Emit a bare file node for skipped data JSON (#2108)

[ayushcodes10]

Summary

Fixes #2108. Data-shaped .json (eval fixtures, parity corpora, i18n catalogues, GeoJSON) is deliberately skipped by extract_json's AST pass — the right call for structure, since walking it exploded into hundreds of orphan key-nodes (#1224). But the skip was total: the file contributed no node at all, so it was entirely absent from graph.json and unreachable from query/explain/affected, with no warning that anything was missing.

Root cause

extract_json already builds the file node (file_nid = _make_id(str(path)); add_node(file_nid, path.name, 1)) before deciding whether the document is a recognized config/manifest. Both skip branches then discarded it, returning a literal {"nodes": [], ...} instead of the nodes list — which at that point held exactly that one file node and nothing else.

Fix

Both skip paths (non-config object root, and non-object top-level root) now return the already-built nodes list instead of an empty one. Since nothing else has been added to it by that point, this yields exactly one bare file node — no per-key traversal, no children, no edges — keeping the file discoverable without reintroducing the node explosion #1224 fixed. Verified the size-limit and invalid-JSON early-return paths are unaffected (they return before the file node is ever built).

Test plan

• Updated test_extract_json_data_file_skipped and test_extract_json_top_level_array_skipped in tests/test_extract.py, which previously pinned an empty node list, to assert the new single bare-file-node behavior.
• Added test_extract_json_data_file_node_is_a_real_file_node (same id scheme, file_type: "code" matching .json's CODE_EXTENSIONS classification, no error key) and test_extract_json_many_data_files_still_one_node_each (a small corpus of data files stays AST pass explodes data .json into orphan key-nodes (CODE_EXTENSIONS includes .json) — 561 isolated nodes on a real repo #1224-safe: exactly one node per file, never per-key nodes).
• Confirmed recognized config/manifest JSON (tsconfig.json, package.json-shaped fixtures) is unaffected — full structural extraction still runs.
• Full suite: python3 -m pytest -q — 5623 passed, 68 skipped, no regressions.

🤖 Generated with Claude Code

[graphify-labs]

Graphify reviewed this change.

Looks safe to merge — no coupling regressions and no blocking issues, checked against the code graph (not a self-assessment).

Formal verification. No changes could be formally verified in this run.

---

Graphify review — findings

Emits the bare file node for data-shaped .json files that fail the config/manifest check in extract_json, instead of returning an empty node list, so eval fixtures, datasets, and array/scalar-rooted JSON stay discoverable via query/explain/affected. The skip path still emits no per-key nodes and no edges, preserving the #1224 orphan-key-explosion fix — one file node per file regardless of corpus size. The file node carries the standard id scheme, file_type "code", and no error key, matching every other file node graphify emits.

No blocking issues surfaced.

Analysis details — impact, health, verification

Impact & health

Graphify review

Impact — 637 functions depend on the 637 functions this change touches.

Health — this change adds coupling hotspots:

• new: extract_json() — 18 callers, 7 callees
• new: walk_object() — 1 callers, 7 callees

Verification — 637 functions in the blast radius were not formally verified this run (proofs are advisory here).

Gate & verification

graphify gate

PASS — objectively clean (no health regressions, tests not run — proofs not run this pass (advisory)). Grounded, not self-assessed.

Advisory (not blocking):

• verification_scope: 637 function(s) in the blast radius were not formally verified this run

Test selection

Test selection

286 of 286 test file(s) selected (100%) via static blast radius.

Escalated to a full run for safety — the selection is not trustworthy on its own (see below). CI should run the whole suite.

• tests/test_affected_cli.py — full-run-safety
• tests/test_affected_member_seed.py — full-run-safety
• tests/test_agents_platform.py — full-run-safety
• tests/test_analyze.py — full-run-safety
• tests/test_anthropic_custom_endpoint.py — full-run-safety
• tests/test_antigravity_install.py — full-run-safety
• tests/test_apm_fallback_version.py — full-run-safety
• tests/test_architecture_doc.py — full-run-safety
• tests/test_astro_extraction.py — full-run-safety
• tests/test_astro_import_ids.py — full-run-safety
• tests/test_atomic_canvas_export.py — full-run-safety
• tests/test_atomic_version_stamp.py — full-run-safety
• tests/test_atomic_writes.py — full-run-safety
• tests/test_backend_env_isolation.py — full-run-safety
• tests/test_backend_extras.py — full-run-safety
• tests/test_benchmark.py — full-run-safety
• tests/test_benchmark_raw_graph.py — full-run-safety
• tests/test_build.py — full-run-safety
• tests/test_build_merge_dedup_scope.py — full-run-safety
• tests/test_build_merge_hyperedges_and_prune.py — full-run-safety
• tests/test_build_merge_shrink_guard.py — full-run-safety
• tests/test_builtin_global_type_refs.py — full-run-safety
• tests/test_cache.py — full-run-safety
• tests/test_callflow_html.py — full-run-safety
• tests/test_cargo_introspect.py — full-run-safety
• tests/test_carried_hyperedge_remap.py — full-run-safety
• tests/test_case_sensitive_resolution.py — full-run-safety
• tests/test_charmap_encoding.py — full-run-safety
• tests/test_chunking.py — full-run-safety
• tests/test_cjs_module_extension.py — full-run-safety
• tests/test_claude_cli_backend.py — full-run-safety
• tests/test_claude_md.py — full-run-safety
• tests/test_cli_broken_pipe.py — full-run-safety
• tests/test_cli_export.py — full-run-safety
• tests/test_cli_help.py — full-run-safety
• tests/test_cluster.py — full-run-safety
• tests/test_codebuddy.py — full-run-safety
• tests/test_community_hub_labels.py — full-run-safety
• tests/test_community_labels_skill.py — full-run-safety
• tests/test_confidence.py — full-run-safety
• tests/test_corrupt_graph_json.py — full-run-safety
• tests/test_cpp_nested_and_cli.py — full-run-safety
• tests/test_cpp_objc_cross_file_calls.py — full-run-safety
• tests/test_cpp_preprocess.py — full-run-safety
• tests/test_cross_extension_reexport_self_cycle.py — full-run-safety
• tests/test_cross_language_call_resolution.py — full-run-safety
• tests/test_cross_repo_external_call_guards.py — full-run-safety
• tests/test_cross_repo_member_calls.py — full-run-safety
• tests/test_cross_repo_shared_types.py — full-run-safety
• tests/test_csharp_call_site_generic_args.py — full-run-safety
• … and 236 more

non-code file(s) changed (CHANGELOG.md) → running the full suite for safety (a code graph can't see config/fixture/data deps)

changed code file(s) with no mapped test (CHANGELOG.md) — a coverage gap or a missing link — running the full suite rather than only the selected tests

Selection is safe under the controlled-regression assumption; always-run tests + a periodic full run are the backstops. Advisory — it never changes the check verdict.

Formal verification

Could not verify: Could not verify extract\_json.

The verifier did not have enough to check extract\_json, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: no capturable inputs from the test suite; property tier: parameter `path` is annotated `Path` — outside the synthesizable primitive/collection set

· 2 more finding(s) on lines outside this diff (see the check run).