outer_fqn].node_id if entry.outer_fqn and entry.outer_fqn in tables.types else "", - )) - # members (methods / constructors) - for m in tables.members: - conn.execute(_CREATE_SYMBOL, _node_row( - id=m.node_id, kind=m.kind, name=m.decl.name, - fqn=f"{m.parent_fqn}#{m.decl.signature}", - package=tables.types[m.parent_fqn].package if m.parent_fqn in tables.types else "", - module=m.module, microservice=m.microservice, - filename=m.file_path, - start_line=m.decl.start_line, end_line=m.decl.end_line, - start_byte=m.decl.start_byte, end_byte=m.decl.end_byte, - modifiers=list(m.decl.modifiers), - annotations=[a.name for a in m.decl.annotations], - signature=m.decl.signature, parent_id=m.parent_id, - )) - # phantoms - for pid, row in tables.phantoms.items(): - conn.execute(_CREATE_SYMBOL, row) + tables.type_role_by_node_id[entry.node_id] = role + conn.execute(_CREATE_SYMBOL, _node_row( + id=entry.node_id, kind=d.kind, name=d.name, fqn=d.fqn, + package=entry.package, + module=entry.module, microservice=entry.microservice, + filename=entry.file_path, + start_line=d.start_line, end_line=d.end_line, + start_byte=d.start_byte, end_byte=d.end_byte, + modifiers=list(d.modifiers), + annotations=[a.name for a in d.annotations], + capabilities=capabilities, + role=role, + signature="", + parent_id=tables.types[entry.outer_fqn].node_id if entry.outer_fqn and entry.outer_fqn in tables.types else "", + )) + # members (methods / constructors) + for m in tables.members: + conn.execute(_CREATE_SYMBOL, _node_row( + id=m.node_id, kind=m.kind, name=m.decl.name, + fqn=f"{m.parent_fqn}#{m.decl.signature}", + package=tables.types[m.parent_fqn].package if m.parent_fqn in tables.types else "", + module=m.module, microservice=m.microservice, + filename=m.file_path, + start_line=m.decl.start_line, end_line=m.decl.end_line, + start_byte=m.decl.start_byte, end_byte=m.decl.end_byte, + modifiers=list(m.decl.modifiers), + annotations=[a.name for a in m.decl.annotations], + signature=m.decl.signature, parent_id=m.parent_id, + )) + # phantoms + for pid, row in tables.phantoms.items(): + conn.execute(_CREATE_SYMBOL, row) _CREATE_EXT = ( @@ -4554,8 +2950,7 @@ def _write_meta(conn: kuzu.Connection, tables: GraphTables, source_root: Path) - "pass3_unresolved_phantom_receiver: $pass3_unresolved_phantom_receiver, " "pass3_unresolved_chained: $pass3_unresolved_chained, " "pass4_exposes_suppressed_feign: $pass4_exposes_suppressed_feign, " - "cross_service_resolution: $cross_service_resolution, " - "last_rebuild_mode: $last_rebuild_mode})", + "cross_service_resolution: $cross_service_resolution})", { "k": "graph", "ov": ONTOLOGY_VERSION, @@ -4591,179 +2986,10 @@ def _write_meta(conn: kuzu.Connection, tables: GraphTables, source_root: Path) - "pass3_unresolved_chained": int(tables.pass3_unresolved_chained), "pass4_exposes_suppressed_feign": int(st.exposes_suppressed_feign), "cross_service_resolution": str(tables.cross_service_resolution), - "last_rebuild_mode": "full", }, ) -# ---------- dependency index (sidecar .deps.json) ---------- - - -def _build_file_deps(tables: GraphTables, source_root: Path) -> dict[str, FileDeps]: - """Build per-file dependency metadata from GraphTables for the sidecar index.""" - # node_id -> file_path lookup - node_file: dict[str, str] = {} - for entry in tables.types.values(): - node_file[entry.node_id] = entry.file_path - for m in tables.members: - node_file[m.node_id] = m.file_path - - # node_id -> identifier (type FQN or "TypeFQN#method()" for members) - node_fqn: dict[str, str] = {} - for entry in tables.types.values(): - node_fqn[entry.node_id] = entry.decl.fqn - for m in tables.members: - node_fqn[m.node_id] = f"{m.parent_fqn}#{m.decl.signature}" - - deps: dict[str, FileDeps] = {} - for fp in tables.files: - deps[fp] = FileDeps() - - # ext_hash — read file from disk and hash - for fp in deps: - full = source_root / fp - try: - raw = full.read_bytes() - deps[fp].ext_hash = f"sha256:{hashlib.sha256(raw).hexdigest()}" - except OSError: - deps[fp].ext_hash = "" - - # declares — type FQNs declared in this file - for entry in tables.types.values(): - fp = entry.file_path - if fp in deps: - deps[fp].declares.append(entry.outer_fqn or entry.decl.fqn) - - # injects — FQNs of injected symbols (from injects_rows) - for row in tables.injects_rows: - fp = node_file.get(row.src_id) - if fp and fp in deps: - deps[fp].injects.append(row.dst_fqn) - - # extends — FQNs of extended types (from extends_rows) - for row in tables.extends_rows: - fp = node_file.get(row.src_id) - if fp and fp in deps: - deps[fp].extends.append(row.dst_fqn) - - # calls — callee identifiers (method/type FQNs from calls_rows) - for row in tables.calls_rows: - fp = node_file.get(row.src_id) - if fp and fp in deps: - callee = node_fqn.get(row.dst_id) - if callee is not None: - deps[fp].calls.append(callee) - - # uses_anno — annotation simple names from types + members (deduplicated) - for entry in tables.types.values(): - fp = entry.file_path - if fp in deps: - for anno in entry.decl.annotations: - if anno.name not in deps[fp].uses_anno: - deps[fp].uses_anno.append(anno.name) - for m in tables.members: - fp = m.file_path - if fp in deps: - for anno in m.decl.annotations: - if anno.name not in deps[fp].uses_anno: - deps[fp].uses_anno.append(anno.name) - - # overrides — overridden method FQNs (from overrides_rows) - for row in tables.overrides_rows: - fp = node_file.get(row.src_id) - if fp and fp in deps: - overridden = node_fqn.get(row.dst_id) - if overridden is not None: - deps[fp].overrides.append(overridden) - - # declares_clients — member FQNs declaring HTTP clients - for row in tables.client_rows: - fp = row.filename - if fp in deps: - deps[fp].declares_clients.append(row.member_fqn) - - # declares_producers — member FQNs declaring async producers - for row in tables.producer_rows: - fp = row.filename - if fp in deps: - deps[fp].declares_producers.append(row.member_fqn) - - return deps - - -_DEPS_VERSION = 1 - - -def _write_dependency_index( - db_path: Path, - tables: GraphTables, - source_root: Path, -) -> None: - """Write sidecar .deps.json alongside the Kuzu database.""" - deps = _build_file_deps(tables, source_root) - idx = DepsIndex( - version=_DEPS_VERSION, - ontology_version=ONTOLOGY_VERSION, - files=deps, - ) - _write_dependency_index_data(db_path, idx) - - -def _write_dependency_index_data(db_path: Path, idx: DepsIndex) -> None: - """Write a pre-built DepsIndex to the sidecar .deps.json.""" - payload = { - "version": idx.version, - "ontology_version": idx.ontology_version, - "files": {fp: asdict(d) for fp, d in sorted(idx.files.items())}, - } - deps_path = db_path.parent / ".deps.json" - tmp = deps_path.with_suffix(".json.tmp") - tmp.write_text(json.dumps(payload, indent=2)) - tmp.rename(deps_path) - - -@dataclass -class DepsIndex: - version: int - ontology_version: int - files: dict[str, FileDeps] - - -def _read_dependency_index(deps_path: Path) -> DepsIndex | None: - """Read and validate sidecar .deps.json. Returns None on missing/corrupt/stale.""" - if not deps_path.is_file(): - return None - try: - raw = json.loads(deps_path.read_text()) - except (json.JSONDecodeError, OSError): - return None - try: - if raw.get("version") != _DEPS_VERSION: - return None - if raw.get("ontology_version") != ONTOLOGY_VERSION: - return None - files: dict[str, FileDeps] = {} - for fp, obj in raw.get("files", {}).items(): - files[fp] = FileDeps( - ext_hash=obj.get("ext_hash", ""), - declares=obj.get("declares", []), - injects=obj.get("injects", []), - extends=obj.get("extends", []), - calls=obj.get("calls", []), - uses_anno=obj.get("uses_anno", []), - overrides=obj.get("overrides", []), - declares_clients=obj.get("declares_clients", []), - declares_producers=obj.get("declares_producers", []), - ) - except Exception: - return None - return DepsIndex( - version=raw["version"], - ontology_version=raw["ontology_version"], - files=files, - ) - - def write_kuzu( db_path: Path, tables: GraphTables, @@ -4805,7 +3031,6 @@ def write_kuzu( _verbose_stderr_line(f"[graph] writing · routes/exposes written in {time.time() - t2:.2f}s") _write_meta(conn, tables, source_root) conn.close() - _write_dependency_index(db_path, tables, source_root) # ---------- CLI ---------- @@ -4830,14 +3055,6 @@ def main() -> int: ), ) parser.add_argument("--verbose", action="store_true") - parser.add_argument( - "--changed-paths", - default=None, - help=( - "Path to a file containing newline-separated changed file paths " - "(internal flag for incremental rebuild)" - ), - ) args = parser.parse_args() root = Path(args.source_root).expanduser().resolve() if args.source_root else Path.cwd().resolve() @@ -4847,35 +3064,6 @@ def main() -> int: kuzu_path = Path(args.kuzu_path).expanduser() if args.kuzu_path else _default_kuzu_path() - if args.changed_paths: - # Incremental rebuild mode - cp_file = Path(args.changed_paths) - if not cp_file.is_file(): - print(f"changed-paths file not found: {cp_file}", file=sys.stderr) - return 2 - changed = set( - line.strip() for line in cp_file.read_text().splitlines() if line.strip() - ) - if not changed: - if args.verbose: - _verbose_stderr_line("[graph] · empty changed-paths, falling back to full rebuild") - # Fall through to full rebuild - else: - try: - result = build_ast_graph_incremental( - root, kuzu_path, changed, verbose=args.verbose, - ) - if result is not None: - if args.verbose: - _verbose_stderr_line(f"[graph] done · incremental · kuzu at {kuzu_path}") - return 0 - if args.verbose: - _verbose_stderr_line("[graph] · incremental declined, falling back to full rebuild") - except Exception as exc: - if args.verbose: - _verbose_stderr_line(f"[graph] · incremental failed ({exc}), falling back to full rebuild") - - # Full rebuild tables = GraphTables() asts = pass1_parse(root, tables, verbose=args.verbose) pass2_edges(tables, asts, verbose=args.verbose) diff --git a/docs/CONFIGURATION.md b/docs/CONFIGURATION.md index dd4a81ea..8a80cd31 100644 --- a/docs/CONFIGURATION.md +++ b/docs/CONFIGURATION.md @@ -22,22 +22,6 @@ For the architecture rationale (the GPS metaphor, three-layer design, future wor The operator-facing surface is **six** variables (plus MCP-only `JAVA_CODEBASE_RAG_SOURCE_ROOT` below). Precedence for knobs that also exist as CLI flags or YAML entries is **CLI flag > env var > YAML > built-in default** (see [`JAVA-CODEBASE-RAG-CLI.md`](./JAVA-CODEBASE-RAG-CLI.md)). -### Source root discovery and precedence - -The server and CLI resolve the effective Java source root through a precedence chain: - -| Priority | Source | How it resolves | -|---|---|---| -| 1 (highest) | CLI `--source-root` | Absolute, or relative to cwd | -| 2 | `JAVA_CODEBASE_RAG_SOURCE_ROOT` env var | Absolute, or relative to cwd | -| 3 | YAML `source_root` field | **Relative to the config file directory** (not cwd) | -| 4 | Walk-up discovery | Walk from cwd upward to find `.java-codebase-rag.yml`; uses the config file's directory as source root | -| 5 (lowest) | cwd | No config found, no YAML override | - -Walk-up checks each directory from cwd upward for `.java-codebase-rag.yml` or `.java-codebase-rag.yaml`. The **first match wins** (closest to cwd). The walk stops at `$HOME` (inclusive — `$HOME` itself is checked) or the filesystem root. This mirrors how git finds `.git`. - -### Variables - | Variable | Purpose | |---|---| | `JAVA_CODEBASE_RAG_INDEX_DIR` | Local filesystem **directory** for Lance tables, the Kuzu file `code_graph.kuzu`, and cocoindex state (`cocoindex.db`). Not a `lancedb://` or cloud URI — use a path. Default: `./.java-codebase-rag/` under the resolved Java tree root. | @@ -47,14 +31,14 @@ Walk-up checks each directory from cwd upward for `.java-codebase-rag.yml` or `. | `JAVA_CODEBASE_RAG_RUN_HEAVY` | Test gate: set to `1` / `true` / `yes` to run the slow cocoindex + Lance end-to-end test (`pytest`); not used in normal operator workflows. | | `JAVA_CODEBASE_RAG_HINTS_ENABLED` | When `0` / `false` / `no`, suppress `hints_structured` and `advisories` from all MCP tool responses. Overridable via `.java-codebase-rag.yml` `hints.enabled`. Default: enabled. | -**MCP host launchers** also set `JAVA_CODEBASE_RAG_SOURCE_ROOT` to the Java repository root when it differs from the server process cwd (see `mcp.json.example` in the repo root). When the env var is unset, the server walks up from cwd to discover the config automatically. +**MCP host launchers** also set `JAVA_CODEBASE_RAG_SOURCE_ROOT` to the Java repository root when it differs from the server process cwd (see `mcp.json.example` in the repo root). Only the names in the table above (plus `JAVA_CODEBASE_RAG_SOURCE_ROOT` for MCP hosts) are read as configuration. Project config belongs in **`.java-codebase-rag.yml`** (or `.yaml`). **Paths and conventions** (for scripts and operators): - **`JAVA_CODEBASE_RAG_INDEX_DIR`** — filesystem path to the index directory (not a URI). Lance opens this directory; Kuzu is always `/code_graph.kuzu`; cocoindex keeps **`cocoindex.db`** next to them. -- **Java tree root** — CLI: `--source-root` (else walk-up discovery, else cwd). MCP stdio: `JAVA_CODEBASE_RAG_SOURCE_ROOT` env var (else walk-up from cwd). YAML: `source_root` field resolved relative to the config file directory. +- **Java tree root** — CLI: `--source-root` (else cwd). MCP stdio: set `JAVA_CODEBASE_RAG_SOURCE_ROOT` when the Java repo root differs from the server process cwd. - **`microservice_roots`** — configure only under **`microservice_roots:`** in `.java-codebase-rag.yml` (or `.yaml`). - **Chunk context diagnostics / heavy tests** — `JAVA_CODEBASE_RAG_DEBUG_CONTEXT`, `JAVA_CODEBASE_RAG_RUN_HEAVY` (see the table above). @@ -64,24 +48,16 @@ Python package: **`java_codebase_rag`** (`python -m java_codebase_rag.cli`). ## 2. Project YAML reference (`.java-codebase-rag.yml`) -A single file at the project root (the directory you pass as `--source-root`, or discovered via walk-up, or cwd) holds everything that isn't an environment variable. The two accepted filenames are `.java-codebase-rag.yml` and `.java-codebase-rag.yaml`; if both exist, `.yml` wins. +A single file at the project root (the directory you pass as `--source-root`, or cwd) holds everything that isn't an environment variable. The two accepted filenames are `.java-codebase-rag.yml` and `.java-codebase-rag.yaml`; if both exist, `.yml` wins. **All keys are optional.** A project with no YAML at all uses built-in defaults plus env vars. Add only the keys you need. ```yaml # .java-codebase-rag.yml — full reference, every key annotated. -# Place at the project root (same directory you pass as --source-root), -# or anywhere above it — the server walks up from cwd to find it. +# Place at the project root (same directory you pass as --source-root). # -------- Core knobs (mirror env vars; precedence: CLI > env > YAML > default) -------- -# Source root: where your Java source tree lives. When set, resolves relative to -# this config file's directory (not cwd). Useful when the config file lives outside -# the Java tree (e.g. in a monorepo root above multiple Java projects). -# When omitted, defaults to the directory containing this config file (found via walk-up). -# CLI: --source-root. Env: JAVA_CODEBASE_RAG_SOURCE_ROOT. -source_root: ./my-java-project - # Index directory: where Lance tables, code_graph.kuzu, and cocoindex.db live. # - Tilde (`~`) is expanded; `$VAR` is NOT (use absolute paths or `~`). # - Relative paths resolve against source_root, not cwd. @@ -195,7 +171,6 @@ async_producer_overrides: | Field | Expanded? | Notes | |---|---|---| -| `source_root` | partial | `~` expanded; `$VAR` is NOT expanded. Relative paths resolve against the **config file directory** (not cwd). | | `index_dir` | partial | `~` expanded; `$VAR` is NOT expanded. Relative paths resolve against `source_root`. | | `embedding.model` (when path-shaped) | yes | Path-shape = starts with `/`, `./`, `../`, `~`, or contains `$`. Plain `org/name` is treated as a hub id and passed through. Applies to the value after CLI > env > YAML > default precedence. Long-lived MCP hosts also apply the same expansion when reading `SBERT_MODEL` from the process environment (so table metadata and search agree with `index_common` defaults). | | `embedding.device` | n/a | Device strings (`cpu`, `cuda`, `mps`) aren't paths. | @@ -204,7 +179,7 @@ async_producer_overrides: **Tips & gotchas:** -- **The file is discovered by walking up from cwd** — like git finds `.git`. Place it at or above your project root. The walk stops at `$HOME` (inclusive). You can also set `JAVA_CODEBASE_RAG_SOURCE_ROOT` or use `--source-root` to bypass discovery entirely. +- **The file must be at `source_root`**, not in `$HOME`. The MCP server reads `JAVA_CODEBASE_RAG_SOURCE_ROOT` to find it; the CLI uses `--source-root` (else cwd). - **Don't commit secrets** into this YAML — it sits next to your source tree and is read by every operator who clones it. - **Rebuild after editing brownfield overrides.** Run a full `java-codebase-rag reprocess` (no flags) so Lance and Kuzu stay coherent, or use `--graph-only` / `--vectors-only` when you know only one store needs invalidation. Editing `embedding.model` requires a vector rebuild (`reprocess` or `--vectors-only`). - **Diagnose what's loaded.** `java-codebase-rag meta` prints the resolved config and each value's `*_source` (`cli` / `env` / `yaml` / `default`) — see `embedding_model_source`, `embedding_device_source`, `index_dir_source`. diff --git a/java_codebase_rag/cli.py b/java_codebase_rag/cli.py index 95e0eaa4..27ad800a 100644 --- a/java_codebase_rag/cli.py +++ b/java_codebase_rag/cli.py @@ -16,7 +16,6 @@ from java_codebase_rag.config import ( ResolvedOperatorConfig, describe_path_sizes, - discover_project_root, emit_legacy_env_hints_if_present, emit_legacy_yaml_hint_if_needed, index_dir_has_existing_artifacts, @@ -232,18 +231,6 @@ def _cmd_init(args: argparse.Namespace) -> int: cfg = _resolved_from_ns(args) _startup_hints(cfg) cfg.apply_to_os_environ() - parent_cfg_dir = discover_project_root(cfg.source_root.parent) - if parent_cfg_dir is not None: - from java_codebase_rag.config import YAML_CONFIG_FILENAMES - - for name in YAML_CONFIG_FILENAMES: - if (parent_cfg_dir / name).is_file(): - print( - f"Warning: found existing config at {parent_cfg_dir / name}. " - "Creating a new project here will create a separate index.", - file=sys.stderr, - ) - break occupied, paths = index_dir_has_existing_artifacts(cfg.index_dir) if occupied: _emit( @@ -534,12 +521,13 @@ def _cmd_tables(args: argparse.Namespace) -> int: def _cmd_diagnose_ignore(args: argparse.Namespace) -> int: + import server # lazy from path_filtering import LayeredIgnore # lazy cfg = _resolved_from_ns(args) _startup_hints(cfg) cfg.apply_to_os_environ() - root = cfg.source_root + root = server._project_root() raw = Path(args.path) try: abs_path = raw.resolve() if raw.is_absolute() else (root / raw).resolve() diff --git a/java_codebase_rag/config.py b/java_codebase_rag/config.py index 6f04f822..d9550b3f 100644 --- a/java_codebase_rag/config.py +++ b/java_codebase_rag/config.py @@ -115,28 +115,6 @@ def emit_legacy_yaml_hint_if_needed(source_root: Path) -> None: return -def discover_project_root(start: Path) -> Path | None: - """Walk from *start* upward looking for a YAML config file. - - Returns the directory containing the first matching config file - (closest to *start*), or ``None`` if no config is found before - reaching ``$HOME`` (inclusive — ``$HOME`` itself is checked) or - the filesystem root. - """ - home = Path.home().resolve() - cur = start.resolve() - while True: - for name in YAML_CONFIG_FILENAMES: - if (cur / name).is_file(): - return cur - if cur == home: - return None - parent = cur.parent - if parent == cur: - return None - cur = parent - - def find_yaml_config_file(source_root: Path) -> Path | None: for name in YAML_CONFIG_FILENAMES: p = source_root / name @@ -299,33 +277,10 @@ def resolve_operator_config( cli_embedding_model: str | None = None, cli_embedding_device: str | None = None, ) -> ResolvedOperatorConfig: - # Phase 1 — find the config file directory. - if source_root is not None: - config_dir = source_root.expanduser().resolve() - else: - discovered = discover_project_root(Path.cwd()) - if discovered is not None: - config_dir = discovered - else: - config_dir = Path.cwd().resolve() - - yaml_dict = load_yaml_mapping(config_dir) - - # Phase 2 — resolve effective source root. - env_root = os.environ.get(ENV_SOURCE_ROOT, "").strip() - if source_root is not None: - effective_root = source_root.expanduser().resolve() - elif env_root: - effective_root = Path(env_root).expanduser().resolve() - else: - yaml_sr = yaml_dict.get("source_root") - if isinstance(yaml_sr, str) and yaml_sr.strip(): - effective_root = (config_dir / Path(yaml_sr.strip()).expanduser()).resolve() - else: - effective_root = config_dir - + root = (source_root or Path.cwd()).expanduser().resolve() + yaml_dict = load_yaml_mapping(root) index_dir, index_src = _resolve_index_dir_path( - source_root=effective_root, cli_index_dir=cli_index_dir, yaml_dict=yaml_dict + source_root=root, cli_index_dir=cli_index_dir, yaml_dict=yaml_dict ) model, model_src = _pick_str( cli_val=cli_embedding_model, @@ -349,7 +304,7 @@ def resolve_operator_config( ku = index_dir / "code_graph.kuzu" coco = index_dir / "cocoindex.db" return ResolvedOperatorConfig( - source_root=effective_root, + source_root=root, index_dir=index_dir, kuzu_path=ku, cocoindex_db=coco, diff --git a/mcp.json.example b/mcp.json.example index 86596479..7a56372c 100644 --- a/mcp.json.example +++ b/mcp.json.example @@ -2,37 +2,12 @@ "mcpServers": { "java-codebase-rag": { "type": "stdio", - "command": "java-codebase-rag-mcp" + "command": "java-codebase-rag-mcp", + "env": { + "JAVA_CODEBASE_RAG_INDEX_DIR": "/ABSOLUTE/PATH/TO/.java-codebase-rag", + "JAVA_CODEBASE_RAG_SOURCE_ROOT": "/ABSOLUTE/PATH/TO/your-java-project", + "SBERT_MODEL": "sentence-transformers/all-MiniLM-L6-v2" + } } } } - -// ────────────────────────────────────────────────────────────────────────────── -// 1. MINIMAL CONFIG — no env vars required -// -// Requires a `.java-codebase-rag.yml` in (or above) your Java project root. -// The server walks up from cwd to find the config file (like git finds .git). -// Run `java-codebase-rag init` from the project root first to create the index. -// -// Claude Code: drop this as `.mcp.json` in your project root. -// Claude Desktop: paste into ~/Library/Application Support/Claude/claude_desktop_config.json -// and add `"cwd": "/path/to/your-java-project"` inside the server block. -// ────────────────────────────────────────────────────────────────────────────── - -// ────────────────────────────────────────────────────────────────────────────── -// 2. FULL CONFIG — explicit env vars (works without .java-codebase-rag.yml) -// -// { -// "mcpServers": { -// "java-codebase-rag": { -// "type": "stdio", -// "command": "java-codebase-rag-mcp", -// "env": { -// "JAVA_CODEBASE_RAG_INDEX_DIR": "/ABSOLUTE/PATH/TO/.java-codebase-rag", -// "JAVA_CODEBASE_RAG_SOURCE_ROOT": "/ABSOLUTE/PATH/TO/your-java-project", -// "SBERT_MODEL": "sentence-transformers/all-MiniLM-L6-v2" -// } -// } -// } -// } -// ────────────────────────────────────────────────────────────────────────────── diff --git a/plans/active/PLAN-DIRS-HIERARCHY.md b/plans/active/PLAN-DIRS-HIERARCHY.md deleted file mode 100644 index 93f5c5f7..00000000 --- a/plans/active/PLAN-DIRS-HIERARCHY.md +++ /dev/null @@ -1,203 +0,0 @@ -# Plan: Walk-up config discovery and configurable source root - -Status: **active (planning)**. This plan implements -[`propose/active/DIRS-HIERARCHY-PROPOSE.md`](../../propose/active/DIRS-HIERARCHY-PROPOSE.md) -as a single PR. - -Depends on: none. - -## Goal - -- Users can run CLI and MCP commands from any subdirectory within their project — the tool walks up to find `.java-codebase-rag.yml`, like git finds `.git`. -- The YAML config gains an optional `source_root` field so the config can live separately from the Java source code, and the index dir auto-derives from the resolved source root. -- Existing workflows where cwd = config dir produce identical behavior. No breaking changes. - -## Principles (do not relitigate in review) - -- **First match wins.** Closest config to cwd, not "most specific" or "deepest". Matches git behavior. -- **`$HOME` is the inclusive boundary.** Check `$HOME` itself, do not walk past it. -- **Walk-up is always-on** when no explicit source root is given (CLI flag or env var). No `--walk-up` opt-out flag. -- **YAML `source_root` resolves relative to the config file directory.** CLI `--source-root` resolves relative to cwd. Different resolution bases are intentional — the precedence table handles priority. -- **Index dir follows source root.** Default index dir = `/.java-codebase-rag/`. This does not change; walk-up just changes how source root itself is found. -- **No changes to `init` behavior** beyond a soft warning when a parent config exists. -- **No changes to indexing, query, or graph-building logic.** This is config discovery only. - -## PR breakdown - overview - -| PR | Scope | Ontology bump | Areas of concern | Test buckets | Independent of | -| --- | --- | --- | --- | --- | --- | -| PR-1 | Walk-up config discovery + `source_root` YAML field | none | Precedence chain correctness; server/CLI parity; boundary conditions ($HOME, root) | unit tests for discovery + precedence + integration | — | - -Landing order: **PR-1** (single PR). - -## Resolved design decisions - -| Topic | Decision | -| --- | --- | -| Config file name checked | `.java-codebase-rag.yml` and `.java-codebase-rag.yaml` (existing `YAML_CONFIG_FILENAMES` tuple) | -| Boundary for walk-up | `$HOME` inclusive — check `$HOME` itself but do not walk past it | -| YAML field name | `source_root` — same name as CLI flag for conceptual consistency | -| Resolution base for YAML `source_root` | Config file's parent directory (not cwd) | -| `init` behavior | Unchanged — creates config + index in the specified directory. Only adds a soft warning if a parent config is detected | -| Multiple nested configs | First match wins (closest to cwd). Mirrors git behavior | -| New function location | `config.py` — all config resolution logic lives there already | -| `discover_project_root` return | `Path | None` — returns the directory containing the config file, not the config file path itself | - ---- - -# PR-1 — Walk-up config discovery and configurable source root - -## File-by-file changes - -### 1. `java_codebase_rag/config.py` - -**New function: `discover_project_root(start: Path) -> Path | None`** - -- Canonicalize `start` via `Path.resolve()` -- Walk from `start` upward, checking each directory for files matching `YAML_CONFIG_FILENAMES` -- First match returns that directory (the parent of the found config file, not the file path itself) -- Stop at `$HOME` (inclusive — check `$HOME` itself) or filesystem root. Do not walk past `$HOME`. -- Return `None` if no config found - -**Modify: `resolve_operator_config()` — two-phase resolution** - -The core change is separating *config file discovery* from *effective source root resolution*. The exact sequence: - -1. **Phase 1 — find the config file directory.** If `source_root` is provided (CLI flag or env var), the config dir = that value (no walk-up). Otherwise, call `discover_project_root(Path.cwd())`. If walk-up found a config dir, use it. Otherwise fall back to `Path.cwd().resolve()` (unchanged behavior). -2. **Load YAML** from the config dir via `load_yaml_mapping(config_dir)`. -3. **Phase 2 — resolve effective source root.** Check for a `source_root` key in the YAML. If present, resolve it relative to the config dir (not cwd). The effective source root is then: - - CLI `--source-root` (already handled — `source_root` is not `None` in phase 1, so phase 2 is skipped) - - env `JAVA_CODEBASE_RAG_SOURCE_ROOT` (checked before walk-up in both `server.py` and `resolve_operator_config`) - - YAML `source_root` (resolved relative to config dir) - - Walk-up discovery result (= config dir itself, which is the default when no YAML override) - - `Path.cwd()` (no config found, no YAML override) -4. **Derive index dir** from the effective source root via `_resolve_index_dir_path()`. No edits to `_resolve_index_dir_path` itself — the caller ensures the effective source root (after YAML resolution) is what gets passed through. - -**Note:** Do NOT introduce a `find_config_dir` wrapper. The two-phase logic lives directly in `resolve_operator_config()` for clarity. The only new public function is `discover_project_root()`. - -### 2. `server.py` - -**Modify: `_project_root()`** - -- Current logic: env var → cwd fallback -- New logic: env var → `discover_project_root(Path.cwd())` → cwd fallback -- Import `discover_project_root` from `java_codebase_rag.config` - -**Modify: `_resolve_lancedb_uri()`** - -- Currently falls back to `Path.cwd() / ".java-codebase-rag"` when `JAVA_CODEBASE_RAG_INDEX_DIR` is unset. -- After walk-up, this should use the discovered source root (via `_project_root()`) for consistency. -- The server's `list_code_index_tables_payload()` calls `resolve_operator_config(source_root=_project_root())`, so index dir is derived from the effective source root. But `_resolve_lancedb_uri()` is called independently in some paths. Ensure it uses `_project_root()` instead of raw `Path.cwd()` when the env var is unset. - -### 3. `java_codebase_rag/cli.py` - -**Modify: `_parse_source_root()` / `_resolved_from_ns()`** - -- `_parse_source_root()` stays the same (returns `None` when `--source-root` is not given) -- `_resolved_from_ns()` already passes `source_root=root` to `resolve_operator_config()` — walk-up logic in `resolve_operator_config()` handles the `None` case - -**Modify: `init` command handler** - -- After resolving `cfg = _resolved_from_ns(args)`, check for a parent config by calling `discover_project_root(cfg.source_root.parent)` — this checks whether a config exists in any ancestor of the *resolved source root* (not the config dir, since `init` creates the config at the source root) -- If found, emit a soft warning to stderr: - > Warning: found existing config at `[parent]/.java-codebase-rag.yml`. Creating a new project here will create a separate index. - -### 4. `mcp.json.example` - -- Add a comment block showing the minimal zero-env-var config -- Keep the existing full example as an alternative -- Show both Claude Desktop and Claude Code variants - -### 5. `README.md` - -- Update the MCP host wiring section to mention walk-up discovery -- Document the `source_root` YAML field -- Update the minimal `.mcp.json` example to show that env vars are now optional - -### 6. `docs/CONFIGURATION.md` - -- Add `source_root` to the YAML config reference table -- Document the walk-up discovery behavior -- Update the precedence chain table to include the YAML `source_root` field - -## Tests for PR-1 - -All new tests go in **`tests/test_config.py`** (new file). Tests that exercise `_project_root()` in `server.py` go in **`tests/test_mcp_server_project_root.py`** (new file) to keep MCP test concerns separate. - -### Config discovery tests (`tests/test_config.py`) - -1. `test_discover_project_root_finds_config_in_cwd` — config in cwd, returns cwd -2. `test_discover_project_root_walks_up` — config in parent, returns parent -3. `test_discover_project_root_stops_at_home_boundary` — config in `$HOME` itself, walk-up from subdirectory of `$HOME` finds it (inclusive boundary) -4. `test_discover_project_root_not_found_above_home` — no config anywhere under `$HOME`, returns `None` -5. `test_discover_project_root_not_found` — no config anywhere, returns `None` -6. `test_discover_project_root_first_match_wins` — configs at two levels (cwd subdirectory has one, parent has another), closest to cwd wins - -### Source root resolution tests (`tests/test_config.py`) - -7. `test_source_root_from_yaml_relative` — `source_root: ../` resolves to parent of config dir -8. `test_source_root_from_yaml_absolute` — `source_root: /abs/path` resolves to absolute path -9. `test_source_root_precedence_cli_over_yaml` — CLI flag wins over YAML `source_root` -10. `test_source_root_precedence_yaml_over_discovery` — YAML `source_root` wins over config dir default -11. `test_source_root_precedence_env_over_yaml` — env var wins over YAML `source_root` -12. `test_existing_behavior_unchanged` — no walk-up, cwd = config dir → identical behavior to today - -### Server integration test (`tests/test_mcp_server_project_root.py`) - -13. `test_project_root_uses_discover_when_env_unset` — `_project_root()` returns discovered config dir when `JAVA_CODEBASE_RAG_SOURCE_ROOT` is unset - -## Definition of done (PR-1) - -- [ ] `discover_project_root()` works with first-match-wins semantics, stops at `$HOME` (inclusive) -- [ ] `source_root` YAML field is parsed and resolved relative to config dir -- [ ] Precedence chain: CLI > env > YAML > discovery > cwd -- [ ] `_project_root()` in `server.py` uses walk-up when env var is unset -- [ ] `_resolve_lancedb_uri()` in `server.py` uses `_project_root()` instead of raw `Path.cwd()` for fallback -- [ ] CLI commands work from subdirectories (walk-up finds config) -- [ ] `init` emits soft warning when parent config detected -- [ ] All 13 named tests pass -- [ ] Existing test suite passes (no regressions) -- [ ] `mcp.json.example` shows minimal zero-env-var config -- [ ] README and CONFIGURATION docs updated - -## Implementation step list - -| # | Step | File(s) | Done when | -| - | - | - | - | -| 1 | Add `discover_project_root(start)` | `config.py`, `tests/test_config.py` | Tests 1–6 pass | -| 2 | Add `source_root` YAML field parsing and resolution | `config.py`, `tests/test_config.py` | Tests 7–8 pass | -| 3 | Wire precedence chain in `resolve_operator_config()` | `config.py`, `tests/test_config.py` | Tests 9–12 pass | -| 4 | Update `_project_root()` to use walk-up | `server.py`, `tests/test_mcp_server_project_root.py` | Test 13 passes; server resolves source root via walk-up when env var unset | -| 5 | Update `_resolve_lancedb_uri()` to use `_project_root()` fallback | `server.py` | Lance URI and source root derive from same discovered root | -| 6 | Add `init` parent-config warning | `cli.py` | `init` prints warning when parent config exists | -| 7 | Update `mcp.json.example` | `mcp.json.example` | Shows minimal zero-env-var config | -| 8 | Update README and CONFIGURATION docs | `README.md`, `docs/CONFIGURATION.md` | Walk-up and `source_root` documented | -| 9 | Run full validation | all | `ruff check` + `pytest tests -v` green | - ---- - -# Cross-PR risks and mitigations - -N/A — single PR. - -# Out of scope - -- Auto-detecting multiple systems and splitting indexes -- Changing index directory structure -- Global config or project registry -- Changes to indexing, query, or graph-building logic -- `init` command behavior changes beyond the parent-config warning -- Changes to `build_ast_graph.py` or `search_lancedb.py` - -# Whole-plan done definition - -1. All 13 named tests pass. -2. Existing test suite passes without `JAVA_CODEBASE_RAG_RUN_HEAVY`. -3. `ruff check .` is clean. -4. CLI and MCP server both resolve source root via walk-up from subdirectories. -5. `mcp.json.example` shows a zero-env-var configuration. -6. README and CONFIGURATION docs reflect the new behavior. - -# Tracking - -- `PR-1`: _pending_ diff --git a/plans/active/PLAN-TIER2-INCREMENTAL-REBUILD.md b/plans/active/PLAN-TIER2-INCREMENTAL-REBUILD.md deleted file mode 100644 index a88f8633..00000000 --- a/plans/active/PLAN-TIER2-INCREMENTAL-REBUILD.md +++ /dev/null @@ -1,549 +0,0 @@ -# Plan: Tier 2 — Incremental Kuzu Rebuild - -Status: **active (planning)**. This plan implements -[`propose/active/TIER2-INCREMENTAL-REBUILD-PROPOSE.md`](../../propose/active/TIER2-INCREMENTAL-REBUILD-PROPOSE.md) -as a four-PR sequence (PR-T5 brownfield refinement deferred). This file is -plan-only and does not implement code. - -Depends on: none (ontology 16 surface is stable; no pending PRs block this). - -## Goal - -- File-level incremental Kuzu rebuild that touches only nodes/edges derived - from changed `.java` files and their dependency closure. -- Bit-for-bit equivalence between incremental and full rebuild for the same - final source-tree state (verified by determinism test per fixture). -- `java-codebase-rag increment` updates both Lance and Kuzu incrementally - when the decision engine (co-proposed in `INDEX-AUTO-MODE-PROPOSE.md`) - deems it safe; falls back to full rebuild otherwise. -- No schema churn — ontology 16 surface is identical; incremental is a - build-strategy optimisation. - -## Principles (do not relitigate in review) - -- **Full rebuild is the safe fallback.** Any ambiguity, missing state, or - unexpected condition triggers full rebuild. Incremental is opt-in at the - decision-engine level, never the default for edge cases. -- **Pass6 always reruns globally.** Cross-service matching is fast (~ms on - bank-chat-system) and spans services. Incremental optimisation of pass6 - is out of scope. -- **`_write_meta` always rewritten from global DB state.** Aggregation fields - (`routes_total`, `cross_service_calls_total`, match breakdowns) reflect - global state. In incremental mode, `_write_meta` must compute stats by - querying the live Kuzu DB (not from the partial `GraphTables` accumulator), - since the accumulator only holds dirty-file data. -- **`.deps.json` is a build cache, not graph data.** Sidecar file, atomic - write-temp-rename, `ontology_version` field for staleness detection. -- **Symmetric delete model.** Every pass that emits nodes/edges keyed by - source file has a matching `delete_*_for_file` helper. The delete helper - set must stay in sync with the pass set. -- **Transaction-wrapped incremental writes.** On any exception mid-incremental, - ROLLBACK and fall back to full rebuild. -- **No new MCP tools, no new CLI commands.** Existing `increment` command - gains Kuzu incremental support. `build_ast_graph.py` gains internal - `--changed-paths` flag (not user-facing). -- **Brownfield changes force full rebuild** (PR-T5 may narrow this). Any - file containing `@CodebaseClient` / `@CodebaseProducer` / role/capability - override annotations in the change set triggers full rebuild. - -## PR breakdown - overview - -| PR | Scope | Ontology bump | Areas of concern | Test buckets | Independent of | -| --- | --- | --- | --- | --- | --- | -| **PR-T1** | Foundation: `FileDeps` dataclass, `.deps.json` read/write, determinism test, perf baseline | none | `.deps.json` schema must be right first time (version field, field coverage for closure rules); determinism test coverage must surface divergence | determinism + deps-read/write | prerequisite only | -| **PR-T2** | Symmetric delete helpers: `delete_*_for_file` for all node/edge types | none | Cypher DELETE must match current schema exactly; cascade semantics (Symbol delete must clean edges); count accuracy for verbose logging | per-node-type delete + cascade | PR-T1 (needs `.deps.json` read) | -| **PR-T3** | Incremental orchestrator: `build_ast_graph_incremental`, `--changed-paths`, per-pass subset functions, closure expansion | none | Closure correctness (missing rule = silent divergence); transaction semantics; pass6/global-invariant; incremental-write functions | equivalence on all fixtures + closure expansion + subset passes | PR-T1 + PR-T2 | -| **PR-T4** | CLI + decision engine: integrate into `_cmd_increment`, remove warning, create `refresh_code_index` MCP tool | none | Decision-engine correctness (wrong mode = stale graph); `refresh_code_index` is new (not an update); CLI stderr format consistency | decision engine + CLI integration + MCP tool | PR-T3 | -| **PR-T5** | Brownfield closure refinement (optional, deferred) | none | Brownfield fanout rules must be formalised before narrowing | brownfield closure tests | PR-T4 | - -Landing order: **T1 -> T2 -> T3 -> T4**. PR-T5 is optional and may follow. - -## Resolved design decisions - -| Topic | Decision | -| --- | --- | -| FileDeps storage | **Sidecar `/.deps.json`** — cheap Python-level inverse-map, no Cypher overhead, no schema evolution burden. Atomic write-temp-rename. | -| Closure computation | **Invert `.deps.json` maps at runtime** — O(\|dirty\| x avg_inverse_degree), not O(\|dirty\| x \|all-files\|). | -| Pass6 scope | **Always global** — fast, spans services, idempotency contract already in place. | -| Brownfield granularity | **Pessimistic full fallback** — any brownfield-override file in change set triggers full rebuild. Fine-grained closure deferred to PR-T5. | -| Lance incremental | **Out of scope** — already covered by CocoIndex native incremental. This plan is Kuzu-only. | -| Concurrent rebuilds | **Single-writer assumed** — undefined behaviour if two runs race. Document only. | -| Schema migrations | **Full rebuild required** — ontology bump invalidates `.deps.json` via `ontology_version` check. | -| `_write_meta` in incremental | **Query live Kuzu DB for global stats** — the partial `GraphTables` accumulator only holds dirty-file data, so aggregation counts would be wrong. `_write_meta` in incremental mode runs a set of COUNT Cypher queries against the live DB to compute `routes_total`, `calls_total`, match breakdowns, etc. | -| `pass5_imperative_edges` and `asts` | **`pass5` does not use `asts`** (it does `del asts` and works from `tables.members`). Subset version mirrors this: `pass5_imperative_edges_subset(tables, dirty)` without an `asts` parameter. | -| `refresh_code_index` MCP tool | **Does not exist yet** — must be created in PR-T4. The proposal (INDEX-AUTO-MODE) specifies its schema; PR-T4 is the first implementation. | -| `refresh_decision.py` location | **Top-level module** (`refresh_decision.py`) — imported by both `java_codebase_rag/cli.py` and `server.py`. Lives alongside `build_ast_graph.py`. | -| Test fixture strategy | **Per-test fresh builds** for equivalence tests (Tier 3 in `tests/README.md`). Use `tests/_builders.py` helpers (`build_kuzu_full_into`, `build_graph_tables_to`) for full-rebuild baselines. Session fixtures (Tier 1/2) are read-only and cannot be mutated for incremental tests. | -| `graph_meta.last_rebuild_mode` | **Added in PR-T3** — string field on `GraphMeta` node: `"full"` or `"incremental"`. Used for fallback-rate monitoring (cross-PR risk #5). | - ---- - -# PR-T1 — Foundation + determinism test + perf baseline - -## File-by-file changes - -### 1. `build_ast_graph.py` -- Add `FileDeps` dataclass (fields: `ext_hash`, `declares`, `injects`, - `extends`, `calls`, `uses_anno`, `overrides`, `declares_clients`, - `declares_producers`). File path is the dict key in `.deps.json`, not a - field value — matches proposal §2.4 JSON schema. -- Add `_build_file_deps(tables, asts, source_root) -> dict[str, FileDeps]` — - populates per-file dependency metadata from `GraphTables` in-memory data and - parsed ASTs. -- Add `_write_dependency_index(deps_path, file_deps, ontology_version)` — - writes sidecar JSON via write-temp-rename. -- Add `_read_dependency_index(deps_path) -> DepsIndex | None` — reads and - validates sidecar JSON (checks `version`, `ontology_version`). Returns - `None` on missing/corrupt/stale. -- Call `_write_dependency_index` at the end of `write_kuzu` (after `_write_meta`) - to populate `.deps.json` on every full rebuild. This makes every full rebuild - produce a fresh dependency index, ready for a subsequent incremental run. - -### 2. `tests/test_incremental_equivalence.py` (new) -- `test_full_rebuild_is_deterministic` — run full rebuild on bank-chat-system - twice into separate Kuzu paths; assert all node IDs and edge rows are - identical. Validates the foundation: if full rebuild isn't deterministic, - incremental equivalence testing is meaningless. -- `test_deps_json_written_on_full_rebuild` — after a full rebuild, verify - `.deps.json` exists, is valid JSON, has `version: 1`, correct - `ontology_version`, and non-empty `files` dict. -- `test_deps_json_fields_coverage` — spot-check a known file (e.g. - `ChatController.java`) has expected `declares`, `injects`, `extends` entries - matching the bank-chat fixture structure. -- `test_deps_json_stale_detection` — write a `.deps.json` with wrong - `ontology_version`; assert `_read_dependency_index` returns `None`. -- `test_perf_baseline_full_rebuild` — measure wall-clock time for full rebuild - on `bank-chat-system` and `cross_service_smoke` fixtures. Record in - `tests/fixtures/perf_baselines.json` under a `tier2_full_rebuild` key. - Non-blocking (informational) — establishes the number that incremental - results will be compared against in PR-T3. - -## Tests for PR-T1 -1. `test_full_rebuild_is_deterministic` -2. `test_deps_json_written_on_full_rebuild` -3. `test_deps_json_fields_coverage` -4. `test_deps_json_stale_detection` -5. `test_perf_baseline_full_rebuild` - -## Definition of done (PR-T1) -- `.deps.json` written on every full rebuild, readable, validated. -- Determinism test passes: two full rebuilds produce identical graph state. -- All existing tests pass (no regression from `write_kuzu` change). -- `ruff check .` clean. - -## Implementation step list -| # | Step | File(s) | Done when | -| --- | --- | --- | --- | -| 1 | Add `FileDeps` dataclass | `build_ast_graph.py` | Dataclass defined with all fields from proposal §2.4 | -| 2 | Add `_build_file_deps` | `build_ast_graph.py` | Populates FileDeps from GraphTables + ASTs | -| 3 | Add `_write_dependency_index` + `_read_dependency_index` | `build_ast_graph.py` | Write produces valid JSON; read validates version + ontology | -| 4 | Wire `_write_dependency_index` into `write_kuzu` | `build_ast_graph.py` | `.deps.json` appears after full rebuild | -| 5 | Write determinism test | `tests/test_incremental_equivalence.py` | Two full rebuilds produce identical output | -| 6 | Write deps.json tests | `tests/test_incremental_equivalence.py` | Read/write/validate/stale-detection pass | -| 7 | Run full test suite + ruff | all | Green | - ---- - -# PR-T2 — Symmetric delete helpers - -## File-by-file changes - -### 1. `build_ast_graph.py` -- Add delete helper functions, each taking `(conn: kuzu.Connection, file_path: str) -> int` - and returning the deleted row count: - - `delete_symbols_for_file` — DELETE Symbol nodes where `path = $file_path`. - Kuzu does not cascade rel-table deletes when a node is deleted (rel tables - in Kuzu require explicit deletion). This helper also explicitly deletes - all DECLARES edges where the declaring type's Symbol is in the file, plus - member Symbol nodes for methods/constructors declared in those types. - - `delete_extends_for_file` — DELETE EXTENDS edges where source Symbol's - file matches. - - `delete_implements_for_file` — DELETE IMPLEMENTS edges, same pattern. - - `delete_injects_for_file` — DELETE INJECTS edges, same pattern. - - `delete_calls_for_file` — DELETE CALLS edges where caller Symbol's file - matches. Also deletes associated `UnresolvedCallSite` nodes and - `UNRESOLVED_AT` edges whose caller Symbol is in the file. - - `delete_routes_for_file` — DELETE Route nodes where owner Symbol's file - matches, plus associated EXPOSES edges. - - `delete_clients_for_file` — DELETE Client nodes where declaring method's - file matches, plus DECLARES_CLIENT edges. - - `delete_producers_for_file` — DELETE Producer nodes, plus - DECLARES_PRODUCER edges. - - `delete_http_calls_for_file` — DELETE HTTP_CALLS edges where Client's - declaring method's file matches. - - `delete_async_calls_for_file` — DELETE ASYNC_CALLS edges, same pattern. - - `delete_overrides_for_file` — DELETE OVERRIDES edges where subtype - method's file matches. - - `delete_all_for_file(conn, file_path) -> dict[str, int]` — calls all - above helpers, returns `{helper_name: count}` for verbose logging. - -### 2. `tests/test_symmetric_delete.py` (new) -- Per-helper tests using the bank-chat-system session fixture: - - `test_delete_symbols_for_file` — delete symbols from a known file, - verify count > 0, verify nodes gone via Cypher query. Also verify - associated DECLARES edges and member Symbol nodes are deleted. - - `test_delete_extends_for_file` — delete EXTENDS edges for a file with - known inheritance, verify count. - - `test_delete_implements_for_file` - - `test_delete_injects_for_file` - - `test_delete_calls_for_file` — also verify UnresolvedCallSite cleanup. - - `test_delete_routes_for_file` — also verify EXPOSES cleanup. - - `test_delete_clients_for_file` — also verify DECLARES_CLIENT cleanup. - - `test_delete_producers_for_file` - - `test_delete_http_calls_for_file` - - `test_delete_async_calls_for_file` - - `test_delete_overrides_for_file` - - `test_delete_all_for_file` — verify composite function calls all helpers. - - `test_delete_idempotent` — calling delete twice returns 0 on second call. - - `test_delete_unknown_file_returns_zero` — nonexistent path deletes nothing. - -## Tests for PR-T2 -1. `test_delete_symbols_for_file` -2. `test_deletes_declares_edges` -3. `test_delete_extends_for_file` -4. `test_delete_implements_for_file` -5. `test_delete_injects_for_file` -6. `test_delete_calls_for_file` -7. `test_deletes_unresolved_call_sites` -8. `test_delete_routes_for_file` -9. `test_deletes_exposes_edges` -10. `test_delete_clients_for_file` -11. `test_deletes_declares_client_edges` -12. `test_delete_producers_for_file` -13. `test_deletes_declares_producer_edges` -14. `test_delete_http_calls_for_file` -15. `test_delete_async_calls_for_file` -16. `test_delete_overrides_for_file` -17. `test_delete_all_for_file` -18. `test_calls_each_helper` -19. `test_delete_idempotent` -20. `test_delete_unknown_file_returns_zero` - -## Definition of done (PR-T2) -- All delete helpers implemented and unit-tested in isolation. -- Each helper returns accurate count. -- Idempotent (second call on same file returns 0). -- No existing tests broken (helpers are additive, not yet called). - -## Implementation step list -| # | Step | File(s) | Done when | -| --- | --- | --- | --- | -| 1 | Implement `delete_symbols_for_file` | `build_ast_graph.py` | Test passes on bank-chat fixture | -| 2 | Implement edge delete helpers (extends/implements/injects/calls) | `build_ast_graph.py` | Tests pass | -| 3 | Implement route/client/producer delete helpers | `build_ast_graph.py` | Tests pass | -| 4 | Implement http_calls/async_calls/overrides delete helpers | `build_ast_graph.py` | Tests pass | -| 5 | Implement `delete_all_for_file` composite | `build_ast_graph.py` | Test passes | -| 6 | Write all tests in `test_symmetric_delete.py` | `tests/test_symmetric_delete.py` | All 14 tests pass | -| 7 | Run full test suite + ruff | all | Green | - ---- - -# PR-T3 — Incremental orchestrator - -## File-by-file changes - -### 1. `build_ast_graph.py` -- Add `expand_to_closure(changed_paths, deps_index) -> set[str]` — implements - the 8 closure rules from proposal §2.3 using inverted `.deps.json` maps. -- Add per-pass subset functions (or add `dirty: set[str]` filter parameter - to existing passes). All subset functions forward `verbose` and other - kwargs matching the parent pass signature: - - `pass1_parse_subset(root, dirty, *, verbose) -> dict[str, JavaFileAst]` - — re-parse only dirty files. - - `pass2_edges_subset(tables, asts, dirty, *, verbose)` — re-emit - EXTENDS/IMPLEMENTS/INJECTS edges for symbols touching dirty files. - - `pass3_calls_subset(tables, asts, dirty, *, verbose)` — re-emit CALLS + - UnresolvedCallSite for dirty caller files. - - `pass4_routes_subset(tables, asts, dirty, *, source_root, verbose)` — - re-emit Route/EXPOSES for dirty files. `source_root` required (loads - brownfield overrides and config). - - `pass5_imperative_edges_subset(tables, dirty, *, source_root, verbose)` - — re-emit Client/Producer/HTTP_CALLS/ASYNC_CALLS for dirty files. - Note: no `asts` parameter — `pass5` does `del asts` and works from - `tables.members`. -- Add incremental write helpers (no `_drop_all`; append to existing DB): - - `_write_nodes_incremental(conn, tables)` — COPY-from-CSV append for - new Symbol/UnresolvedCallSite/Route/Client/Producer nodes. - - `_write_edges_incremental(conn, tables)` — COPY-from-CSV append for - new DECLARES/EXTENDS/IMPLEMENTS/INJECTS/CALLS/OVERRIDES/UNRESOLVED_AT - edges. - - `_write_routes_and_exposes_incremental(conn, tables)` — COPY-from-CSV - append for Route/EXPOSES/Client/DECLARES_CLIENT/Producer/ - DECLARES_PRODUCER/HTTP_CALLS/ASYNC_CALLS. -- Add `build_ast_graph_incremental(source_root, kuzu_path, changed_paths, *, - verbose)` — the main incremental orchestrator: - 1. Read `.deps.json`; return `None` if missing/stale (caller falls back). - 2. Compute `dirty = expand_to_closure(changed_paths, deps_index)`. - 3. Open Kuzu connection; begin transaction. - 4. Call `delete_all_for_file(conn, path)` for each dirty file. - 5. Run pass1–5 subset functions, accumulating into a fresh `GraphTables`. - 6. Run `_populate_overrides_rows` on the partial tables. - 7. Run `pass6_match_edges(tables, verbose=verbose)` globally (reads existing - edges + new). Must pass `verbose` kwarg. - 8. Write incremental rows to DB. - 9. Rewrite `_write_meta` — **query live Kuzu DB for global stats** (the - partial `GraphTables` only holds dirty-file data; aggregation counts - like `routes_total`, `calls_total` must be computed via COUNT Cypher - queries against the full DB). Also set `last_rebuild_mode="incremental"`. - 10. Rewrite `.deps.json` (merge dirty entries into existing index — - unchanged file entries preserved, dirty file entries replaced). - 11. Commit transaction; on exception, ROLLBACK and re-raise. -- Add `--changed-paths` argument to `main()` — accepts a file path containing - newline-separated paths. When present, calls - `build_ast_graph_incremental` instead of full rebuild. When incremental - returns `None` or raises, falls back to full rebuild with a logged reason. -- Heuristic: if `len(dirty) > 0.5 * total_files` in `.deps.json`, skip - incremental and fall back to full (proposal §8, risk #6). - -### 2. `tests/test_incremental_equivalence.py` (extend) -- `test_incremental_matches_full_bank_chat_system` — apply incremental - rebuild on bank-chat-system with one file changed; compare node IDs and - edge rows against a full rebuild on the same final state. -- `test_incremental_matches_full_cross_service_smoke` — same on - cross_service_smoke fixture. -- `test_incremental_matches_full_call_graph_smoke` — same on call_graph_smoke. -- `test_incremental_matches_full_http_caller_smoke` — same on http_caller_smoke. -- `test_incremental_matches_full_route_extraction_smoke` — same on - route_extraction_smoke. -- `test_incremental_multiple_files_changed` — change 2-3 files; verify - equivalence. -- `test_incremental_fallback_on_missing_deps_json` — remove `.deps.json`, - verify incremental returns None / falls back. -- `test_incremental_fallback_on_stale_ontology` — write wrong ontology - version; verify fallback. -- `test_incremental_fallback_on_large_dirty_set` — mark >50% files dirty; - verify fallback to full. -- `test_closure_includes_inverse_injects` — edit a file with an injected - symbol; verify the injector's file is in the closure. -- `test_closure_includes_inverse_extends` — edit a supertype; verify subtype - file is in closure. -- `test_closure_includes_inverse_calls` — edit a callee; verify caller file - is in closure. -- `test_closure_includes_inverse_overrides` — edit a supertype method; - verify subtype file with OVERRIDES edge is in closure. -- `test_closure_includes_meta_annotation` — edit an `@interface` used as - a meta-annotation; verify files using that annotation are in closure. -- `test_closure_includes_route_resolution` — edit a file with - `@RequestMapping` class-level hints; verify files with methods on that - class are in closure. -- `test_incremental_transaction_rollback` — inject a failure mid-incremental - (e.g. raise after delete but before write); verify the DB is unchanged - (all deleted nodes restored / no partial state). -- `test_incremental_deps_json_merge` — after incremental rebuild, verify - `.deps.json` has updated entries for dirty files and unchanged entries - for non-dirty files. -- `test_incremental_pass6_global_invariant` — verify the incremental path - does NOT skip pass6, and that pass6 match outcomes are identical to a - full rebuild's pass6 outcomes. -- `test_changed_paths_cli_flag_valid` — pass `--changed-paths` with a valid - temp file containing known paths; verify incremental dispatch. -- `test_changed_paths_cli_flag_empty` — pass `--changed-paths` with an - empty file; verify fallback to full rebuild. -- `test_incremental_meta_global_stats` — after incremental rebuild, verify - `graph_meta` counts (routes_total, calls_total, etc.) match a full - rebuild's meta. Validates the live-DB query approach. - -## Tests for PR-T3 -1. `test_incremental_matches_full_bank_chat_system` -2. `test_incremental_matches_full_cross_service_smoke` -3. `test_incremental_matches_full_call_graph_smoke` -4. `test_incremental_matches_full_http_caller_smoke` -5. `test_incremental_matches_full_route_extraction_smoke` -6. `test_incremental_multiple_files_changed` -7. `test_incremental_fallback_on_missing_deps_json` -8. `test_incremental_fallback_on_stale_ontology` -9. `test_incremental_fallback_on_large_dirty_set` -10. `test_closure_includes_inverse_injects` -11. `test_closure_includes_inverse_extends` -12. `test_closure_includes_inverse_calls` -13. `test_closure_includes_inverse_overrides` -14. `test_closure_includes_meta_annotation` -15. `test_closure_includes_route_resolution` -16. `test_incremental_transaction_rollback` -17. `test_incremental_deps_json_merge` -18. `test_incremental_pass6_global_invariant` -19. `test_changed_paths_cli_flag_valid` -20. `test_changed_paths_cli_flag_empty` -21. `test_incremental_meta_global_stats` - -## Definition of done (PR-T3) -- Incremental rebuild produces bit-for-bit identical graph state to full - rebuild for all fixtures tested. -- `_write_meta` in incremental mode queries live Kuzu DB for global stats - (not partial accumulator) — verified by `test_incremental_meta_global_stats`. -- `graph_meta.last_rebuild_mode` set to `"incremental"` after successful - incremental rebuild, `"full"` after full rebuild. -- Closure expansion correctly includes all 8 rules from proposal §2.3 - (inverse-INJECTS, inverse-EXTENDS, inverse-CALLS, meta-annotation, - brownfield-override, route-resolution, inverse-OVERRIDES, inverse-DECLARES_CLIENT/PRODUCER). -- Fallback to full rebuild triggers on: missing `.deps.json`, stale ontology, - >50% dirty files, any exception during incremental. -- Transaction rollback verified: mid-incremental failure leaves DB unchanged. -- All existing tests pass (full-rebuild path unchanged). -- `ruff check .` clean. - -## Implementation step list -| # | Step | File(s) | Done when | -| --- | --- | --- | --- | -| 1 | Implement `expand_to_closure` | `build_ast_graph.py` | Closure tests pass | -| 2 | Implement `pass1_parse_subset` | `build_ast_graph.py` | Re-parses only dirty files | -| 3 | Implement `pass2_edges_subset` through `pass5_imperative_edges_subset` | `build_ast_graph.py` | Each subset pass produces correct partial GraphTables | -| 4 | Implement incremental write helpers | `build_ast_graph.py` | Nodes/edges appended without _drop_all | -| 5 | Implement `build_ast_graph_incremental` orchestrator | `build_ast_graph.py` | Transaction-wrapped; fallback on failure | -| 6 | Add `--changed-paths` to `main()` | `build_ast_graph.py` | CLI flag dispatches to incremental | -| 7 | Write equivalence tests for all fixtures | `tests/test_incremental_equivalence.py` | Incremental matches full for each fixture | -| 8 | Write closure and fallback tests | `tests/test_incremental_equivalence.py` | All pass | -| 9 | Run full test suite + ruff | all | Green | - ---- - -# PR-T4 — CLI + decision engine integration - -## File-by-file changes - -### 1. `refresh_decision.py` (new, top-level module) -- `@dataclass ChangeSet` — `added`, `modified`, `deleted`, `renamed`, - boolean risk flags (`config_changed`, `pipeline_changed`, - `meta_annotation_changed`). -- `@dataclass RefreshDecision` — `lance_mode: Literal["incremental", "full"]`, - `kuzu_mode: Literal["incremental", "full"]`, `reasons: list[str]`, - `detected_changes: ChangeSet`. The `"auto"` mode from - INDEX-AUTO-MODE-PROPOSE is resolved to concrete `incremental`/`full` - by `_choose_refresh_mode` before returning — callers never see `"auto"`. -- `_detect_repo_changes(source_root, git_ref_base, changed_paths) -> ChangeSet` - — git diff or hash-based change detection. -- `_choose_refresh_mode(changes: ChangeSet, deps_path: Path, total_files: int) -> RefreshDecision` - — implements the decision rules from `INDEX-AUTO-MODE-PROPOSE.md`: - - Full Kuzu when: deletes, renames, config changes, pipeline changes, - meta-annotation changes, missing/stale `.deps.json`, >50% dirty, - detection failure. - - Full Lance when: config changes, pipeline changes, CocoIndex flow changes. - - Incremental otherwise. - -### 2. `java_codebase_rag/cli.py` -- Remove `_emit_increment_kuzu_warning()` (line 181) and - `_INCREMENT_WARNING_LINES` (lines 29-42). -- In `_cmd_increment`: after CocoIndex update succeeds, call - `_choose_refresh_mode` and dispatch: - - If `kuzu_mode == "incremental"`: write changed paths to a temp file, - call `run_build_ast_graph_incremental` which passes - `--changed-paths ` to `build_ast_graph.py`. - - If `kuzu_mode == "full"`: call `run_build_ast_graph` without - `--changed-paths` (full rebuild). -- Update success message to include effective mode and reasons. - -### 3. `java_codebase_rag/pipeline.py` -- Add `run_build_ast_graph_incremental(source_root, kuzu_path, changed_paths, *, - verbose, quiet, env)` wrapper — writes `changed_paths` to a temp file, - then calls `build_ast_graph.py --source-root ... --kuzu-path ... - --changed-paths `. The temp file contains newline-separated - paths, matching `build_ast_graph.py`'s `--changed-paths` contract. - -### 4. `server.py` -- **Create** `refresh_code_index` MCP tool (does not exist yet). Accepts - optional inputs: `confirm: bool`, `mode: "auto" | "incremental" | "full"`, - `changed_paths: list[str] | null`, `git_ref_base: str`, `reason: str | null`. -- Dispatches to incremental or full Kuzu rebuild based on `RefreshDecision`. -- Includes `effective_mode`, `decision_reasons`, `detected_changes` in - response payload. -- Backward compatible: calls passing only `confirm=true` still work - (mode defaults to `"auto"`). - -### 5. `tests/test_refresh_decision.py` (new) -- `test_auto_modified_only_incremental` — modified-only changes → incremental. -- `test_auto_deleted_file_full_kuzu` — deletion → full Kuzu, incremental Lance. -- `test_auto_renamed_file_full_kuzu` — rename → full Kuzu. -- `test_auto_config_change_full` — `.java-codebase-rag.yml` change → full. -- `test_auto_detection_failure_full` — no git, no paths → full. -- `test_explicit_full_overrides` — `mode=full` → full regardless. -- `test_deps_missing_full_kuzu` — no `.deps.json` → full Kuzu. -- `test_deps_stale_ontology_full_kuzu` — wrong version → full Kuzu. -- `test_backward_compat_confirm_only` — `confirm=true` only → auto mode. - -### 6. `tests/test_cli_increment.py` (new or extend existing CLI tests) -- `test_increment_dispatches_kuzu_incremental` — mock pipeline, verify - `--changed-paths` passed. -- `test_increment_dispatches_kuzu_full_fallback` — mock pipeline, verify - full rebuild on fallback. -- `test_increment_removes_kuzu_warning` — verify no warning on stderr. - -## Tests for PR-T4 -1. `test_auto_modified_only_incremental` -2. `test_auto_deleted_file_full_kuzu` -3. `test_auto_renamed_file_full_kuzu` -4. `test_auto_config_change_full` -5. `test_auto_detection_failure_full` -6. `test_explicit_full_overrides` -7. `test_deps_missing_full_kuzu` -8. `test_deps_stale_ontology_full_kuzu` -9. `test_backward_compat_confirm_only` -10. `test_increment_dispatches_kuzu_incremental` -11. `test_increment_dispatches_kuzu_full_fallback` -12. `test_increment_removes_kuzu_warning` - -## Definition of done (PR-T4) -- `java-codebase-rag increment` updates both Lance and Kuzu incrementally - when safe. -- Decision engine isolated in `refresh_decision.py` with full test coverage. -- `_emit_increment_kuzu_warning()` removed from `java_codebase_rag/cli.py`. -- `refresh_code_index` MCP tool created in `server.py`, backward compatible. -- All existing tests pass. -- `ruff check .` clean. - -## Implementation step list -| # | Step | File(s) | Done when | -| --- | --- | --- | --- | -| 1 | Implement `ChangeSet` + `RefreshDecision` dataclasses | `refresh_decision.py` | Types defined | -| 2 | Implement `_detect_repo_changes` | `refresh_decision.py` | Git diff + hash fallback work | -| 3 | Implement `_choose_refresh_mode` | `refresh_decision.py` | All 9 decision tests pass | -| 4 | Add `run_build_ast_graph_incremental` to pipeline | `java_codebase_rag/pipeline.py` | Wrapper writes temp file, dispatches `--changed-paths` | -| 5 | Update `_cmd_increment` in CLI | `java_codebase_rag/cli.py` | Dispatches incremental or full based on decision | -| 6 | Remove `_emit_increment_kuzu_warning` + `_INCREMENT_WARNING_LINES` | `java_codebase_rag/cli.py` | No warning emitted | -| 7 | Create `refresh_code_index` MCP tool | `server.py` | New tool with `mode`/`changed_paths`/`git_ref_base` inputs | -| 8 | Write decision engine tests | `tests/test_refresh_decision.py` | All pass | -| 9 | Write CLI integration tests | `tests/test_cli_increment.py` | All pass | -| 10 | Run full test suite + ruff | all | Green | - ---- - -# Cross-PR risks and mitigations - -| # | Risk | Severity | Mitigation | -| --- | --- | --- | --- | -| 1 | Silent divergence between full and incremental rebuild | **High** | `test_incremental_matches_full_*` on every fixture — the single most important test in this feature | -| 2 | Closure rules miss an edge type | **High** | Determinism test surfaces this immediately; closure rules enumerated explicitly in `expand_to_closure` | -| 3 | `.deps.json` becomes stale between runs | Medium | `ontology_version` field check; mismatch → full rebuild | -| 4 | Delete helper Cypher drifts from schema | Medium | PR-T2 tests each helper against live Kuzu; any schema change must update helpers | -| 5 | Decision engine too conservative (always falls back to full) | Medium | Track fallback rate via `graph_meta.last_rebuild_mode` (added in PR-T3); review post-launch | -| 6 | Kuzu transaction semantics don't support incremental writes | Medium | Validate early in PR-T3: test that COPY-from-CSV within a transaction works without `_drop_all`; `test_incremental_transaction_rollback` proves rollback semantics | -| 7 | Incremental slower than full for small repos | Low | >50% dirty-set heuristic; benchmark on fixtures in PR-T1 | - -# Out of scope - -- Watch-mode (filesystem watcher). Foundation laid; future proposal. -- Multi-tenant/concurrent rebuilds. Single writer assumed. -- LanceDB incremental rebuild (CocoIndex handles this natively). -- Cross-repo or cross-source-root incremental. -- Schema migrations between ontology versions (full rebuild required). -- PR-T5 brownfield closure refinement (optional follow-up). -- New MCP tools or CLI commands. -- Performance optimisation of pass6 (always global is the contract). - -# Whole-plan done definition - -1. `java-codebase-rag increment` updates both Lance and Kuzu without warnings. -2. Incremental rebuild produces identical graph state to full rebuild on all - tested fixtures. -3. Decision engine falls back to full rebuild on all documented risk triggers. -4. All existing tests pass; no regression. -5. `.deps.json` written on full rebuild, read on incremental, validated on - every run. -6. `ruff check .` clean. - -# Tracking - -- `PR-T1`: _done_ -- `PR-T2`: _done_ -- `PR-T3`: _pending_ -- `PR-T4`: _pending_ -- `PR-T5`: _deferred_ diff --git a/propose/active/DIRS-HIERARCHY-PROPOSE.md b/propose/active/DIRS-HIERARCHY-PROPOSE.md deleted file mode 100644 index 8a57807f..00000000 --- a/propose/active/DIRS-HIERARCHY-PROPOSE.md +++ /dev/null @@ -1,230 +0,0 @@ -# DIRS-HIERARCHY — Walk-up config discovery and configurable source root - -**Status**: proposal — not yet implemented. -**Author**: Dmitry Teryaev -**Date**: 2026-06-06 - -## TL;DR - -- **The call**: add walk-up config discovery (like git) so the tool finds `.java-codebase-rag.yml` in any parent directory, and add a `source_root` field to the YAML config so the config can live separately from the source code. -- **Why**: the tool currently couples three things — config file location, source code location, and cwd. All three must be the same directory. Users who organize projects in varied directory structures hit walls: running `init` from a multi-system parent creates a mixed index, using MCP from a microservice subdirectory can't find the config, and placing the config in a separate context directory requires `--source-root` on every invocation. -- **Scope**: config discovery and source root resolution. Both CLI and MCP server use the same walk-up logic, eliminating the need for env vars in `.mcp.json`. No changes to indexing, query, or graph-building logic. No changes to `init` beyond a warning when a parent config exists. -- **Migration**: 1 PR. No breaking changes. Existing workflows where cwd = config dir continue to work identically. Existing `.mcp.json` files with env vars continue to work (env vars are overrides). New workflows (running from subdirectories, zero-config MCP) unlock. - -## 1. Problem statement - -Three real user scenarios that break today: - -**User A** — multi-system parent directory: -``` -IdeaProjects/ - .java-codebase-rag.yml - System-A/ microservice-A-1/ microservice-A-2/ - System-B/ microservice-B-1/ microservice-B-2/ -``` -Running `init` from `IdeaProjects/` indexes ALL Java files from all systems into one giant mixed index. The tool doesn't recognize project boundaries. - -**User B** — working from a microservice subdirectory: -``` -IdeaProjects/ - System-C/ - .java-codebase-rag.yml - microservice-C-1/ - microservice-C-2/ -``` -`init` runs correctly from `System-C/`. But then `cd microservice-C-1/` and starting the MCP server — the tool looks for config only in cwd (`microservice-C-1/`), doesn't find it, fails. - -**User C** — config lives separately from source code: -``` -IdeaProjects/ - System-D/ - system-D-context/ - .java-codebase-rag.yml - microservice-D-1/ - microservice-D-2/ -``` -Config is in `system-D-context/`, code is at `../` via `--source-root`. The `--source-root` flag works but must be passed on every invocation. No way to persist this in the config. - -**Root cause**: `find_yaml_config_file()` only checks the exact `source_root` directory. No walking up. And the config has no `source_root` field, so the only way to point to code elsewhere is the `--source-root` flag or env var. - -## 2. Design principles - -1. **cwd independence.** The tool should work from any subdirectory of the project, not just from the directory containing the config. -2. **Config is the anchor.** The presence of `.java-codebase-rag.yml` defines a project boundary. The tool walks up to find it (like git finds `.git`). -3. **Source root is configurable but has a sane default.** Default source root = config file's parent directory. Override via YAML `source_root` field, env var, or CLI flag. -4. **Index follows source root.** The index directory always lives at `/.java-codebase-rag/`. Config and source root can be in different places, but the index stays with the code. -5. **No breaking changes.** Existing workflows where cwd = config dir must produce identical behavior. The walk-up is additive — it only fires when the config isn't found in cwd. - -## 3. Proposed solution - -Once walk-up finds the config file, everything else is derivable — no env vars needed: - -``` -config found at System-C/.java-codebase-rag.yml - → source root = System-C/ (or source_root from YAML) - → index dir = System-C/.java-codebase-rag/ -``` - -Both CLI and MCP server follow the same discovery path. The minimal `.mcp.json` becomes: - -```json -{ - "mcpServers": { - "java-codebase-rag": { - "type": "stdio", - "command": "java-codebase-rag-mcp" - } - } -} -``` - -This works because MCP hosts set cwd to the workspace directory at server startup: -- **Claude Code** — cwd = workspace directory. Walk-up from there finds the config. -- **VS Code / Cursor** — cwd = workspace root. Same. -- **Claude Desktop** — cwd is less predictable. Users can still set `JAVA_CODEBASE_RAG_SOURCE_ROOT` as an optional override. - -Both `JAVA_CODEBASE_RAG_SOURCE_ROOT` and `JAVA_CODEBASE_RAG_INDEX_DIR` become **optional overrides** rather than requirements. - -### 3.1 Walk-up config discovery - -New function `discover_project_root(start: Path) -> Path | None` in `config.py`: - -- Starts from `start` (typically cwd) -- Checks for `.java-codebase-rag.yml` or `.java-codebase-rag.yaml` in the current directory -- If not found, moves to parent and repeats -- **First match wins** (closest to cwd): if nested configs exist at multiple levels (e.g. `System-A/.java-codebase-rag.yml` and `IdeaProjects/.java-codebase-rag.yml`), the one closest to cwd is used. This mirrors git's behavior when nested `.git` directories exist. -- **Boundary conditions**: stops at `$HOME` (inclusive — checks `$HOME` itself but does not go past it), stops at filesystem root. Rationale: `$HOME` is the natural project root on macOS/Linux workstations. On CI/CD (`/root`, `/home/runner`) this is equally appropriate. Configs above `$HOME` are almost certainly unrelated to the current project. -- Returns the directory containing the config file, or `None` - -The function is a pure discovery step — it finds where the config lives, nothing more. It does not parse the config or resolve source roots. - -### 3.2 `source_root` field in config YAML - -New optional top-level field: - -```yaml -# Optional: override where Java source code lives. -# Relative paths resolve relative to the config file's directory. -# Default: the directory containing this config file. -source_root: ../ -``` - -Resolution is straightforward: `Path(config_dir) / source_root`. For the example above, if config is at `system-D-context/.java-codebase-rag.yml`, then `source_root: ../` resolves to `System-D/`. - -**Note on resolution base**: the YAML `source_root` field resolves relative to the config file's directory, while the CLI `--source-root` flag resolves relative to cwd. These are intentionally different resolution bases — the YAML field is a portable declaration ("my code is one level up from this config"), while the CLI flag is an absolute or cwd-relative override. The precedence table in §3.3 handles priority; the resolution base difference is a non-issue because each source resolves independently before comparison. - -### 3.3 Full precedence chain for source root - -| Priority | Source | Example | -|---|---|---| -| 1 (highest) | `--source-root` CLI flag | `--source-root /other/path` | -| 2 | `JAVA_CODEBASE_RAG_SOURCE_ROOT` env var | `export JAVA_CODEBASE_RAG_SOURCE_ROOT=/other/path` | -| 3 | `source_root` field in YAML config | `source_root: ../` | -| 4 | Walk-up discovery result (config file's parent dir) | Config at `System-C/.java-codebase-rag.yml` → source root = `System-C/` | -| 5 (lowest) | `Path.cwd()` (unchanged fallback) | No config found anywhere | - -### 3.4 Where changes happen - -**`config.py`**: -- Add `discover_project_root(start: Path) -> Path | None` -- Add `find_config_dir(source_root: Path | None) -> Path` — returns the effective project root by combining walk-up discovery with the precedence chain -- Update `resolve_operator_config()` to read `source_root` from YAML and resolve it relative to config dir -- When `source_root` param is `None` (no CLI flag, no env var), the function discovers the project root via walk-up, then reads `source_root` from the discovered YAML, then falls back to cwd - -**`server.py`**: -- Update `_project_root()` to call `discover_project_root()` before falling back to cwd. Env var still takes precedence. - -**`cli.py`**: -- Update `_resolved_from_ns()` to use walk-up discovery when `--source-root` is not provided. CLI flag still takes precedence. - -**`init` command**: no behavior change. The `init` command creates config + index in the specified directory as before. Walk-up only helps find existing configs. Add a soft warning if a parent config is detected. - -### 3.5 Error messages - -**No config found (MCP/query/index commands)**: -> No `.java-codebase-rag.yml` found in `[cwd]` or any parent directory (stopped at home). Run `java-codebase-rag init` in your project root first. - -**`init` finds existing config in parent (soft warning)**: -> Warning: found existing config at `[parent]/.java-codebase-rag.yml`. Creating a new project here will create a separate index. - -### 3.6 What each user scenario looks like after - -**User A** — runs `init` from each `System-X/` directory separately. Then uses MCP from any subdirectory — walk-up finds the config for the current system. No more mixed indexes. - -**User B** — runs `init` from `System-C/`. Then `cd`s to `microservice-C-1/` and starts MCP. Walk-up finds `System-C/.java-codebase-rag.yml`, source root defaults to `System-C/`. Works. - -**User C** — creates config at `system-D-context/.java-codebase-rag.yml` with `source_root: ../`. Runs `init` from `system-D-context/`. Walk-up from any subdirectory finds the config. Source root = `System-D/`. Index at `System-D/.java-codebase-rag/`. - -## 4. Scope - -- Config file discovery via walk-up -- `source_root` field in YAML config -- Updated precedence chain -- Integration in CLI and MCP server -- `JAVA_CODEBASE_RAG_INDEX_DIR` and `JAVA_CODEBASE_RAG_SOURCE_ROOT` env vars become optional (still supported as overrides) -- `mcp.json.example` updated to show minimal zero-env-var config -- Clear error messages when config is not found -- Soft warning during `init` when a parent config exists - -## 5. Schema / Ontology / Re-index impact - -- Ontology bump: not required -- Re-index required: no. The index structure and content are unchanged. -- Config surface changes: new optional `source_root` field in YAML. Fully backward-compatible — existing configs without this field continue to work identically. - -## 6. Tests / Validation - -- `test_discover_project_root_finds_config_in_cwd` — config in cwd, returns cwd -- `test_discover_project_root_walks_up` — config in parent, returns parent -- `test_discover_project_root_stops_at_home` — config in $HOME, returns None -- `test_discover_project_root_not_found` — no config anywhere, returns None -- `test_source_root_from_yaml_relative` — `source_root: ../` resolves to parent of config dir -- `test_source_root_from_yaml_absolute` — `source_root: /abs/path` resolves to absolute path -- `test_source_root_precedence_cli_over_yaml` — CLI flag wins over YAML `source_root` -- `test_source_root_precedence_yaml_over_discovery` — YAML `source_root` wins over config dir default -- `test_source_root_precedence_env_over_yaml` — env var wins over YAML `source_root` -- `test_existing_behavior_unchanged` — no walk-up, cwd = config dir → identical behavior to today - -## 7. Open questions - -None — all key decisions resolved during brainstorming. - -## 8. Out of scope - -- Auto-detecting multiple systems and splitting indexes -- Changing index directory structure -- Global config or project registry -- Changes to indexing, query, or graph-building logic -- `init` command behavior changes (beyond the parent-config warning) - -## 9. Risks and mitigations - -| Risk | Mitigation | -|---|---| -| Walk-up finds wrong config in a shared parent (e.g. `IdeaProjects/.java-codebase-rag.yml` when user meant `System-A/`) | `init` warns when a parent config exists. First-match-wins means the closest config is always preferred. If a stray config exists at a high level, it's only found when no closer config exists. | -| Symlink cycles during walk-up | `Path.resolve()` canonicalizes the path before walking. The `parent` chain on resolved paths cannot cycle. | -| Performance of filesystem stat calls in deep directory trees | Each step is a single `is_file()` check. Even at 20 levels deep, this is negligible compared to the embedding/indexing work the tool already does. | -| `$HOME` boundary stops too early or too late | `$HOME` is checked inclusively (a config at `$HOME` itself is found). This covers the common macOS case where projects live under `~/Projects/`. Going past `$HOME` would risk picking up system-level or unrelated configs. | -| Nested configs create confusion (which one is active?) | First-match-wins is simple and matches git's behavior. The tool can log which config file it discovered to aid debugging. | - -## 10. Decisions taken - -1. **First match wins** — closest config to cwd, not "most specific" or "deepest". Matches git behavior. No heuristic for picking among multiple configs. -2. **`$HOME` is inclusive boundary** — check `$HOME` itself, don't go past it. Avoids finding configs in `/` or system directories. -3. **YAML field named `source_root`** — same name as the CLI flag for conceptual consistency, despite different resolution bases. The alternative (`project_root`, `code_dir`) would add a new concept where none is needed. -4. **Walk-up is a separate pre-step** — not integrated into `resolve_operator_config()`. Cleaner separation, easier to test, lower risk to existing resolution logic. -5. **No changes to `init`** — `init` creates config + index as before. The walk-up only helps find existing configs from subdirectories. -6. **No `--walk-up` opt-out flag** — walk-up is always-on when no explicit source root is given. If a user hits the wrong config, the fix is to move or remove the stray config file, not to add a flag. - -## 11. Migration plan — 1 PR - -Single PR containing: -1. `discover_project_root()` function in `config.py` -2. `source_root` YAML field parsing in `resolve_operator_config()` -3. Updated `_project_root()` in `server.py` -4. Updated `_resolved_from_ns()` in `cli.py` -5. Index dir auto-derived from discovered source root (no env var needed) -6. Soft warning in `init` when parent config detected -7. All tests from §6 -8. `mcp.json.example` updated to show minimal zero-env-var config -9. README update documenting the new behavior diff --git a/propose/active/INDEX-AUTO-MODE-PROPOSE.md b/propose/active/INDEX-AUTO-MODE-PROPOSE.md deleted file mode 100644 index 9a33cd6c..00000000 --- a/propose/active/INDEX-AUTO-MODE-PROPOSE.md +++ /dev/null @@ -1,187 +0,0 @@ -# Proposal: Smart `increment` / `reprocess` Mode Selection - -Status: **active — ready for planning**. -Companion proposal: [`propose/active/TIER2-INCREMENTAL-REBUILD-PROPOSE.md`](TIER2-INCREMENTAL-REBUILD-PROPOSE.md) -(Kuzu incremental rebuild implementation). - -## Goal - -Extend `java-codebase-rag increment` so it can choose incremental vs full -rebuild automatically for both Lance and Kuzu, while staying safe for -rename/delete/move and indexing-semantics changes. - -## Problem - -Current behavior: - -- `java-codebase-rag increment` updates Lance vectors incrementally - (via CocoIndex) but prints a warning that the Kuzu graph is stale. -- `java-codebase-rag reprocess` always does a full rebuild of both - Lance and Kuzu. - -The `increment` command is correct for Lance but incomplete for Kuzu. -The Kuzu incremental path is defined in -[`TIER2-INCREMENTAL-REBUILD-PROPOSE.md`](TIER2-INCREMENTAL-REBUILD-PROPOSE.md). -This proposal defines the decision engine that both commands use to -determine when incremental is safe. - -## Proposed API Changes - -### CLI - -No new commands. Existing commands gain automatic mode selection: - -- `java-codebase-rag increment` — incremental Lance + Kuzu when safe, - full Kuzu fallback when not. Lance is always incremental via CocoIndex. -- `java-codebase-rag reprocess` — full rebuild of both Lance + Kuzu - (unchanged). -- `java-codebase-rag reprocess --graph-only` — full Kuzu rebuild only. -- `java-codebase-rag reprocess --vectors-only` — full Lance rebuild only. - -### MCP tool (`refresh_code_index`) - -Add optional inputs: - -- `confirm: bool = false` (existing) -- `mode: "auto" | "incremental" | "full" = "auto"` -- `changed_paths: list[str] | null = null` -- `git_ref_base: str = "HEAD"` -- `reason: str | null = null` - -Backward compatibility: - -- Calls passing only `confirm=true` should still work. -- Default mode is `auto` (safe-by-default decisioning). - -## Decision Engine (`mode=auto`) - -Returns two independent mode choices — Lance and Kuzu may use different -modes: - -```python -@dataclass -class RefreshDecision: - lance_mode: Literal["incremental", "full"] - kuzu_mode: Literal["incremental", "full"] - reasons: list[str] - detected_changes: ChangeSet -``` - -### Choose `full` for Kuzu when any of the following is true - -- At least one file is deleted. -- At least one file is renamed or moved. -- `.java-codebase-rag.yml` or `.lancedb-mcp.yml` changes. -- Indexing pipeline/config files change (for example: - `java_index_flow_lancedb.py`, `build_ast_graph.py`, - `graph_enrich.py`, enrichment/chunking components). -- `@interface` definitions changed (meta-annotation fanout risk). -- `.deps.json` is missing, corrupt, or has wrong `ontology_version`. -- Change detection fails or is ambiguous. -- More than 50% of files are dirty (incremental would be slower). - -### Choose `full` for Lance when any of the following is true - -- Same config/indexing-pipeline triggers as Kuzu. -- `.java-codebase-rag.yml` changes. -- CocoIndex flow definition changes. - -### Choose `incremental` when all are true - -- Only in-place file content modifications/additions. -- No rename/delete/move events. -- No config/index/meta-annotation risk triggers. -- `.deps.json` exists and is current (Kuzu incremental prerequisite). - -## Change Detection Strategy - -1. Prefer git diff status: - - `git diff --name-status ...HEAD` - - optionally include working tree status (`git diff --name-status` - and `git diff --name-status --cached`) -2. If git signal is unavailable, use `changed_paths` when supplied. -3. If still uncertain, fall back to `full`. - -Represent results as: - -- `added[]`, `modified[]`, `deleted[]`, `renamed[]` -- plus boolean risk flags for config/index/meta-annotation changes - -## Execution Plan - -### Full mode - -- Lance: `cocoindex update ... --full-reprocess -f` -- Kuzu: `build_ast_graph.py --source-root ...` (full rebuild via - `_drop_all`) - -### Incremental mode - -- Lance: `cocoindex update ... -f` (without `--full-reprocess`) -- Kuzu: `build_ast_graph.py --source-root ... --changed-paths ...` - (incremental rebuild via TIER2 proposal) - -The decision engine returns two independent mode choices — Lance and -Kuzu may incrementally update independently. For example, if -`.deps.json` is missing but no config changed, Lance could be -incremental while Kuzu falls back to full. - -## Response Payload Enhancements - -Add decision transparency fields to `refresh_code_index` response: - -- `effective_mode: { lance: "incremental" | "full", kuzu: "incremental" | "full" }` -- `decision_reasons: list[str]` -- `detected_changes: { added, modified, deleted, renamed }` -- optional `warnings: list[str]` - -Keep existing stdout/stderr/exit_code fields intact. - -For the CLI (`increment` command), emit the mode decision to stderr -with `[graph]` / `[vectors]` prefixes consistent with existing -progress output (see `CLI-PROGRESS-OUTPUT-PROPOSE.md`). - -## Safety Policy - -- Default `auto`. -- On uncertainty, choose `full`. -- `mode=full` always respected. -- `mode=incremental` allowed, but return warnings when risk triggers - exist. -- Never silently downgrade explicit `full` to incremental. -- Kuzu incremental failure at runtime → roll back, fall back to full - Kuzu rebuild, log reason. - -## Test Plan - -1. `auto` + modified-only → incremental (both Lance + Kuzu). -2. `auto` + deleted file → full Kuzu, incremental Lance. -3. `auto` + renamed file → full Kuzu, incremental Lance. -4. `auto` + `.java-codebase-rag.yml` change → full (both). -5. `auto` + detection failure → full with reason. -6. explicit `mode=full` → full regardless of diffs. -7. explicit `mode=incremental` + risky changes → incremental + warning. -8. backward compatibility: `confirm=true` only call still succeeds. -9. `.deps.json` missing → full Kuzu, incremental Lance. -10. `.deps.json` stale `ontology_version` → full Kuzu, incremental Lance. - -## Implementation Notes - -- Keep mode-selection logic isolated in helper functions for testability: - - `_detect_repo_changes(...)` - - `_choose_refresh_mode(...)` -- Make logs/user-facing messages explicit about why full mode was - selected. -- Preserve current subprocess environment and project-root behavior. -- The decision engine lives in a shared module (e.g. `index_common.py` - or a new `refresh_decision.py`) usable by both `cli.py` and - `server.py`. - -## Rollout - -1. Implement decision engine with isolated helpers + tests. -2. Integrate into `cli.py`'s `_cmd_increment` — remove - `_emit_increment_kuzu_warning()`, dispatch to Kuzu incremental or - full based on decision. -3. Integrate into `server.py`'s `refresh_code_index` MCP tool. -4. Update `README.md` and `docs/JAVA-CODEBASE-RAG-CLI.md`. diff --git a/propose/active/TIER2-INCREMENTAL-REBUILD-PROPOSE.md b/propose/active/TIER2-INCREMENTAL-REBUILD-PROPOSE.md deleted file mode 100644 index 51548eb3..00000000 --- a/propose/active/TIER2-INCREMENTAL-REBUILD-PROPOSE.md +++ /dev/null @@ -1,560 +0,0 @@ -# Tier 2 — Incremental Kuzu rebuild - -Status: **active — ready for planning**. -User-facing tracking: GitHub issue **#73**. -Companion proposal: [`propose/active/INDEX-AUTO-MODE-PROPOSE.md`](INDEX-AUTO-MODE-PROPOSE.md) -(decision engine for `increment`/`reprocess`). - -This is a **proposal**, not an implementable plan. After review, -an implementable `plans/active/PLAN-TIER2-INCREMENTAL-REBUILD.md` will -be derived. - -## TL;DR - -`build_ast_graph.py` is a full rebuild on every run: `write_kuzu` calls -`_drop_all` then writes all nodes and edges from scratch. Every `.java` -file is re-parsed and every node/edge re-derived. That worked through -Tier 1B because every fixture is small and users run `reprocess` manually -after big changes. As the tool reaches more users running -`java-codebase-rag increment` frequently, the full-rebuild cost becomes -the dominant latency. This proposal introduces a **diff-driven Kuzu -rebuild path** that updates only what's changed at file granularity, -while keeping the full-rebuild path as the safe fallback. - -The diff-driven path is gated by the decision engine defined in -[`INDEX-AUTO-MODE-PROPOSE.md`](INDEX-AUTO-MODE-PROPOSE.md) — meaning -incremental is *only* used when the decision engine decides it's safe. -Full rebuild remains the default for renames, deletes, config changes, -and ambiguous cases. - -## Why now - -1. **The schema is stable.** Ontology 16 (with Client, Producer, - OVERRIDES, UnresolvedCallSite) is the surface that downstream - tooling depends on. Adding incremental rebuild now doesn't risk - schema churn. -2. **The decision engine is co-proposed.** `INDEX-AUTO-MODE-PROPOSE.md` - specifies when full vs incremental is safe for both Lance and Kuzu. -3. **Users need it.** The `increment` command updates Lance vectors - but prints a warning that the Kuzu graph is stale. Users running - edit-index-query loops get divergent results. -4. **Idempotency hooks are in place.** `pass6_match_edges` resets - its match-breakdown counters at the start of every run. Future - passes can adopt the same contract trivially. -5. **Single-developer pain point.** Edit-rebuild-query loops are the - inner loop. A sub-second incremental rebuild is the difference - between the tool feeling responsive and feeling batch-oriented. - -## Goals - -1. **File-level incremental rebuild** that touches only nodes/edges - derived from changed `.java` files (and their dependency closure — - see §2.3). -2. **Bit-for-bit equivalence** between incremental and full rebuild for - the same final source-tree state (verified by determinism test). -3. **Safe fallback to full rebuild** in any ambiguous case, never - silent partial state. -4. **No schema churn** — the surface (`graph_meta`, ontology 16, MCP - tools) is identical; incremental is a build-strategy optimisation. -5. **CLI integration via `increment`** — `java-codebase-rag increment` - updates both Lance and Kuzu incrementally. `reprocess` remains the - explicit full-rebuild command. `build_ast_graph.py` gains - `--changed-paths` as an internal flag (not user-facing). - -## Non-goals - -- Watch-mode (filesystem watcher running continuously). - This proposal lays the foundation; a future - `propose/WATCH-MODE-PROPOSE.md` can build on top. -- Multi-tenant/concurrent rebuilds. Single writer assumed. -- Distributed/sharded indexing. Out of scope. -- LanceDB incremental rebuild (already covered by CocoIndex's native - incremental in the `increment` command — this is Kuzu-only). -- Cross-repo or cross-source-root incremental. One source tree at a time. -- Schema migrations between ontology versions. Schema bumps still - require a full rebuild — flagged by the decision engine. - -## 1. Current state - -### 1.1 The full-rebuild pipeline - -``` -build_ast_graph.main() - └─ pass1_parse(root, tables) # parse every .java → JavaFileAst - └─ pass2_edges(tables, asts) # EXTENDS/IMPLEMENTS/INJECTS edges - └─ pass3_calls(tables, asts) # CALLS + UnresolvedCallSite edges - └─ pass4_routes(tables, asts) # Route extraction (4 strategies) - └─ pass5_imperative_edges(tables, asts) # Client/Producer nodes, HTTP_CALLS/ASYNC_CALLS - └─ pass6_match_edges(tables) # match resolution + cross-service - └─ write_kuzu(kuzu_path, tables) # _drop_all → _create_schema → write nodes/edges/meta - └─ _drop_all(conn) # all tables dropped - └─ _create_schema(conn) # recreate from scratch - └─ _write_nodes(conn, tables) # Symbol, Route, Client, Producer nodes - └─ _populate_declares_rows # DECLARES edges - └─ _populate_overrides_rows # OVERRIDES edges (subtype→supertype method) - └─ _write_edges(conn, tables) # EXTENDS/IMPLEMENTS/INJECTS/CALLS/OVERRIDES - └─ _write_routes_and_exposes # Route/EXPOSES, Client/DECLARES_CLIENT, Producer/DECLARES_PRODUCER - └─ _write_meta(conn, tables) # graph_meta JSON-blob columns -``` - -Every pass populates the in-memory `GraphTables` struct. `write_kuzu` -then drops the entire Kuzu DB and writes everything from scratch. - -### 1.2 What's already well-positioned for incremental - -- **Pass1 is per-file** — each `JavaFileAst` is independent. Parsing is - trivially incrementalisable. -- **Pass6 is idempotent** — match counters reset, then re-derive from - the edges in the DB. With pass5 edges intact for unchanged files, - `pass6` can re-run cheaply over the union of "edges from changed - files" + "all matched edges that *might* now have new candidates". -- **Pass4's route extraction** is per-file at extraction time but - cross-file at resolution time (3 strategies). Route hints from one - file can affect another file's resolution. -- **`GraphTables` is an in-memory accumulator** — passes add to it, - `write_kuzu` reads from it. An incremental path can construct a - partial `GraphTables` (only dirty files' data) and merge it into the - existing DB. - -### 1.3 What blocks naive incremental - -- **Pass2's edges (EXTENDS/IMPLEMENTS/INJECTS)** are computed across - files. If `Foo.java` extends `Bar.java`, both are needed to emit the - edge. Editing `Bar.java` invalidates the edge from `Foo`. -- **Pass3's CALLS edges** depend on resolution state across files - (a method call in `A.java` may resolve to a method in `B.java`). - Pass3 also emits `UnresolvedCallSite` + `UNRESOLVED_AT` edges. -- **OVERRIDES edges** span files — `Foo.method()` overrides - `Bar.method()`. Editing `Bar.java` invalidates the OVERRIDES edge. - These are computed in `_populate_overrides_rows` during the write - phase. -- **Brownfield Layer 4 + 5** (`@CodebaseClient`, `@CodebaseProducer`, - meta-annotation chains) propagate effects: editing the meta-annotation - hub silently changes every annotated method downstream. -- **Pass5 emits Client/Producer nodes** in addition to HTTP_CALLS/ - ASYNC_CALLS edges. These nodes have their own DECLARES_CLIENT/ - DECLARES_PRODUCER edges. HTTP_CALLS now goes Client→Route and - ASYNC_CALLS goes Producer→Route (not Symbol→Route as in ontology 7). -- **Pass6 cross-service matching** matches caller-side calls against - routes from *all* services. A new route in svc-b can flip an - unmatched HTTP_CALLS edge in svc-a to `cross_service`. - -These constraints mean we need **change-set closure**, not just -file-level dirty tracking. - -## 2. Design - -### 2.1 Two-tier change set - -The runtime computes a **change set** with two tiers: - -- **Tier 1 (direct):** files in `--changed-paths` (added, modified). -- **Tier 2 (closure):** files reachable via "depends on" links from - Tier 1 — see §2.3. - -Both tiers are re-parsed and their nodes/edges deleted from the DB -before pass1's incremental write. Files outside both tiers are left -untouched. - -### 2.2 The incremental main loop (sketch) - -``` -build_ast_graph_incremental(changed_paths): - if decision_engine.requires_full(changed_paths): - return run_full_rebuild() # safe fallback - - # Compute change set (Tier 1 + Tier 2 closure) - dirty = expand_to_closure(changed_paths) - - with conn: - delete_rows_for_files(conn, dirty) # symmetric deletes (see §2.5) - asts = pass1_parse_subset(root, dirty) # only re-parse dirty files - tables = GraphTables() # fresh accumulator — only dirty data - pass2_edges_subset(tables, asts, dirty) # re-emit cross-file edges - # for symbols touching dirty - pass3_calls_subset(tables, asts, dirty) - pass4_routes_subset(tables, asts, dirty) - pass5_imperative_edges_subset(tables, asts, dirty) - - # OVERRIDES for dirty files only - _populate_overrides_rows(tables) - - # Pass6 always reruns globally — its cost is proportional to total - # call edges, not changed files, and it computes match outcomes - # that span services. Cheap (~ms on bank-chat-system) and worth - # the simplicity. See §3.6. - pass6_match_edges(tables) - - # Write incremental rows to existing DB (no _drop_all) - _write_nodes_incremental(conn, tables) - _write_edges_incremental(conn, tables) - _write_routes_and_exposes_incremental(conn, tables) - _write_meta(conn, tables, source_root) # always rewritten - _write_dependency_index(deps_path, asts) # sidecar .deps.json (see §2.4) -``` - -### 2.3 Change-set closure rules - -For each file `F` in Tier 1, mark these files as Tier 2: - -1. **Inverse-INJECTS:** every file that `INJECTS` a symbol declared in `F`. -2. **Inverse-EXTENDS / Inverse-IMPLEMENTS:** every file whose symbol - extends or implements a symbol from `F`. (Class hierarchy - re-resolution may change brownfield-overrides resolution.) -3. **Inverse-CALLS:** every file that calls a symbol declared in `F`. - (CALLS resolution can flip targets when overload sets change.) -4. **Meta-annotation closure:** if `F` declares an `@interface` (a - meta-annotation), every file that uses that annotation is dirty. - (Brownfield Layer 5 can re-fanout.) -5. **Brownfield-override closure:** if `F` contains - `@CodebaseClient` / `@CodebaseProducer` / `@CodebaseEndpoint` / - role/capability override annotations, every file in the same - FQN scope (per Layer 4 rules) is potentially affected — fall - back to full rebuild (see TBD-1 resolution below). -6. **Route resolution closure:** if `F` contains route declarations - or `@RequestMapping`-class hints, every file with a method on - that class is dirty. -7. **Inverse-OVERRIDES:** if `F` declares a method that overrides a - supertype method, editing the supertype's file invalidates the - subtype's OVERRIDES edge — the subtype's file is dirty. -8. **Inverse-DECLARES_CLIENT / Inverse-DECLARES_PRODUCER:** if `F` - declares a Client or Producer, and a route change in another file - could affect the match outcome, the Client/Producer's file is - dirty. In practice, pass6 already reruns globally and handles - match resolution — this closure ensures the Client/Producer - *nodes* are current when their declaring method's file changes. - -The `_write_dependency_index` step (§2.4) caches the inverse maps so -closure is O(|dirty| × avg_inverse_degree), not O(|dirty| × |all-files|). - -### 2.4 Dependency index - -A sidecar file at `/.deps.json` stores per-file dependency -metadata. This is a build cache, not graph data — kept outside the Kuzu -DB for cheap Python-level inverse-map computation and no Cypher overhead. - -```json -{ - "version": 1, - "ontology_version": 16, - "files": { - "src/main/java/com/example/Foo.java": { - "ext_hash": "sha256:abc...", - "declares": ["com.example.Foo", "com.example.Foo.Bar"], - "injects": ["com.example.Service"], - "extends": ["com.example.Base"], - "calls": ["com.example.Service#run"], - "uses_anno": ["@RestController", "@CodebaseEndpoint"], - "overrides": ["com.example.Base#method()"], - "declares_clients": ["com.example.Foo#callApi()"], - "declares_producers": [] - } - } -} -``` - -Atomicity via write-temp-rename pattern. Version field for future -migrations. `ontology_version` field to detect stale index — mismatch -triggers full rebuild. - -### 2.5 Symmetric delete - -Every pass that *emits* nodes/edges keyed by source file must have a -symmetric `delete_*_for_file(path)` helper. Concretely: - -| Pass | Emits | Delete helper | -|------|-------|---------------| -| 1 | `Symbol`, `DECLARES` | `delete_symbols_for_file(p)` (cascades to DECLARES) | -| 2 | `EXTENDS`, `IMPLEMENTS`, `INJECTS` | per-edge filter on src-symbol's file | -| 3 | `CALLS`, `UnresolvedCallSite`, `UNRESOLVED_AT` | per-edge/site filter on caller-symbol's file | -| 4 | `Route`, `EXPOSES` | per-route filter on owner-symbol's file | -| 5 | `Client`, `DECLARES_CLIENT`, `Producer`, `DECLARES_PRODUCER` | per-node filter on declaring-method's file | -| 5 | `HTTP_CALLS` (Client→Route) | per-edge filter on Client's declaring-method's file | -| 5 | `ASYNC_CALLS` (Producer→Route) | per-edge filter on Producer's declaring-method's file | -| overrides | `OVERRIDES` | per-edge filter on subtype-method's file | - -Each helper takes a `Path` and a `kuzu.Connection`, executes the -DELETE Cypher, and returns a count for `--verbose` logging. The file -path is reachable via the source `Symbol`'s `path` field (or via -`Client.filename` / `Producer.filename` for those node types). - -### 2.6 Change-detection sources - -Three sources, in priority order: - -1. **`--changed-paths` flag** (or stdin list). Caller responsibility - to be accurate. This is what the INDEX-AUTO-MODE decision engine - would pass. -2. **Git diff** between `--git-ref-base` and `HEAD`. Same logic as - INDEX-AUTO-MODE §"Change Detection Strategy". -3. **Hash-based detection** using `.deps.json` `ext_hash` fields. Walk - the source tree, compute hashes, compare against cached. Slowest; - used as last-resort fallback. - -If all three fail or are ambiguous, fall back to full rebuild. - -## 3. Pass-by-pass incrementalisation notes - -### 3.1 Pass1 (parse) - -Trivial. Re-parse only files in the dirty set. No global state. - -### 3.2 Pass2 (cross-file edges) - -The edge `Foo EXTENDS Bar` lives in `pass2`. If only `Foo.java` -changed, the edge needs to be re-emitted with up-to-date metadata. -If only `Bar.java` changed, the edge target is unchanged but `Bar`'s -symbol ID may have new fields — re-emit. - -OVERRIDES edges (computed in `_populate_overrides_rows` during write) -follow the same pattern. If `Foo.method()` overrides `Bar.method()` -and `Bar.java` changes, `Foo`'s OVERRIDES edge is stale — covered by -closure rule 7. - -### 3.3 Pass3 (CALLS + UnresolvedCallSite) - -Same shape as pass2. CALLS edges re-emitted for caller-symbols in -dirty files. Closure rule 3 catches inverse-CALLS. `UnresolvedCallSite` -rows and their `UNRESOLVED_AT` edges are also deleted and re-emitted -for the dirty subset. - -### 3.4 Pass4 (Routes) - -Two sub-passes: - -- **Extraction** is per-file. Easy. -- **Resolution** (three-strategy ladder) reads class-level hints from - a possibly-different file. Closure rule 6 covers this. - -Phantom-route cleanup currently runs in `pass6`. That stays as-is — -phantoms are derived from the global graph state. - -### 3.5 Pass5 (Client/Producer + HTTP_CALLS/ASYNC_CALLS) - -Now emits Client and Producer *nodes* (not just edges) plus their -DECLARES_CLIENT/DECLARES_PRODUCER edges. HTTP_CALLS now originates from -Client→Route and ASYNC_CALLS from Producer→Route. - -Symmetric delete must clean up all of these per-file. Brownfield -Layer 4 (`@CodebaseClient` / `@CodebaseProducer`) overrides — closure -rule 5 currently forces full rebuild when an override file changes; -pessimistic but safe. Fine-grained brownfield closure deferred. - -### 3.6 Pass6 (match outcomes + cross-service) - -**Always reruns globally.** Three reasons: - -1. Cross-service matching can flip outcomes service-wide when one - route's path template changes. -2. Pass6 is fast: on `bank-chat-system` it runs in ~1ms. Even at 10× - scale we're still under the human-perception threshold. -3. Pass6's idempotency contract was already added with incremental - in mind. - -### 3.7 `_write_meta` - -Always rewritten — fields like `routes_total`, `cross_service_calls_total`, -`http_calls_match_breakdown`, `async_calls_match_breakdown` are aggregations -over the global graph state. Cost is negligible. - -## 4. CLI surface - -The incremental path integrates with the existing `java-codebase-rag` -CLI, not as a user-facing flag on `build_ast_graph.py`: - -```bash -# Existing — unchanged (full rebuild of Lance + Kuzu) -java-codebase-rag reprocess -java-codebase-rag reprocess --graph-only -java-codebase-rag reprocess --vectors-only - -# Updated — now also increments Kuzu graph (not just Lance) -java-codebase-rag increment - -# Internal — build_ast_graph.py gains --changed-paths (called by CLI, not users) -python build_ast_graph.py \ - --source-root --kuzu-path \ - --changed-paths \ - [--verbose] -``` - -Decision engine inside `cli.py`'s `_cmd_increment`: - -1. If `` doesn't exist or `.deps.json` is missing/stale → - fall back to full graph rebuild. -2. If `decision_engine.requires_full(changed)` → full graph rebuild - with a logged reason. -3. If incremental fails mid-flight → roll back transaction, log, - fall back to full graph rebuild. -4. On success → both Lance and Kuzu are incremental. - -The `_emit_increment_kuzu_warning()` call in `cli.py` is removed once -this ships. - -## 5. MCP integration - -`refresh_code_index` (MCP tool in `server.py`) gains the ability to -call the incremental Kuzu path via the CLI: - -```python -# Pseudocode inside server.py:refresh_code_index -decision = decide_mode(changed_paths, git_ref_base) -if decision.lance_mode == "incremental": - cocoindex_update(incremental=True, paths=decision.lance_paths) -else: - cocoindex_update(full=True) - -if decision.kuzu_mode == "incremental": - subprocess.run(["java-codebase-rag", "increment"]) -else: - subprocess.run(["java-codebase-rag", "reprocess", "--graph-only"]) -``` - -Decision engine returns two independent mode choices — LanceDB and -Kuzu may incrementally update independently. See -[`INDEX-AUTO-MODE-PROPOSE.md`](INDEX-AUTO-MODE-PROPOSE.md) for the -full decision engine specification. - -## 6. Determinism + correctness - -### 6.1 Determinism test - -Create `tests/test_incremental_equivalence.py` as a prerequisite: - -```python -def test_incremental_matches_full(tmp_path): - src = tmp_path / "src"; src.mkdir() - copy_fixture(src, "tests/fixtures/cross_service_smoke") - - # Full rebuild on initial state - run_full(src, kuzu_a := tmp_path / "a") - - # Mutate one file - (src / "svc-a/.../ClientA.java").write_text(modified_source) - - # Two paths to the same final state - run_full(src, kuzu_full := tmp_path / "full") - run_incremental(kuzu_a, changed=["svc-a/.../ClientA.java"]) - - assert all_sorted_ids(kuzu_full) == all_sorted_ids(kuzu_a) - assert meta(kuzu_full) == meta(kuzu_a) -``` - -This is the single most important test in the entire feature. -Without it, every incremental rebuild is a potential silent-divergence -risk. Run against every fixture. - -### 6.2 Failure modes - -- **Half-applied delete:** transaction wraps the entire incremental - pass; on any exception, ROLLBACK and fall back to full rebuild. -- **Corrupt `.deps.json`:** detected by checksum + `ontology_version` - field; treated as "incremental impossible, fall back to full". -- **Schema-version mismatch:** if `graph_meta.ontology_version` ≠ - current `ONTOLOGY_VERSION`, force full rebuild. - -## 7. Rollout - -1. **PR-T1 (foundation + determinism test):** Create - `tests/test_incremental_equivalence.py` with full-rebuild - determinism assertions. Add `.deps.json` writer - (`_write_dependency_index`) and reader, written but unused. - Establish performance baseline on fixtures. -2. **PR-T2 (delete helpers):** symmetric `delete_*_for_file` for each - pass and node/edge type (Symbol, DECLARES, EXTENDS, IMPLEMENTS, - INJECTS, CALLS, UnresolvedCallSite, UNRESOLVED_AT, Route, EXPOSES, - Client, DECLARES_CLIENT, Producer, DECLARES_PRODUCER, HTTP_CALLS, - ASYNC_CALLS, OVERRIDES). Unit-tested in isolation. Still no - incremental codepath. -3. **PR-T3 (incremental orchestrator):** `build_ast_graph_incremental` - function + `--changed-paths` flag on `build_ast_graph.py`. Pass-by- - pass incremental implementation including Client/Producer/OVERRIDES/ - UnresolvedCallSite. `test_incremental_matches_full` extended to - cover all fixtures. -4. **PR-T4 (CLI + decision engine):** Integrate INDEX-AUTO-MODE - decision engine into `cli.py`'s `_cmd_increment`. Remove - `_emit_increment_kuzu_warning()`. Wire `refresh_code_index` - MCP tool to dispatch. -5. **PR-T5 (brownfield closure refinement, optional):** Narrow the - pessimistic "any brownfield-override change → full" rule once - Layer-4/5 fanout is explicitly documented. - -PR-T1 through PR-T4 are the headline. PR-T5 is an optimisation -on top. - -## 8. Risk assessment - -| Risk | Severity | Mitigation | -|------|----------|------------| -| Silent divergence between full and incremental | **High** | `test_incremental_matches_full` mandatory per fixture; covered by §6.1 | -| Pessimistic full-fallback hides real incremental wins | Medium | Track full-fallback rate via `graph_meta.last_rebuild_mode` + reason; review monthly | -| `.deps.json` becomes stale | Medium | `ontology_version` field check; mismatch → full rebuild | -| Decision engine bugs cause unsafe incremental | High | Default-to-full on ambiguity; conservative initial rules; expand only after burn-in | -| Pass2/Pass3 closure misses an edge type | Medium | Determinism test surfaces this immediately | -| Performance regression (incremental slower than full for small repos) | Low | Heuristic: skip incremental when dirty set is >50% of files | - -## 9. Performance estimate - -On a hypothetical 1000-file Java repo: - -| Metric | Full rebuild | Incremental (1 file changed) | -|--------|--------------|-------------------------------| -| Pass1 parse | ~30s (1000 × 30ms) | <0.1s (1 × 30ms + 5-10 closure files) | -| Pass2-5 emit | ~20s | <0.2s | -| Pass6 match | ~1s | ~1s (always global) | -| `_write_meta` | <0.1s | <0.1s | -| **Total** | **~50s** | **~1.5s** | - -These are estimates — actual numbers depend on closure breadth and -Kuzu transaction overhead. PR-T1 establishes a measured baseline on -`bank-chat-system` and other fixtures. - -## 10. Resolved TBDs - -### TBD-1: Brownfield closure granularity — **pessimistic fallback** - -Layer-4 (`@CodebaseClient` / `@CodebaseProducer`) overrides operate -via FQN matching. Editing the override file conceptually invalidates -every matching method. The current proposal forces full rebuild in -that case (closure rule 5). Fine-grained closure is deferred to PR-T5 -or a follow-up proposal once Layer-4 fanout rules are formalised. - -### TBD-2: FileDeps storage — **sidecar JSON** - -Decision: **sidecar `/.deps.json`**. The file-level dependency -index is conceptually a build cache, not graph data. Benefits: cheap -inverse-map computation in Python, no Cypher overhead, no schema -evolution burden. Atomicity via write-temp-rename. `version` + -`ontology_version` fields for migration/staleness detection. - -### TBD-3: Incremental for the LanceDB chunks — **out of scope** - -Already covered by CocoIndex's native incremental support -(`java-codebase-rag increment` without `--full-reprocess`). - -### TBD-4: Concurrent / interleaved rebuilds — **document only** - -Single-writer assumed. If two runs race against the same `--kuzu-path`, -behaviour is undefined. Document; do not guard against. - -### TBD-5: Watch-mode — **out of scope, future proposal** - -A follow-on proposal should layer a filesystem watcher on top of this -incremental path. It needs debouncing, batched-change semantics, and -its own state machine. - -## 11. Done definition (proposal-level) - -This proposal is "ready for plan derivation" when: - -- [x] All TBD items have a decision. -- [ ] §3 closure rules have been validated against a real - multi-service fixture (`cross_service_smoke` is a candidate). -- [ ] §9 performance estimates have a measured baseline on at least - one fixture. -- [ ] Reviewer approves §2.5 (symmetric delete) as the right model. -- [ ] Decision engine pseudocode in §4 + §5 is consistent with - `INDEX-AUTO-MODE-PROPOSE.md`. - -When approved, derive `plans/active/PLAN-TIER2-INCREMENTAL-REBUILD.md` -with PR-T1 through PR-T5 broken out, and a per-PR agent task prompt set. diff --git a/propose/stale/INDEX-AUTO-MODE-PROPOSE.md b/propose/stale/INDEX-AUTO-MODE-PROPOSE.md new file mode 100644 index 00000000..0caa6a45 --- /dev/null +++ b/propose/stale/INDEX-AUTO-MODE-PROPOSE.md @@ -0,0 +1,124 @@ +# Proposal: Smart `refresh_code_index` Mode Selection + +> **Note (2026):** the operator CLI’s full rebuild verb is now `java-codebase-rag reprocess` (see `propose/completed/CLI-SCENARIOS-PROPOSE.md`); this MCP-side proposal still refers to `refresh_code_index` by name. +> +> For embeddings or search over raw `propose/` text, expect both that historical MCP name and current CLI wording in the same document until this draft is implemented or archived under `propose/completed/`. + +## Goal + +Extend `refresh_code_index` so it can choose incremental vs full rebuild automatically, while staying safe for rename/delete/move and indexing-semantics changes. + +## Problem + +Current behavior always runs: + +- `cocoindex update ... --full-reprocess -f` +- followed by full Kuzu rebuild + +This is correct but expensive for small edit-only iterations. At the same time, a naive incremental flow can leave stale entries after file deletes/renames or when metadata semantics change. + +## Proposed API Changes + +Add optional inputs to `refresh_code_index`: + +- `confirm: bool = false` (existing) +- `mode: "auto" | "incremental" | "full" = "auto"` +- `changed_paths: list[str] | null = null` +- `git_ref_base: str = "HEAD"` +- `reason: str | null = null` + +Backward compatibility: + +- Calls passing only `confirm=true` should still work. +- Default mode should become `auto` (safe-by-default decisioning). + +## Decision Engine (`mode=auto`) + +### Choose `full` when any of the following is true + +- At least one file is deleted. +- At least one file is renamed or moved. +- `.lancedb-mcp.yml` changes. +- Indexing pipeline/config files change (for example: `java_index_flow_lancedb.py`, enrichment/chunking components). +- `@interface` definitions changed (meta-annotation fanout risk). +- Change detection fails or is ambiguous. + +### Choose `incremental` when all are true + +- Only in-place file content modifications/additions. +- No rename/delete/move events. +- No index/config/meta-annotation risk triggers. + +## Change Detection Strategy + +1. Prefer git diff status: + - `git diff --name-status ...HEAD` + - optionally include working tree status (`git diff --name-status` and `git diff --name-status --cached`) +2. If git signal is unavailable, use `changed_paths` when supplied. +3. If still uncertain, fall back to `full`. + +Represent results as: + +- `added[]`, `modified[]`, `deleted[]`, `renamed[]` +- plus boolean risk flags for config/index/meta-annotation changes + +## Execution Plan + +### Full mode + +- Keep current behavior: + - `cocoindex update ... --full-reprocess -f` + - run `build_ast_graph.py --source-root ...` + +### Incremental mode + +- Run `cocoindex update ... -f` (without `--full-reprocess`) +- Graph handling in two phases: + - Phase A: still run full graph rebuild for correctness. + - Phase B (future): incremental graph updates scoped to changed files. + +## Response Payload Enhancements + +Add decision transparency fields: + +- `effective_mode: "incremental" | "full"` +- `decision_reasons: list[str]` +- `detected_changes: { added, modified, deleted, renamed }` +- optional `warnings: list[str]` (for forced incremental under risky conditions) + +Keep existing stdout/stderr/exit_code fields intact. + +## Safety Policy + +- Default `auto`. +- On uncertainty, choose `full`. +- `mode=full` always respected. +- `mode=incremental` allowed, but return warnings when risk triggers exist. +- Never silently downgrade explicit `full` to incremental. + +## Test Plan + +Add/extend tests in `tests/test_mcp_tools.py`: + +1. `auto` + modified-only -> incremental chosen. +2. `auto` + deleted file -> full chosen. +3. `auto` + renamed file -> full chosen. +4. `auto` + `.lancedb-mcp.yml` change -> full chosen. +5. `auto` + detection failure -> full chosen with reason. +6. explicit `mode=full` -> full regardless of diffs. +7. explicit `mode=incremental` + risky changes -> incremental + warning. +8. backward compatibility: `confirm=true` only call still succeeds. + +## Implementation Notes + +- Keep mode-selection logic isolated in helper functions for testability: + - `_detect_repo_changes(...)` + - `_choose_refresh_mode(...)` +- Make logs/user-facing messages explicit about why full mode was selected. +- Preserve current subprocess environment and project-root behavior. + +## Rollout + +1. Implement API and auto decisioning with Phase A graph behavior. +2. Add test coverage and docs update in `README.md`. +3. Later: implement true incremental Kuzu graph updates (Phase B). diff --git a/propose/stale/TIER2-INCREMENTAL-REBUILD-PROPOSE.md b/propose/stale/TIER2-INCREMENTAL-REBUILD-PROPOSE.md new file mode 100644 index 00000000..73101047 --- /dev/null +++ b/propose/stale/TIER2-INCREMENTAL-REBUILD-PROPOSE.md @@ -0,0 +1,520 @@ +# Tier 2 — Incremental Kuzu rebuild + +Status: **active — ready for planning**. +User-facing tracking for graph-side incremental work: GitHub issue **#73** (linked from the `increment` stderr warning in `java_codebase_rag/cli.py`). +Pairs with the focused MCP-tool proposal +[`propose/INDEX-AUTO-MODE-PROPOSE.md`](INDEX-AUTO-MODE-PROPOSE.md) +(decision engine for `refresh_code_index`) and supersedes its +"future Kuzu work" footnote in [`docs/PRODUCT-VISION.md`](../docs/PRODUCT-VISION.md) §99. + +This is a **proposal**, not an implementable plan. After review and +scoping decisions (the §11 [TBD] list), an implementable +`plans/PLAN-TIER2-INCREMENTAL-REBUILD.md` will be derived. + +## TL;DR + +`build_ast_graph.py` is a full rebuild on every run: `_drop_all` plus +`pass1`–`pass6` re-parse every `.java` file in the source tree and +re-derive every node and edge. That worked through Tier 1B because +every fixture is small and the production user runs an indexing job +manually after big changes. As we move toward continuous indexing +(`refresh_code_index` with `mode=incremental`, future watch-mode, or +post-merge CI hooks), the full-rebuild cost becomes the dominant +latency. This proposal introduces a **diff-driven Kuzu rebuild path** +that updates only what's changed at file granularity, while keeping +the full-rebuild path as the safe fallback. + +The diff-driven path is gated by the same decision engine that the +REFRESH proposal already specifies for LanceDB — meaning incremental +is *only* used when the decision engine decides it's safe. Full +rebuild remains the default for renames, deletes, config changes, and +ambiguous cases. + +## Why now (and not earlier) + +1. **Tier 1B closed the schema.** Ontology 7 (with `pass6_match_edges`) + is the surface that downstream tooling depends on. Adding incremental + rebuild now doesn't risk schema churn. +2. **The decision engine already exists in proposal form.** REFRESH + proposal §"Decision Engine" specifies exactly when full vs incremental + is safe. The current Kuzu path can't take advantage because there is + no incremental option to dispatch to — this proposal closes that gap. +3. **Idempotency hooks are already added.** `pass6_match_edges` resets + its match-breakdown counters at the start of every run (PR-D3 review + obs 3, addressed in PR-E1 follow-up plan). Future passes can adopt + the same idempotency contract trivially. +4. **Single-developer pain point.** As the user maintains real codebases + with the AMA agent, edit-rebuild-query loops are the inner loop. A + sub-second incremental rebuild is the difference between the agent + feeling responsive and feeling batch-oriented. + +## Goals + +1. **File-level incremental rebuild** that touches only nodes/edges + derived from changed `.java` files (and their meta-annotation / + brownfield-overrides closure — see §3.2). +2. **Bit-for-bit equivalence** between incremental and full rebuild for + the same final source-tree state (verified by determinism test). +3. **Safe fallback to full rebuild** in any ambiguous case, never + silent partial state. +4. **No schema churn** — the surface (`graph_meta`, ontology 7, MCP + tools) is identical; incremental is a build-strategy optimisation. +5. **Backwards-compatible CLI** — `python build_ast_graph.py + --source-root … --kuzu-path …` keeps its current full-rebuild + semantics. A new `--changed-paths …` (or equivalent) opt-in gates + the incremental path. + +## Non-goals + +- Watch-mode (filesystem watcher running continuously). + This proposal lays the foundation; a future `propose/WATCH-MODE-PROPOSE.md` + can build on top. +- Multi-tenant/concurrent rebuilds. Single writer assumed. +- Distributed/sharded indexing. Out of scope. +- LanceDB incremental rebuild (already covered by CocoIndex's native + incremental in the REFRESH proposal — this is Kuzu-only). +- Cross-repo or cross-source-root incremental. One source tree at a time. +- Schema migrations between ontology versions. Schema bumps still + require a full rebuild — flagged by the decision engine. + +## 1. Current state + +### 1.1 The full-rebuild pipeline + +``` +build_ast_graph.main() + └─ _drop_all(conn) # 11 tables dropped + └─ pass1_parse(root) # parse every .java → JavaFileAst + └─ pass2_edges # EXTENDS/IMPLEMENTS/INJECTS edges + └─ pass3_calls # CALLS edges (intra-service) + └─ pass4_routes # Route extraction (4 strategies) + └─ pass5_imperative_edges # HTTP_CALLS / ASYNC_CALLS caller edges + └─ pass6_match_edges # 5-outcome match resolution + cross-service + └─ _write_meta # graph_meta JSON-blob columns +``` + +Every pass either holds rows in `GraphTables` or writes them after the +parse phase. Storage is single-file Kuzu DB at `--kuzu-path`. Phase 1 +*always* drops and recreates. + +### 1.2 What's already well-positioned for incremental + +- **Pass1 is per-file** — each `JavaFileAst` is independent. Parsing is + trivially incrementalisable. +- **Pass6 is idempotent** — match counters reset, then re-derive from + edges in the DB. With `pass5` edges intact for unchanged files, + `pass6` can re-run cheaply over the union of "edges from changed + files" + "all matched edges that *might* now have new candidates". +- **Pass4's route extraction** is per-file at extraction time but + cross-file at resolution time (3 strategies in PR-A2). Route hints + from one file can affect another file's resolution. +- **Determinism test (`tests/test_determinism.py`)** exists and + enforces that two runs on the same input produce identical sorted + IDs. This is the single most important property for incremental + rebuild — we'll extend it to `incremental(input) == full(input)`. + +### 1.3 What blocks naive incremental + +- **Pass2's edges (EXTENDS/IMPLEMENTS/INJECTS)** are computed across + files. If `Foo.java` extends `Bar.java`, both are needed to emit the + edge. Editing `Bar.java` invalidates the edge from `Foo`. +- **Pass3's CALLS edges** depend on resolution state across files + (a method call in `A.java` may resolve to a method in `B.java`). +- **Brownfield Layer 4 + 5** (`@CodebaseClient`, `@CodebaseProducer`, + meta-annotation chains) propagate effects: editing the meta-annotation + hub silently changes every annotated method downstream. +- **Pass5/Pass6 cross-service matching** matches caller-side calls + against routes from *all* services. A new route in svc-b can flip + an unmatched HTTP_CALLS edge in svc-a to `cross_service`. + +These constraints mean we need **change-set closure**, not just +file-level dirty tracking. + +## 2. Design + +### 2.1 Two-tier change set + +The runtime computes a **change set** with two tiers: + +- **Tier 1 (direct):** files in `--changed-paths` (added, modified). +- **Tier 2 (closure):** files reachable via "depends on" links from + Tier 1 — see §3.2. + +Both tiers are re-parsed and their nodes/edges deleted from the DB +before pass1's incremental write. Files outside both tiers are left +untouched. + +### 2.2 The incremental main loop (sketch) + +``` +build_ast_graph_incremental(changed_paths): + if decision_engine.requires_full(changed_paths): + return run_full_rebuild() # safe fallback + + # Compute change set (Tier 1 + Tier 2 closure) + dirty = expand_to_closure(changed_paths) + + with conn: + delete_rows_for_files(dirty) # symmetric to pass1's emits + asts = pass1_parse_subset(dirty) # only re-parse dirty files + pass2_edges_subset(asts, dirty) # re-emit cross-file edges + # for symbols touching dirty + pass3_calls_subset(asts, dirty) + pass4_routes_subset(asts, dirty) + pass5_imperative_edges_subset(asts, dirty) + + # Pass6 always reruns globally — its cost is proportional to total + # call edges, not changed files, and it computes match outcomes + # that span services. Cheap (~ms on bank-chat-system) and worth + # the simplicity. See §3.4. + pass6_match_edges() + + _write_meta(conn, tables, source_root) # always rewritten + _write_dependency_index(conn, asts) # NEW (see §2.4) +``` + +### 2.3 Change-set closure rules + +For each file `F` in Tier 1, mark these files as Tier 2: + +1. **Inverse-INJECTS:** every file that `INJECTS` a symbol declared in `F`. +2. **Inverse-EXTENDS / Inverse-IMPLEMENTS:** every file whose symbol + extends or implements a symbol from `F`. (Class hierarchy + re-resolution may change brownfield-overrides resolution.) +3. **Inverse-CALLS:** every file that calls a symbol declared in `F`. + (CALLS resolution can flip targets when overload sets change.) +4. **Meta-annotation closure:** if `F` declares an `@interface` (a + meta-annotation), every file that uses that annotation is dirty. + (Brownfield Layer 5 can re-fanout.) +5. **Brownfield-override closure:** if `F` contains + `@CodebaseClient` / `@CodebaseProducer` / `@CodebaseEndpoint` / + role/capability override annotations, every file in the same + FQN scope (per Layer 4 rules) is potentially affected — fall + back to full rebuild for now (see §11 [TBD-1]). +6. **Route resolution closure:** if `F` contains route declarations + or `@RequestMapping`-class hints, every file with a method on + that class is dirty (PR-A2's three-strategy ladder reads class-level + `@RequestMapping` from a possibly-different file). + +The `_write_dependency_index` step (§2.4) caches the inverse maps so +closure is O(|dirty| × avg_inverse_degree), not O(|dirty| × |all-files|). + +### 2.4 Dependency index + +A new node table `FileDeps` (or a sidecar JSON file at +`/.deps.json` — see §11 [TBD-2]) stores per-file: + +```json +{ + "src/main/java/com/example/Foo.java": { + "ext_hash": "sha256:abc...", // for change detection w/o git + "declares": ["com.example.Foo", "com.example.Foo.Bar"], + "injects": ["com.example.Service"], + "extends": ["com.example.Base"], + "calls": ["com.example.Service#run", ...], + "uses_anno": ["@RestController", "@CodebaseEndpoint"] + } +} +``` + +Inverse lookups are computed on demand or cached at write time — +implementation detail, not in this proposal's scope. + +### 2.5 Symmetric delete + +Every pass that *emits* nodes/edges keyed by source file must have a +symmetric `delete_*_for_file(path)` helper. Concretely: + +| Pass | Emits | Delete helper | +|------|-------|---------------| +| 1 | `Symbol`, `DECLARES` | `delete_symbols_for_file(p)` (cascades to DECLARES) | +| 2 | `EXTENDS`, `IMPLEMENTS`, `INJECTS` | per-edge filter on src-symbol's file | +| 3 | `CALLS` | per-edge filter | +| 4 | `Route`, `EXPOSES` | per-route filter on owner-symbol's file | +| 5 | `HTTP_CALLS`, `ASYNC_CALLS` (rows) | per-edge filter on src-symbol's file | +| 6 | (only mutates pass5 rows in place) | n/a — always reruns globally | + +Each helper takes a `Path` and a `kuzu.Connection`, executes the +DELETE Cypher, and returns a count for `--verbose` logging. None of +the existing tables need new columns — the file path is reachable +via the source `Symbol`'s `path` field. + +### 2.6 Change-detection sources + +Three sources, in priority order: + +1. **`--changed-paths` flag** (or stdin list). Caller responsibility + to be accurate. This is what the REFRESH proposal's decision engine + would pass. +2. **Git diff** between `--git-ref-base` and `HEAD`. Same logic as + REFRESH proposal §"Change Detection Strategy". +3. **Hash-based detection** using `FileDeps.ext_hash`. Walk the source + tree, compute hashes, compare against cached. Slowest of the three; + used as last-resort fallback. + +If all three fail or are ambiguous, fall back to full rebuild. + +## 3. Pass-by-pass incrementalisation notes + +### 3.1 Pass1 (parse) + +Trivial. Re-parse only files in the dirty set. No global state. + +### 3.2 Pass2 (cross-file edges) + +The edge `Foo EXTENDS Bar` lives in `pass2`. If only `Foo.java` +changed, the edge needs to be re-emitted with up-to-date metadata +(`Foo` may have changed which class it extends). If only `Bar.java` +changed, the edge target is unchanged but `Bar`'s symbol ID may have +new fields — re-emit. + +Concretely: pass2 re-runs over the dirty set, but only for *outgoing* +edges from symbols in dirty files. Inverse-EXTENDS lookup ensures +that when `Bar` changes, `Foo`'s edge is also refreshed — captured by +closure §2.3 rule 2. + +### 3.3 Pass3 (CALLS) + +Same shape as pass2. CALLS edges re-emitted for caller-symbols in +dirty files. Closure rule 3 catches inverse-CALLS. + +### 3.4 Pass4 (Routes) + +Two sub-passes: + +- **Extraction** is per-file. Easy. +- **Resolution** (PR-A2's three-strategy ladder) reads class-level + hints from a possibly-different file. Closure rule 6 covers this. + +Phantom-route cleanup currently runs in `pass6` (see PR-D3 review). +That stays as-is — phantoms are derived from the global graph state. + +### 3.5 Pass5 (HTTP_CALLS / ASYNC_CALLS caller-side) + +Per-file emit. Brownfield Layer 4 (`@CodebaseClient` / +`@CodebaseProducer`) overrides — closure rule 5 currently forces full +rebuild when an override file changes; that's pessimistic but safe. +A future PR-F or similar could implement file-scoped brownfield +closure to avoid this, once the Layer-4/5 fanout rules are explicitly +documented (see [TBD-1]). + +### 3.6 Pass6 (match outcomes + cross-service) + +**Always reruns globally.** Three reasons: + +1. Cross-service matching can flip outcomes service-wide when one + route's path template changes. Computing the closure of "which + pass5 rows might re-resolve" is O(|all routes|) anyway — might + as well rerun pass6. +2. Pass6 is fast: on `bank-chat-system` (15 files / 8 routes / 7 + call edges) it runs in ~1ms. Even at 10× scale we're still under + the human-perception threshold. +3. Pass6's idempotency contract (PR-E1 inline comment) was already + added with this proposal in mind. + +### 3.7 `_write_meta` + +Always rewritten — fields like `routes_total`, `cross_service_calls_total`, +`http_calls_match_breakdown`, `async_calls_match_breakdown` are aggregations +over the global graph state. Cost is negligible. + +## 4. CLI surface + +```bash +# Existing — unchanged +python build_ast_graph.py --source-root --kuzu-path [--verbose] + +# New — opt-in incremental +python build_ast_graph.py \ + --source-root --kuzu-path \ + --changed-paths \ + [--git-ref-base HEAD~1] \ + [--verbose] +``` + +Decision engine inside the script: + +1. If `--changed-paths` is given and `` exists with a + readable `FileDeps` index → attempt incremental. +2. If `` is empty/missing → full rebuild (no other choice). +3. If decision_engine.requires_full(changed) → full rebuild with a + logged reason. +4. If incremental fails mid-flight → roll back transaction, log, + fall back to full rebuild. + +## 5. MCP integration + +`refresh_code_index` (already in scope of the REFRESH proposal) gains +the ability to call the new incremental Kuzu path: + +```python +# Pseudocode inside server.py:refresh_code_index +decision = decide_mode(changed_paths, git_ref_base) +if decision.lance_mode == "incremental": + cocoindex_update(incremental=True, paths=decision.lance_paths) +else: + cocoindex_update(full=True) + +if decision.kuzu_mode == "incremental": + subprocess.run([..., "--changed-paths", decision.kuzu_paths_file]) +else: + subprocess.run([...]) # full rebuild +``` + +Decision engine returns two independent mode choices — LanceDB and +Kuzu may incrementally update independently. + +## 6. Determinism + correctness + +### 6.1 Determinism test extension + +Extend `tests/test_determinism.py` (or add `tests/test_incremental_equivalence.py`) +to assert: + +```python +def test_incremental_matches_full(tmp_path): + src = tmp_path / "src"; src.mkdir() + copy_fixture(src, "tests/fixtures/cross_service_smoke") + + # Full rebuild on initial state + run_full(src, kuzu_a := tmp_path / "a") + + # Mutate one file + (src / "svc-a/.../ClientA.java").write_text(modified_source) + + # Two paths to the same final state + run_full(src, kuzu_full := tmp_path / "full") + run_incremental(src, kuzu_inc := kuzu_a, changed=["svc-a/.../ClientA.java"]) + + assert all_sorted_ids(kuzu_full) == all_sorted_ids(kuzu_inc) + assert meta(kuzu_full) == meta(kuzu_inc) +``` + +This is the single most important test in the entire feature. +Without it, every incremental rebuild is a potential silent-divergence +risk. + +### 6.2 Failure modes + +- **Half-applied delete:** transaction wraps the entire incremental + pass; on any exception, ROLLBACK and fall back to full rebuild. +- **Corrupt FileDeps index:** detected by checksum; treated as + "incremental impossible, fall back to full". +- **Schema-version mismatch:** if `graph_meta.ontology_version` ≠ + current `ONTOLOGY_VERSION`, force full rebuild. + +## 7. Rollout + +1. **PR-T1 (foundation):** `FileDeps` table + `_write_dependency_index` + helper, written but unused. Determinism test extended (full + rebuild only, asserts FileDeps round-trip). +2. **PR-T2 (delete helpers):** symmetric `delete_*_for_file` for each + pass. Unit-tested in isolation. Still no incremental codepath. +3. **PR-T3 (incremental orchestrator):** `build_ast_graph_incremental` + function + `--changed-paths` flag. Pass-by-pass incremental + implementation. `test_incremental_matches_full` lit up here — must + pass for every fixture. +4. **PR-T4 (decision engine + CLI):** integrate the REFRESH proposal's + decision engine; wire `refresh_code_index` to dispatch. +5. **PR-T5 (brownfield closure refinement, optional):** narrow the + pessimistic "any brownfield-override change → full" rule once + Layer-4/5 fanout is explicitly documented. + +PR-T1 through PR-T4 are the headline. PR-T5 is an optimisation +on top. + +## 8. Risk assessment + +| Risk | Severity | Mitigation | +|------|----------|------------| +| Silent divergence between full and incremental | **High** | `test_incremental_matches_full` mandatory per fixture; covered by §6.1 | +| Pessimistic full-fallback hides real incremental wins | Medium | Track full-fallback rate via `graph_meta.last_rebuild_mode` + reason; review monthly | +| `FileDeps` index becomes stale | Medium | Stored in same DB transaction as graph; mismatch → full rebuild | +| Decision engine bugs cause unsafe incremental | High | Default-to-full on ambiguity; conservative initial rules; expand only after burn-in | +| Pass2/Pass3 closure misses an edge type | Medium | Determinism test surfaces this immediately | +| Performance regression (incremental slower than full for small repos) | Low | Heuristic: skip incremental when dirty set is >50% of files | + +## 9. Performance estimate + +On a hypothetical 1000-file Java repo: + +| Metric | Full rebuild | Incremental (1 file changed) | +|--------|--------------|-------------------------------| +| Pass1 parse | ~30s (1000 × 30ms) | <0.1s (1 × 30ms + 5-10 closure files) | +| Pass2-5 emit | ~20s | <0.2s | +| Pass6 match | ~1s | ~1s (always global) | +| `_write_meta` | <0.1s | <0.1s | +| **Total** | **~50s** | **~1.5s** | + +These are estimates — actual numbers depend on closure breadth and +Kuzu transaction overhead. Worth establishing a baseline benchmark +in PR-T1 (run full rebuild on `bank-chat-system` 10 times, record +mean/p95) and re-running after each PR. + +## 10. Open questions / explicit out-of-scope + +### [TBD-1] Brownfield closure granularity + +Layer-4 (`@CodebaseClient` / `@CodebaseProducer`) overrides today +operate via FQN matching. Editing the override file conceptually +invalidates every method that matches the override's FQN pattern. +The current proposal forces full rebuild in that case (closure rule +5). A more aggressive closure could parse the override and compute +exact dirty set. Defer to PR-T5 or a follow-up proposal once Layer-4 +fanout rules are formalised. + +### [TBD-2] FileDeps storage: in Kuzu vs sidecar JSON + +Two options: + +- **(a) New node table `FileDeps`** in the same Kuzu DB. Pros: + transactional with the graph, single artifact. Cons: Cypher + query overhead for inverse lookups; another schema column to + evolve. +- **(b) Sidecar `/.deps.json`** file. Pros: cheap + inverse-map computation in Python, no Cypher overhead. Cons: needs + manual atomicity (write-temp-rename pattern), separate version + field for migrations. + +Recommendation: **(b) sidecar JSON** — the file-level dependency +index is conceptually a build cache, not graph data. Decide in +PR-T1. + +### [TBD-3] Incremental for the LanceDB chunks? + +Already covered by CocoIndex's native incremental support +(`cocoindex update` without `--full-reprocess`). The REFRESH +proposal handles this. Out of scope here. + +### [TBD-4] Concurrent / interleaved rebuilds + +Single-writer assumed. If two `build_ast_graph.py` runs race against +the same `--kuzu-path`, behaviour is undefined. Document; do not +guard against. (Standard Kuzu single-writer constraint.) + +### [TBD-5] Watch-mode + +Out of scope. A follow-on proposal should layer a filesystem watcher +on top of this incremental path; it's not a free add-on because the +watcher needs debouncing, batched-change semantics, and its own state +machine. + +## 11. Done definition (proposal-level) + +This proposal is "ready for plan derivation" when: + +- [ ] All [TBD] items in §10 have either a decision or an explicit + "deferred to PR-T5+" tag. +- [ ] §3 closure rules have been validated against a real + multi-service fixture (`cross_service_smoke` is a candidate). +- [ ] §9 performance estimates have a measured baseline on at least + one fixture. +- [ ] Reviewer (you, principal engineer) approves §2.5 (symmetric + delete) as the right model — alternative is "wipe-and-rebuild + the dirty closure", which has similar correctness but worse + performance. +- [ ] Decision engine pseudocode in §4 + §5 is consistent with the + REFRESH proposal. + +When approved, derive `plans/PLAN-TIER2-INCREMENTAL-REBUILD.md` with +PR-T1 through PR-T5 broken out, and a per-PR Cursor task prompt set. diff --git a/server.py b/server.py index cbe40964..31f67306 100644 --- a/server.py +++ b/server.py @@ -16,7 +16,7 @@ emit_vectors_finish, emit_vectors_start, ) -from java_codebase_rag.config import discover_project_root, emit_legacy_env_hints_if_present, resolved_sbert_model_for_process_env, resolve_operator_config +from java_codebase_rag.config import emit_legacy_env_hints_if_present, resolved_sbert_model_for_process_env, resolve_operator_config from kuzu_queries import KuzuGraph, resolve_kuzu_path from mcp.server.fastmcp import FastMCP from pydantic import BaseModel, Field @@ -94,7 +94,7 @@ class IndexInfoOutput(BaseModel): def _resolve_lancedb_uri() -> str: raw = os.environ.get("JAVA_CODEBASE_RAG_INDEX_DIR", "").strip() if not raw: - raw = str((_project_root() / ".java-codebase-rag").resolve()) + raw = str((Path.cwd() / ".java-codebase-rag").resolve()) p = Path(raw).expanduser() if not str(raw).startswith(("s3://", "gs://", "az://")): try: @@ -108,9 +108,6 @@ def _project_root() -> Path: env = os.environ.get("JAVA_CODEBASE_RAG_SOURCE_ROOT", "").strip() if env: return Path(env).expanduser().resolve() - discovered = discover_project_root(Path.cwd()) - if discovered is not None: - return discovered return Path.cwd().resolve() @@ -578,10 +575,8 @@ def main() -> None: # Load YAML config and apply embedding settings to environment # This ensures SBERT_MODEL and SBERT_DEVICE from .java-codebase-rag.yml are available - # before any tool handler runs (same behavior as CLI path). - # Pass source_root=None so walk-up + YAML source_root resolution happens - # inside resolve_operator_config (CLI > env > YAML > discovery > cwd). - cfg = resolve_operator_config(source_root=None) + # before any tool handler runs (same behavior as CLI path) + cfg = resolve_operator_config(source_root=_project_root()) cfg.apply_to_os_environ() mcp_v2.set_hints_enabled(cfg.hints_enabled) diff --git a/tests/test_config.py b/tests/test_config.py deleted file mode 100644 index 9df29153..00000000 --- a/tests/test_config.py +++ /dev/null @@ -1,218 +0,0 @@ -"""Tests for config discovery and source root resolution (PR-1 DIRS-HIERARCHY).""" -from __future__ import annotations - -import os -from pathlib import Path -from unittest.mock import patch - -import pytest - -from java_codebase_rag.config import ( - YAML_CONFIG_FILENAMES, - discover_project_root, - resolve_operator_config, -) - - -# --------------------------------------------------------------------------- -# Fixtures -# --------------------------------------------------------------------------- - - -@pytest.fixture() -def config_tree(tmp_path: Path): - """Provide a helper for building nested config trees under tmp_path.""" - - class _Helper: - def write_config(self, directory: Path, content: str = "") -> Path: - directory.mkdir(parents=True, exist_ok=True) - cfg = directory / YAML_CONFIG_FILENAMES[0] - cfg.write_text(content, encoding="utf-8") - return cfg - - return _Helper() - - -@pytest.fixture(autouse=True) -def _clean_source_root_env(): - """Ensure JAVA_CODEBASE_RAG_SOURCE_ROOT is unset during tests.""" - saved = os.environ.pop("JAVA_CODEBASE_RAG_SOURCE_ROOT", None) - try: - yield - finally: - if saved is not None: - os.environ["JAVA_CODEBASE_RAG_SOURCE_ROOT"] = saved - - -# --------------------------------------------------------------------------- -# Tests 1-6: discover_project_root -# --------------------------------------------------------------------------- - - -class TestDiscoverProjectRoot: - def test_discover_project_root_finds_config_in_cwd(self, tmp_path: Path, config_tree): - config_tree.write_config(tmp_path) - assert discover_project_root(tmp_path) == tmp_path - - def test_discover_project_root_walks_up(self, tmp_path: Path, config_tree): - config_tree.write_config(tmp_path) - child = tmp_path / "sub" / "dir" - child.mkdir(parents=True) - assert discover_project_root(child) == tmp_path - - def test_discover_project_root_stops_at_home_boundary(self, tmp_path: Path, config_tree): - """Config in $HOME itself is found when walking up from a subdirectory.""" - home = Path.home().resolve() - cfg_name = YAML_CONFIG_FILENAMES[0] - cfg = home / cfg_name - existed = cfg.exists() - if not existed: - cfg.write_text("", encoding="utf-8") - try: - # Use a direct child of $HOME that isn't tmp_path (which may be - # outside $HOME on macOS: /private/tmp -> /var/folders). - start = home / ".java-codebase-rag-test-walk-up-boundary" - start.mkdir(exist_ok=True) - assert discover_project_root(start) == home - finally: - if not existed: - cfg.unlink() - - def test_discover_project_root_not_found_above_home(self, tmp_path: Path, config_tree): - """No config anywhere between start and $HOME -> None.""" - child = tmp_path / "deep" / "nested" - child.mkdir(parents=True) - # tmp_path is typically under /private/tmp on macOS which is NOT - # under $HOME, so this tests the "not found" path. - # If tmp_path *is* under $HOME, we need a directory without config. - # Use a mock to make $HOME point to something with no config above. - fake_home = tmp_path / "fake_home" - fake_home.mkdir() - start = tmp_path / "work" / "project" - start.mkdir(parents=True) - with patch("java_codebase_rag.config.Path.home", return_value=fake_home): - assert discover_project_root(start) is None - - def test_discover_project_root_not_found(self, tmp_path: Path): - start = tmp_path / "nope" - start.mkdir() - # Mock home to tmp_path so we don't accidentally find real configs - with patch("java_codebase_rag.config.Path.home", return_value=tmp_path): - assert discover_project_root(start) is None - - def test_discover_project_root_first_match_wins(self, tmp_path: Path, config_tree): - parent_dir = tmp_path / "parent" - parent_dir.mkdir() - config_tree.write_config(parent_dir, "index_dir: /parent-idx\n") - child_dir = parent_dir / "child" - config_tree.write_config(child_dir, "index_dir: /child-idx\n") - grandchild = child_dir / "grandchild" - grandchild.mkdir() - # Closest config to grandchild is child_dir - assert discover_project_root(grandchild) == child_dir - # Closest config to child_dir is child_dir itself - assert discover_project_root(child_dir) == child_dir - # From parent_dir, it's parent_dir - assert discover_project_root(parent_dir) == parent_dir - - -# --------------------------------------------------------------------------- -# Tests 7-12: source root resolution -# --------------------------------------------------------------------------- - - -class TestSourceRootResolution: - def test_source_root_from_yaml_relative(self, tmp_path: Path, config_tree): - """YAML source_root: ../ resolves relative to config dir.""" - config_tree.write_config(tmp_path, "source_root: ../\n") - child = tmp_path / "subdir" - child.mkdir() - with patch("java_codebase_rag.config.Path.cwd", return_value=child): - cfg = resolve_operator_config(source_root=None) - # source_root in YAML is "../" relative to config dir (tmp_path) - expected = tmp_path.parent.resolve() - assert cfg.source_root == expected - - def test_source_root_from_yaml_absolute(self, tmp_path: Path, config_tree): - """YAML source_root: /abs/path resolves as-is.""" - target = tmp_path / "actual-java-src" - target.mkdir() - config_tree.write_config(tmp_path, f"source_root: {target}\n") - child = tmp_path / "subdir" - child.mkdir() - with patch("java_codebase_rag.config.Path.cwd", return_value=child): - cfg = resolve_operator_config(source_root=None) - assert cfg.source_root == target.resolve() - - def test_source_root_precedence_cli_over_yaml(self, tmp_path: Path, config_tree): - config_tree.write_config(tmp_path, "source_root: /yaml-path\n") - child = tmp_path / "subdir" - child.mkdir() - with patch("java_codebase_rag.config.Path.cwd", return_value=child): - cfg = resolve_operator_config(source_root=tmp_path / "cli-path") - assert cfg.source_root == (tmp_path / "cli-path").resolve() - - def test_source_root_precedence_yaml_over_discovery(self, tmp_path: Path, config_tree): - """YAML source_root wins over config dir default.""" - target = tmp_path / "real-src" - target.mkdir() - config_tree.write_config(tmp_path, f"source_root: {target}\n") - child = tmp_path / "subdir" - child.mkdir() - with patch("java_codebase_rag.config.Path.cwd", return_value=child): - cfg = resolve_operator_config(source_root=None) - assert cfg.source_root == target.resolve() - - def test_source_root_precedence_env_over_yaml(self, tmp_path: Path, config_tree): - config_tree.write_config(tmp_path, "source_root: /yaml-path\n") - child = tmp_path / "subdir" - child.mkdir() - env_dir = tmp_path / "env-src" - env_dir.mkdir() - with ( - patch("java_codebase_rag.config.Path.cwd", return_value=child), - patch.dict(os.environ, {"JAVA_CODEBASE_RAG_SOURCE_ROOT": str(env_dir)}), - ): - cfg = resolve_operator_config(source_root=None) - assert cfg.source_root == env_dir.resolve() - - def test_existing_behavior_unchanged(self, tmp_path: Path, config_tree): - """When cwd = config dir with no source_root YAML, behavior is identical.""" - config_tree.write_config(tmp_path) - with patch("java_codebase_rag.config.Path.cwd", return_value=tmp_path): - cfg = resolve_operator_config(source_root=None) - assert cfg.source_root == tmp_path.resolve() - - -# --------------------------------------------------------------------------- -# Test 14: init parent-config warning -# --------------------------------------------------------------------------- - - -class TestInitParentConfigWarning: - def test_init_warns_when_parent_config_exists(self, tmp_path: Path, config_tree): - """init prints a warning to stderr when a parent config is detected.""" - config_tree.write_config(tmp_path) - child = tmp_path / "subproject" - child.mkdir() - - from java_codebase_rag.config import YAML_CONFIG_FILENAMES, discover_project_root - - parent_cfg_dir = discover_project_root(child) - assert parent_cfg_dir == tmp_path # parent config found - - for name in YAML_CONFIG_FILENAMES: - if (parent_cfg_dir / name).is_file(): - assert f"Warning: found existing config at {parent_cfg_dir / name}" is not None - break - - def test_init_no_warning_without_parent_config(self, tmp_path: Path, config_tree): - """No warning when no parent config exists.""" - isolated = tmp_path / "isolated" - isolated.mkdir() - - from java_codebase_rag.config import discover_project_root - - with patch("java_codebase_rag.config.Path.home", return_value=tmp_path): - parent_cfg_dir = discover_project_root(isolated) - assert parent_cfg_dir is None # no parent config diff --git a/tests/test_incremental_equivalence.py b/tests/test_incremental_equivalence.py deleted file mode 100644 index b764b0a9..00000000 --- a/tests/test_incremental_equivalence.py +++ /dev/null @@ -1,497 +0,0 @@ -"""PR-T3: Incremental rebuild equivalence, closure, and fallback tests.""" - -from __future__ import annotations - -import json -import shutil -from pathlib import Path - -import kuzu - -from build_ast_graph import ( - ONTOLOGY_VERSION, - DepsIndex, - FileDeps, - GraphTables, - _read_dependency_index, - build_ast_graph_incremental, - expand_to_closure, - pass1_parse, - pass2_edges, - pass3_calls, - pass4_routes, - pass5_imperative_edges, - pass6_match_edges, - write_kuzu, -) - -TESTS_DIR = Path(__file__).resolve().parent -CORPUS = TESTS_DIR / "bank-chat-system" - - -def _full_rebuild_into(corpus: Path, db_path: Path) -> Path: - tables = GraphTables() - asts = pass1_parse(corpus, tables, verbose=False) - pass2_edges(tables, asts, verbose=False) - pass3_calls(tables, asts, verbose=False) - pass4_routes(tables, asts, source_root=corpus, verbose=False) - pass5_imperative_edges(tables, asts, source_root=corpus, verbose=False) - pass6_match_edges(tables, verbose=False) - write_kuzu(db_path, tables, source_root=corpus, verbose=False) - return db_path - - -def _dump_node_ids(db_path: Path) -> set[str]: - db = kuzu.Database(str(db_path)) - conn = kuzu.Connection(db) - ids: set[str] = set() - for kind in ("Symbol", "Route", "Client", "Producer", "UnresolvedCallSite"): - try: - r = conn.execute(f"MATCH (n:{kind}) RETURN n.id AS id") - while r.has_next(): - ids.add(r.get_next()[0]) - except Exception: - pass - conn.close() - return ids - - -def _dump_edge_rows(db_path: Path) -> set[tuple[str, ...]]: - db = kuzu.Database(str(db_path)) - conn = kuzu.Connection(db) - labels = [ - "DECLARES", "EXTENDS", "IMPLEMENTS", "INJECTS", - "CALLS", "OVERRIDES", "EXPOSES", - "DECLARES_CLIENT", "DECLARES_PRODUCER", - "HTTP_CALLS", "ASYNC_CALLS", - ] - rows: set[tuple[str, ...]] = set() - for label in labels: - try: - result = conn.execute( - f"MATCH (a)-[e:{label}]->(b) RETURN a.id AS src, b.id AS dst" - ) - except Exception: - continue - while result.has_next(): - row = result.get_next() - rows.add((row[0], row[1], label)) - conn.close() - return rows - - -def _get_graph_meta(conn: kuzu.Connection) -> dict: - r = conn.execute("MATCH (m:GraphMeta) WHERE m.key = 'graph' RETURN m.*") - if not r.has_next(): - return {} - row = r.get_next() - cols = [d["name"] for d in r.get_column_names()] - # Kuzu returns column names via get_column_names on result - return dict(zip(cols, row)) - - -def _get_any_java_file(corpus: Path) -> str: - """Return a relative path to any .java file in corpus.""" - for p in sorted(corpus.rglob("*.java")): - try: - return str(p.resolve().relative_to(corpus.resolve())) - except ValueError: - continue - raise FileNotFoundError(f"No .java files in {corpus}") - - -def _copy_corpus(src: Path, dst: Path) -> Path: - """Copy corpus to dst for mutation.""" - shutil.copytree(src, dst, dirs_exist_ok=True) - return dst - - -# ---- Equivalence tests ---- - - -class TestIncrementalEquivalence: - """Incremental rebuild must produce identical graph state to full rebuild.""" - - def _assert_equivalence(self, corpus: Path, tmp_path: Path) -> None: - """Run full rebuild, then incremental with one file 'changed', compare.""" - # Full rebuild baseline - full_db = tmp_path / "full" / "code_graph.kuzu" - _full_rebuild_into(corpus, full_db) - full_nodes = _dump_node_ids(full_db) - full_edges = _dump_edge_rows(full_db) - - # Incremental: pick one file as "changed" - changed_file = _get_any_java_file(corpus) - incr_db = tmp_path / "incr" / "code_graph.kuzu" - _full_rebuild_into(corpus, incr_db) - - result = build_ast_graph_incremental( - corpus, incr_db, {changed_file}, verbose=False, - ) - assert result == "incremental" - - incr_nodes = _dump_node_ids(incr_db) - incr_edges = _dump_edge_rows(incr_db) - assert incr_nodes == full_nodes, ( - f"Node sets differ: {len(incr_nodes)} vs {len(full_nodes)}.\n" - f"Missing: {full_nodes - incr_nodes}\n" - f"Extra: {incr_nodes - full_nodes}" - ) - assert incr_edges == full_edges, ( - f"Edge sets differ: {len(incr_edges)} vs {len(full_edges)}.\n" - f"Missing: {full_edges - incr_edges}\n" - f"Extra: {incr_edges - full_edges}" - ) - - def test_incremental_matches_full_bank_chat_system(self, tmp_path: Path) -> None: - self._assert_equivalence(CORPUS, tmp_path / "bank_chat") - - def test_incremental_matches_full_cross_service_smoke(self, tmp_path: Path) -> None: - self._assert_equivalence( - TESTS_DIR / "fixtures" / "cross_service_smoke", - tmp_path / "cross_service", - ) - - def test_incremental_matches_full_call_graph_smoke(self, tmp_path: Path) -> None: - self._assert_equivalence( - TESTS_DIR / "fixtures" / "call_graph_smoke", - tmp_path / "call_graph", - ) - - def test_incremental_matches_full_http_caller_smoke(self, tmp_path: Path) -> None: - self._assert_equivalence( - TESTS_DIR / "fixtures" / "http_caller_smoke", - tmp_path / "http_caller", - ) - - def test_incremental_matches_full_route_extraction_smoke(self, tmp_path: Path) -> None: - self._assert_equivalence( - TESTS_DIR / "fixtures" / "route_extraction_smoke", - tmp_path / "route_extraction", - ) - - def test_incremental_multiple_files_changed(self, tmp_path: Path) -> None: - # Use cross_service_smoke (smaller corpus) to avoid >50% dirty-set heuristic - corpus = TESTS_DIR / "fixtures" / "cross_service_smoke" - full_db = tmp_path / "full" / "code_graph.kuzu" - _full_rebuild_into(corpus, full_db) - - incr_db = tmp_path / "incr" / "code_graph.kuzu" - _full_rebuild_into(corpus, incr_db) - - # Pick all files from one service (small enough to stay under 50%) - java_files = sorted( - str(p.resolve().relative_to(corpus.resolve())) - for p in corpus.rglob("*.java") - if "svc-a" in str(p) - ) - assert len(java_files) >= 2, f"Expected >= 2 svc-a files, got {java_files}" - - result = build_ast_graph_incremental( - corpus, incr_db, set(java_files), verbose=False, - ) - assert result == "incremental" - - assert _dump_node_ids(incr_db) == _dump_node_ids(full_db) - assert _dump_edge_rows(incr_db) == _dump_edge_rows(full_db) - - -# ---- Fallback tests ---- - - -class TestIncrementalFallback: - def test_incremental_fallback_on_missing_deps_json(self, tmp_path: Path) -> None: - corpus = CORPUS - incr_db = tmp_path / "code_graph.kuzu" - _full_rebuild_into(corpus, incr_db) - # Remove .deps.json - deps = incr_db.parent / ".deps.json" - deps.unlink(missing_ok=True) - result = build_ast_graph_incremental( - corpus, incr_db, {"some/File.java"}, verbose=False, - ) - assert result is None - - def test_incremental_fallback_on_stale_ontology(self, tmp_path: Path) -> None: - corpus = CORPUS - incr_db = tmp_path / "code_graph.kuzu" - _full_rebuild_into(corpus, incr_db) - deps = incr_db.parent / ".deps.json" - data = json.loads(deps.read_text()) - data["ontology_version"] = 0 - deps.write_text(json.dumps(data)) - result = build_ast_graph_incremental( - corpus, incr_db, {"some/File.java"}, verbose=False, - ) - assert result is None - - def test_incremental_fallback_on_large_dirty_set(self, tmp_path: Path) -> None: - corpus = CORPUS - incr_db = tmp_path / "code_graph.kuzu" - _full_rebuild_into(corpus, incr_db) - # Mark >50% of files dirty - deps = incr_db.parent / ".deps.json" - idx = _read_dependency_index(deps) - assert idx is not None - all_files = list(idx.files.keys()) - most_files = set(all_files[: int(len(all_files) * 0.6) + 1]) - result = build_ast_graph_incremental( - corpus, incr_db, most_files, verbose=False, - ) - assert result is None - - -# ---- Closure tests ---- - - -class TestClosureExpansion: - def _make_deps_index(self, files: dict[str, FileDeps]) -> DepsIndex: - return DepsIndex(version=1, ontology_version=ONTOLOGY_VERSION, files=files) - - def test_closure_includes_inverse_injects(self) -> None: - idx = self._make_deps_index({ - "a/Foo.java": FileDeps(declares=["com.example.Foo"]), - "a/Bar.java": FileDeps(injects=["com.example.Foo"]), - }) - dirty = expand_to_closure({"a/Foo.java"}, idx) - assert "a/Bar.java" in dirty - - def test_closure_includes_inverse_extends(self) -> None: - idx = self._make_deps_index({ - "a/Base.java": FileDeps(declares=["com.example.Base"]), - "a/Child.java": FileDeps(extends=["com.example.Base"]), - }) - dirty = expand_to_closure({"a/Base.java"}, idx) - assert "a/Child.java" in dirty - - def test_closure_includes_inverse_calls(self) -> None: - idx = self._make_deps_index({ - "a/Service.java": FileDeps(declares=["com.example.Service"]), - "a/Client.java": FileDeps(calls=["com.example.Service#run()"]), - }) - dirty = expand_to_closure({"a/Service.java"}, idx) - assert "a/Client.java" in dirty - - def test_closure_includes_inverse_overrides(self) -> None: - idx = self._make_deps_index({ - "a/Base.java": FileDeps(declares=["com.example.Base"]), - "a/Impl.java": FileDeps(overrides=["com.example.Base#method()"]), - }) - dirty = expand_to_closure({"a/Base.java"}, idx) - assert "a/Impl.java" in dirty - - def test_closure_includes_meta_annotation(self) -> None: - idx = self._make_deps_index({ - "a/CustomAnno.java": FileDeps(declares=["com.example.CustomAnno"]), - "a/User.java": FileDeps(uses_anno=["CustomAnno"]), - }) - dirty = expand_to_closure({"a/CustomAnno.java"}, idx) - assert "a/User.java" in dirty - - def test_closure_includes_forward_deps(self) -> None: - idx = self._make_deps_index({ - "a/Foo.java": FileDeps( - injects=["com.example.Service"], - declares=["com.example.Foo"], - ), - "a/Service.java": FileDeps(declares=["com.example.Service"]), - }) - dirty = expand_to_closure({"a/Foo.java"}, idx) - assert "a/Service.java" in dirty - - def test_closure_empty_changed_returns_empty(self) -> None: - idx = self._make_deps_index({"a/Foo.java": FileDeps()}) - dirty = expand_to_closure(set(), idx) - assert dirty == set() - - def test_closure_unknown_path_ignored(self) -> None: - idx = self._make_deps_index({"a/Foo.java": FileDeps()}) - dirty = expand_to_closure({"nonexistent/File.java"}, idx) - assert dirty == set() - - -# ---- Incremental deps merge ---- - - -class TestIncrementalDepsMerge: - def test_incremental_deps_json_merge(self, tmp_path: Path) -> None: - corpus = CORPUS - incr_db = tmp_path / "code_graph.kuzu" - _full_rebuild_into(corpus, incr_db) - deps = incr_db.parent / ".deps.json" - - idx_before = _read_dependency_index(deps) - assert idx_before is not None - unchanged_file = next(iter(idx_before.files)) - - changed_file = _get_any_java_file(corpus) - result = build_ast_graph_incremental( - corpus, incr_db, {changed_file}, verbose=False, - ) - assert result == "incremental" - - idx_after = _read_dependency_index(deps) - assert idx_after is not None - # Unchanged file entries preserved - assert unchanged_file in idx_after.files - # Changed file entries updated - assert changed_file in idx_after.files - - -# ---- Pass6 global invariant ---- - - -class TestPass6GlobalInvariant: - def test_incremental_pass6_global_invariant(self, tmp_path: Path) -> None: - corpus = TESTS_DIR / "fixtures" / "cross_service_smoke" - full_db = tmp_path / "full" / "code_graph.kuzu" - _full_rebuild_into(corpus, full_db) - - incr_db = tmp_path / "incr" / "code_graph.kuzu" - _full_rebuild_into(corpus, incr_db) - - changed_file = _get_any_java_file(corpus) - result = build_ast_graph_incremental( - corpus, incr_db, {changed_file}, verbose=False, - ) - assert result == "incremental" - - # Compare HTTP_CALLS and ASYNC_CALLS match outcomes - db_full = kuzu.Database(str(full_db)) - conn_full = kuzu.Connection(db_full) - db_incr = kuzu.Database(str(incr_db)) - conn_incr = kuzu.Connection(db_incr) - - for label in ("HTTP_CALLS", "ASYNC_CALLS"): - full_matches: dict[str, str] = {} - r = conn_full.execute( - f"MATCH (a)-[e:{label}]->(b) RETURN a.id, e.match" - ) - while r.has_next(): - row = r.get_next() - full_matches[row[0]] = row[1] - - incr_matches: dict[str, str] = {} - r = conn_incr.execute( - f"MATCH (a)-[e:{label}]->(b) RETURN a.id, e.match" - ) - while r.has_next(): - row = r.get_next() - incr_matches[row[0]] = row[1] - - assert full_matches == incr_matches, ( - f"{label} match outcomes differ: " - f"full={full_matches} vs incr={incr_matches}" - ) - - conn_full.close() - conn_incr.close() - - -# ---- Meta global stats ---- - - -class TestIncrementalMetaStats: - def test_incremental_meta_global_stats(self, tmp_path: Path) -> None: - corpus = CORPUS - full_db = tmp_path / "full" / "code_graph.kuzu" - _full_rebuild_into(corpus, full_db) - - incr_db = tmp_path / "incr" / "code_graph.kuzu" - _full_rebuild_into(corpus, incr_db) - - changed_file = _get_any_java_file(corpus) - result = build_ast_graph_incremental( - corpus, incr_db, {changed_file}, verbose=False, - ) - assert result == "incremental" - - # Compare key meta fields - db_full = kuzu.Database(str(full_db)) - conn_full = kuzu.Connection(db_full) - db_incr = kuzu.Database(str(incr_db)) - conn_incr = kuzu.Connection(db_incr) - - for field in ( - "routes_total", "clients_total", "producers_total", - "http_calls_total", "async_calls_total", - ): - r_full = conn_full.execute( - f"MATCH (m:GraphMeta) WHERE m.key = 'graph' RETURN m.{field}" - ) - val_full = r_full.get_next()[0] if r_full.has_next() else None - r_incr = conn_incr.execute( - f"MATCH (m:GraphMeta) WHERE m.key = 'graph' RETURN m.{field}" - ) - val_incr = r_incr.get_next()[0] if r_incr.has_next() else None - assert val_full == val_incr, f"{field}: full={val_full} vs incr={val_incr}" - - # Check last_rebuild_mode - r = conn_incr.execute( - "MATCH (m:GraphMeta) WHERE m.key = 'graph' RETURN m.last_rebuild_mode" - ) - mode = r.get_next()[0] if r.has_next() else None - assert mode == "incremental" - - r = conn_full.execute( - "MATCH (m:GraphMeta) WHERE m.key = 'graph' RETURN m.last_rebuild_mode" - ) - mode = r.get_next()[0] if r.has_next() else None - assert mode == "full" - - conn_full.close() - conn_incr.close() - - -# ---- CLI flag tests ---- - - -class TestChangedPathsCLI: - def test_changed_paths_cli_flag_valid(self, tmp_path: Path) -> None: - import subprocess - import sys - - corpus = CORPUS - kuzu_path = tmp_path / "code_graph.kuzu" - _full_rebuild_into(corpus, kuzu_path) - - changed_file = _get_any_java_file(corpus) - paths_file = tmp_path / "changed.txt" - paths_file.write_text(changed_file + "\n") - - result = subprocess.run( - [ - sys.executable, "build_ast_graph.py", - "--source-root", str(corpus), - "--kuzu-path", str(kuzu_path), - "--changed-paths", str(paths_file), - ], - capture_output=True, - text=True, - timeout=60, - ) - assert result.returncode == 0 - - def test_changed_paths_cli_flag_empty(self, tmp_path: Path) -> None: - import subprocess - import sys - - corpus = CORPUS - kuzu_path = tmp_path / "code_graph.kuzu" - _full_rebuild_into(corpus, kuzu_path) - - paths_file = tmp_path / "changed.txt" - paths_file.write_text("") - - result = subprocess.run( - [ - sys.executable, "build_ast_graph.py", - "--source-root", str(corpus), - "--kuzu-path", str(kuzu_path), - "--changed-paths", str(paths_file), - ], - capture_output=True, - text=True, - timeout=60, - ) - assert result.returncode == 0 diff --git a/tests/test_java_codebase_rag_cli.py b/tests/test_java_codebase_rag_cli.py index c7483d83..1d67cb77 100644 --- a/tests/test_java_codebase_rag_cli.py +++ b/tests/test_java_codebase_rag_cli.py @@ -941,10 +941,9 @@ def test_mcp_server_loads_yaml_config_at_startup( ) -> None: """MCP server main() loads YAML config and applies to os.environ (issue #238). - Verifies that main() calls resolve_operator_config with source_root=None - (walk-up discovery) and applies the result to os.environ. Uses mocks to - avoid loading real models or leaking env state (e.g. SBERT_DEVICE=cuda) - to subsequent tests. + Verifies that main() calls resolve_operator_config with the correct source_root + and applies the result to os.environ. Uses mocks to avoid loading real models + or leaking env state (e.g. SBERT_DEVICE=cuda) to subsequent tests. """ import server as server_mod from unittest.mock import MagicMock @@ -962,9 +961,8 @@ def fake_asyncio_run(awaitable, *, debug=None): server_mod.main() - # resolve_operator_config should have been called with source_root=None - # so walk-up + YAML source_root resolution happens inside it - server_mod.resolve_operator_config.assert_called_once_with(source_root=None) + # resolve_operator_config should have been called with the project root + server_mod.resolve_operator_config.assert_called_once_with(source_root=server_mod._project_root()) # apply_to_os_environ should have been called to set env vars fake_cfg.apply_to_os_environ.assert_called_once() @@ -972,11 +970,12 @@ def fake_asyncio_run(awaitable, *, debug=None): def test_mcp_server_yaml_config_precedence_env_over_yaml( tmp_path: Path, monkeypatch: pytest.MonkeyPatch, ) -> None: - """MCP server passes source_root=None to resolve_operator_config (issue #238). + """MCP server passes _project_root() to resolve_operator_config (issue #238). - Precedence (env > YAML > default) is handled inside resolve_operator_config - via walk-up discovery. This test verifies that main() delegates correctly - and apply_to_os_environ is called with the resolved config. + Precedence (env > YAML > default) is already tested by + test_embedding_model_precedence_cli_over_env_over_yaml_over_default. + This test verifies that main() delegates to resolve_operator_config + with the correct source root, which handles precedence internally. """ import server as server_mod from unittest.mock import MagicMock @@ -995,4 +994,5 @@ def fake_asyncio_run(awaitable, *, debug=None): server_mod.main() - server_mod.resolve_operator_config.assert_called_once_with(source_root=None) + server_mod.resolve_operator_config.assert_called_once() + assert server_mod.resolve_operator_config.call_args.kwargs["source_root"] == server_mod._project_root() diff --git a/tests/test_mcp_server_project_root.py b/tests/test_mcp_server_project_root.py deleted file mode 100644 index 40a29da6..00000000 --- a/tests/test_mcp_server_project_root.py +++ /dev/null @@ -1,57 +0,0 @@ -"""Tests for _project_root() walk-up discovery in server.py (PR-1 DIRS-HIERARCHY).""" -from __future__ import annotations - -import os -from pathlib import Path -from unittest.mock import patch - -import pytest - - -@pytest.fixture() -def _clean_source_root_env(): - """Ensure JAVA_CODEBASE_RAG_SOURCE_ROOT is unset during the test.""" - with patch.dict(os.environ, {}, clear=False): - os.environ.pop("JAVA_CODEBASE_RAG_SOURCE_ROOT", None) - yield - - -@pytest.mark.usefixtures("_clean_source_root_env") -class TestProjectRootDiscovery: - def test_project_root_uses_discover_when_env_unset(self, tmp_path: Path): - """_project_root() returns discovered config dir when env var is unset.""" - from java_codebase_rag.config import YAML_CONFIG_FILENAMES - - # Write a config in tmp_path - cfg = tmp_path / YAML_CONFIG_FILENAMES[0] - cfg.write_text("", encoding="utf-8") - child = tmp_path / "subdir" - child.mkdir() - - import server - - with patch("server.Path.cwd", return_value=child): - result = server._project_root() - assert result == tmp_path - - def test_resolve_operator_config_honors_yaml_source_root_from_server_path( - self, tmp_path: Path - ): - """resolve_operator_config(source_root=None) resolves YAML source_root. - - This tests the MCP server startup path where source_root=None is passed - (not the discovered config dir directly), so the YAML source_root field - is correctly resolved in Phase 2. - """ - from java_codebase_rag.config import YAML_CONFIG_FILENAMES, resolve_operator_config - - target = tmp_path / "actual-java-src" - target.mkdir() - cfg = tmp_path / YAML_CONFIG_FILENAMES[0] - cfg.write_text(f"source_root: {target}\n", encoding="utf-8") - child = tmp_path / "subdir" - child.mkdir() - - with patch("java_codebase_rag.config.Path.cwd", return_value=child): - result = resolve_operator_config(source_root=None) - assert result.source_root == target.resolve() diff --git a/tests/test_symmetric_delete.py b/tests/test_symmetric_delete.py deleted file mode 100644 index 2e9e50be..00000000 --- a/tests/test_symmetric_delete.py +++ /dev/null @@ -1,509 +0,0 @@ -"""Tests for symmetric delete helpers (PR-T2). - -Each delete helper takes ``(conn, file_path)`` and returns the deleted row -count. The helpers are additive — nothing calls them yet (that's PR-T3). -""" - -from __future__ import annotations - -import kuzu -import pytest - -from _builders import build_kuzu_to - - -# --------------------------------------------------------------------------- -# Fixtures -# --------------------------------------------------------------------------- - -@pytest.fixture -def conn(tmp_path, corpus_root): - """Per-test fresh writeable Kuzu DB from bank-chat-system (pass1-5).""" - db_path = tmp_path / "code_graph.kuzu" - build_kuzu_to(corpus_root, db_path, max_pass=5) - db = kuzu.Database(str(db_path)) - return kuzu.Connection(db) - - -# --------------------------------------------------------------------------- -# Helpers -# --------------------------------------------------------------------------- - -def _count(conn, cypher, params=None): - r = conn.execute(cypher, params or {}) - return int(r.get_next()[0]) if r.has_next() else 0 - - -def _find_file_with(conn, cypher): - r = conn.execute(cypher) - assert r.has_next(), f"no matching rows in fixture: {cypher}" - return str(r.get_next()[0]) - - -# --------------------------------------------------------------------------- -# Per-helper tests -# --------------------------------------------------------------------------- - -class TestDeleteSymbolsForFile: - def test_delete_symbols_for_file(self, conn): - from build_ast_graph import delete_symbols_for_file - - fp = _find_file_with( - conn, - "MATCH (s:Symbol) WHERE s.kind = 'class' " - "RETURN s.filename AS fn LIMIT 1", - ) - before = _count( - conn, - "MATCH (s:Symbol) WHERE s.filename = $fp RETURN count(s) AS n", - {"fp": fp}, - ) - assert before > 0 - - n = delete_symbols_for_file(conn, fp) - assert n > 0 - - after = _count( - conn, - "MATCH (s:Symbol) WHERE s.filename = $fp RETURN count(s) AS n", - {"fp": fp}, - ) - assert after == 0 - - def test_deletes_declares_edges(self, conn): - from build_ast_graph import delete_symbols_for_file - - fp = _find_file_with( - conn, - "MATCH (a:Symbol)-[:DECLARES]->(b:Symbol) " - "RETURN DISTINCT a.filename AS fn LIMIT 1", - ) - delete_symbols_for_file(conn, fp) - - remaining = _count( - conn, - "MATCH (a:Symbol)-[e:DECLARES]->(b:Symbol) " - "WHERE a.filename = $fp OR b.filename = $fp " - "RETURN count(e) AS n", - {"fp": fp}, - ) - assert remaining == 0 - - -class TestDeleteExtendsForFile: - def test_delete_extends_for_file(self, conn): - from build_ast_graph import delete_extends_for_file - - fp = _find_file_with( - conn, - "MATCH (a:Symbol)-[:EXTENDS]->(b:Symbol) " - "RETURN DISTINCT a.filename AS fn LIMIT 1", - ) - before = _count( - conn, - "MATCH (a:Symbol)-[e:EXTENDS]->(b:Symbol) " - "WHERE a.filename = $fp RETURN count(e) AS n", - {"fp": fp}, - ) - assert before > 0 - - n = delete_extends_for_file(conn, fp) - assert n == before - - after = _count( - conn, - "MATCH (a:Symbol)-[e:EXTENDS]->(b:Symbol) " - "WHERE a.filename = $fp RETURN count(e) AS n", - {"fp": fp}, - ) - assert after == 0 - - -class TestDeleteImplementsForFile: - def test_delete_implements_for_file(self, conn): - from build_ast_graph import delete_implements_for_file - - fp = _find_file_with( - conn, - "MATCH (a:Symbol)-[:IMPLEMENTS]->(b:Symbol) " - "RETURN DISTINCT a.filename AS fn LIMIT 1", - ) - before = _count( - conn, - "MATCH (a:Symbol)-[e:IMPLEMENTS]->(b:Symbol) " - "WHERE a.filename = $fp RETURN count(e) AS n", - {"fp": fp}, - ) - assert before > 0 - - n = delete_implements_for_file(conn, fp) - assert n == before - - after = _count( - conn, - "MATCH (a:Symbol)-[e:IMPLEMENTS]->(b:Symbol) " - "WHERE a.filename = $fp RETURN count(e) AS n", - {"fp": fp}, - ) - assert after == 0 - - -class TestDeleteInjectsForFile: - def test_delete_injects_for_file(self, conn): - from build_ast_graph import delete_injects_for_file - - fp = _find_file_with( - conn, - "MATCH (a:Symbol)-[:INJECTS]->(b:Symbol) " - "RETURN DISTINCT a.filename AS fn LIMIT 1", - ) - before = _count( - conn, - "MATCH (a:Symbol)-[e:INJECTS]->(b:Symbol) " - "WHERE a.filename = $fp RETURN count(e) AS n", - {"fp": fp}, - ) - assert before > 0 - - n = delete_injects_for_file(conn, fp) - assert n == before - - after = _count( - conn, - "MATCH (a:Symbol)-[e:INJECTS]->(b:Symbol) " - "WHERE a.filename = $fp RETURN count(e) AS n", - {"fp": fp}, - ) - assert after == 0 - - -class TestDeleteCallsForFile: - def test_delete_calls_for_file(self, conn): - from build_ast_graph import delete_calls_for_file - - fp = _find_file_with( - conn, - "MATCH (a:Symbol)-[:CALLS]->(b:Symbol) " - "RETURN DISTINCT a.filename AS fn LIMIT 1", - ) - before = _count( - conn, - "MATCH (a:Symbol)-[e:CALLS]->(b:Symbol) " - "WHERE a.filename = $fp RETURN count(e) AS n", - {"fp": fp}, - ) - assert before > 0 - - n = delete_calls_for_file(conn, fp) - assert n == before - - after = _count( - conn, - "MATCH (a:Symbol)-[e:CALLS]->(b:Symbol) " - "WHERE a.filename = $fp RETURN count(e) AS n", - {"fp": fp}, - ) - assert after == 0 - - def test_deletes_unresolved_call_sites(self, conn): - from build_ast_graph import delete_calls_for_file - - fp = _find_file_with( - conn, - "MATCH (a:Symbol)-[:UNRESOLVED_AT]->(u:UnresolvedCallSite) " - "RETURN DISTINCT a.filename AS fn LIMIT 1", - ) - delete_calls_for_file(conn, fp) - - remaining = _count( - conn, - "MATCH (a:Symbol)-[e:UNRESOLVED_AT]->(u:UnresolvedCallSite) " - "WHERE a.filename = $fp RETURN count(e) AS n", - {"fp": fp}, - ) - assert remaining == 0 - - -class TestDeleteRoutesForFile: - def test_delete_routes_for_file(self, conn): - from build_ast_graph import delete_routes_for_file - - fp = _find_file_with( - conn, - "MATCH (r:Route) RETURN r.filename AS fn LIMIT 1", - ) - before = _count( - conn, - "MATCH (r:Route) WHERE r.filename = $fp RETURN count(r) AS n", - {"fp": fp}, - ) - assert before > 0 - - n = delete_routes_for_file(conn, fp) - assert n == before - - after = _count( - conn, - "MATCH (r:Route) WHERE r.filename = $fp RETURN count(r) AS n", - {"fp": fp}, - ) - assert after == 0 - - def test_deletes_exposes_edges(self, conn): - from build_ast_graph import delete_routes_for_file - - fp = _find_file_with( - conn, - "MATCH (a:Symbol)-[:EXPOSES]->(r:Route) " - "RETURN DISTINCT r.filename AS fn LIMIT 1", - ) - delete_routes_for_file(conn, fp) - - remaining = _count( - conn, - "MATCH (a:Symbol)-[e:EXPOSES]->(r:Route) " - "WHERE r.filename = $fp RETURN count(e) AS n", - {"fp": fp}, - ) - assert remaining == 0 - - -class TestDeleteClientsForFile: - def test_delete_clients_for_file(self, conn): - from build_ast_graph import delete_clients_for_file - - fp = _find_file_with( - conn, - "MATCH (c:Client) RETURN c.filename AS fn LIMIT 1", - ) - before = _count( - conn, - "MATCH (c:Client) WHERE c.filename = $fp RETURN count(c) AS n", - {"fp": fp}, - ) - assert before > 0 - - n = delete_clients_for_file(conn, fp) - assert n == before - - after = _count( - conn, - "MATCH (c:Client) WHERE c.filename = $fp RETURN count(c) AS n", - {"fp": fp}, - ) - assert after == 0 - - def test_deletes_declares_client_edges(self, conn): - from build_ast_graph import delete_clients_for_file - - fp = _find_file_with( - conn, - "MATCH (a:Symbol)-[:DECLARES_CLIENT]->(c:Client) " - "RETURN DISTINCT c.filename AS fn LIMIT 1", - ) - delete_clients_for_file(conn, fp) - - remaining = _count( - conn, - "MATCH (a:Symbol)-[e:DECLARES_CLIENT]->(c:Client) " - "WHERE c.filename = $fp RETURN count(e) AS n", - {"fp": fp}, - ) - assert remaining == 0 - - -class TestDeleteProducersForFile: - def test_delete_producers_for_file(self, conn): - from build_ast_graph import delete_producers_for_file - - fp = _find_file_with( - conn, - "MATCH (p:Producer) RETURN p.filename AS fn LIMIT 1", - ) - before = _count( - conn, - "MATCH (p:Producer) WHERE p.filename = $fp RETURN count(p) AS n", - {"fp": fp}, - ) - assert before > 0 - - n = delete_producers_for_file(conn, fp) - assert n == before - - after = _count( - conn, - "MATCH (p:Producer) WHERE p.filename = $fp RETURN count(p) AS n", - {"fp": fp}, - ) - assert after == 0 - - def test_deletes_declares_producer_edges(self, conn): - from build_ast_graph import delete_producers_for_file - - fp = _find_file_with( - conn, - "MATCH (a:Symbol)-[:DECLARES_PRODUCER]->(p:Producer) " - "RETURN DISTINCT p.filename AS fn LIMIT 1", - ) - delete_producers_for_file(conn, fp) - - remaining = _count( - conn, - "MATCH (a:Symbol)-[e:DECLARES_PRODUCER]->(p:Producer) " - "WHERE p.filename = $fp RETURN count(e) AS n", - {"fp": fp}, - ) - assert remaining == 0 - - -class TestDeleteHttpCallsForFile: - def test_delete_http_calls_for_file(self, conn): - from build_ast_graph import delete_http_calls_for_file - - fp = _find_file_with( - conn, - "MATCH (c:Client)-[:HTTP_CALLS]->(r:Route) " - "RETURN DISTINCT c.filename AS fn LIMIT 1", - ) - before = _count( - conn, - "MATCH (c:Client)-[e:HTTP_CALLS]->(r:Route) " - "WHERE c.filename = $fp RETURN count(e) AS n", - {"fp": fp}, - ) - assert before > 0 - - n = delete_http_calls_for_file(conn, fp) - assert n == before - - after = _count( - conn, - "MATCH (c:Client)-[e:HTTP_CALLS]->(r:Route) " - "WHERE c.filename = $fp RETURN count(e) AS n", - {"fp": fp}, - ) - assert after == 0 - - -class TestDeleteAsyncCallsForFile: - def test_delete_async_calls_for_file(self, conn): - from build_ast_graph import delete_async_calls_for_file - - fp = _find_file_with( - conn, - "MATCH (p:Producer)-[:ASYNC_CALLS]->(r:Route) " - "RETURN DISTINCT p.filename AS fn LIMIT 1", - ) - before = _count( - conn, - "MATCH (p:Producer)-[e:ASYNC_CALLS]->(r:Route) " - "WHERE p.filename = $fp RETURN count(e) AS n", - {"fp": fp}, - ) - assert before > 0 - - n = delete_async_calls_for_file(conn, fp) - assert n == before - - after = _count( - conn, - "MATCH (p:Producer)-[e:ASYNC_CALLS]->(r:Route) " - "WHERE p.filename = $fp RETURN count(e) AS n", - {"fp": fp}, - ) - assert after == 0 - - -class TestDeleteOverridesForFile: - def test_delete_overrides_for_file(self, conn): - from build_ast_graph import delete_overrides_for_file - - fp = _find_file_with( - conn, - "MATCH (a:Symbol)-[:OVERRIDES]->(b:Symbol) " - "RETURN DISTINCT a.filename AS fn LIMIT 1", - ) - before = _count( - conn, - "MATCH (a:Symbol)-[e:OVERRIDES]->(b:Symbol) " - "WHERE a.filename = $fp RETURN count(e) AS n", - {"fp": fp}, - ) - assert before > 0 - - n = delete_overrides_for_file(conn, fp) - assert n == before - - after = _count( - conn, - "MATCH (a:Symbol)-[e:OVERRIDES]->(b:Symbol) " - "WHERE a.filename = $fp RETURN count(e) AS n", - {"fp": fp}, - ) - assert after == 0 - - -class TestDeleteAllForFile: - def test_delete_all_for_file(self, conn): - from build_ast_graph import delete_all_for_file - - fp = _find_file_with( - conn, - "MATCH (s:Symbol) WHERE s.kind = 'class' " - "RETURN s.filename AS fn LIMIT 1", - ) - result = delete_all_for_file(conn, fp) - - assert isinstance(result, dict) - assert len(result) > 0 - assert all(isinstance(v, int) for v in result.values()) - - # Verify symbols are gone - after = _count( - conn, - "MATCH (s:Symbol) WHERE s.filename = $fp RETURN count(s) AS n", - {"fp": fp}, - ) - assert after == 0 - - def test_calls_each_helper(self, conn): - """delete_all_for_file should return counts from each sub-helper.""" - from build_ast_graph import delete_all_for_file - - fp = _find_file_with( - conn, - "MATCH (s:Symbol) WHERE s.kind = 'class' " - "RETURN s.filename AS fn LIMIT 1", - ) - result = delete_all_for_file(conn, fp) - - expected_keys = { - "symbols", "extends", "implements", "injects", - "calls", "routes", "clients", "producers", - "http_calls", "async_calls", "overrides", - } - assert expected_keys == set(result.keys()) - - -class TestDeleteEdgeCases: - def test_delete_idempotent(self, conn): - from build_ast_graph import delete_extends_for_file - - fp = _find_file_with( - conn, - "MATCH (a:Symbol)-[:EXTENDS]->(b:Symbol) " - "RETURN DISTINCT a.filename AS fn LIMIT 1", - ) - first = delete_extends_for_file(conn, fp) - assert first > 0 - - second = 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