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Support separate bibliography roots in review export

This commit is contained in:
welsberr 2026-05-08 01:18:06 -04:00
parent 2f7696c115
commit 8201dd83ee
2 changed files with 56 additions and 4 deletions
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23
src/groundrecall/review_export.py
View File

@ -177,16 +177,27 @@ def _resolve_source_root(import_dir: Path, source_root: str) -> str:
return str((import_dir.parent.parent / root).resolve())
def _resolve_bibliography_root(import_dir: Path, manifest: dict[str, Any], resolved_source_root: str) -> str:
bibliography_root = str(manifest.get("bibliography_root", "")).strip()
if not bibliography_root:
return resolved_source_root
root = Path(bibliography_root)
if root.is_absolute():
return str(root)
return str((import_dir.parent.parent / root).resolve())
def _artifact_citation_payloads(
artifacts: list[dict[str, Any]],
*,
source_root: str,
bibliography_root: str | None = None,
) -> tuple[list[dict[str, Any]], dict[str, dict[str, Any]]]:
extract_references, backends = _load_citegeist_extract()
artifact_payloads: list[dict[str, Any]] = []
summaries: dict[str, dict[str, Any]] = {}
root = Path(source_root) if source_root else None
bibliography_index = load_bibliography_index(source_root) if source_root else {}
bibliography_index = load_bibliography_index(bibliography_root or source_root) if (bibliography_root or source_root) else {}
for artifact in artifacts:
path = Path(source_root) / artifact["path"] if root is not None else None
@ -280,14 +291,16 @@ def build_citation_review_entries_from_import(import_dir: str | Path) -> list[Ci
base = Path(import_dir)
manifest = _read_json(base / "manifest.json")
resolved_source_root = _resolve_source_root(base, manifest.get("source_root", ""))
resolved_bibliography_root = _resolve_bibliography_root(base, manifest, resolved_source_root)
artifacts = _read_jsonl(base / "artifacts.jsonl")
observations = _read_jsonl(base / "observations.jsonl")
claims = _read_jsonl(base / "claims.jsonl")
bibliography_index = load_bibliography_index(resolved_source_root)
bibliography_index = load_bibliography_index(resolved_bibliography_root)
artifact_payloads, _ = _artifact_citation_payloads(
artifacts,
source_root=resolved_source_root,
bibliography_root=resolved_bibliography_root,
)
observations_by_id = {item["observation_id"]: item for item in observations}
artifact_claim_links: dict[str, dict[str, set[str]]] = defaultdict(lambda: {"claim_ids": set(), "concept_ids": set()})
@ -357,7 +370,8 @@ def build_citation_review_entries_from_import(import_dir: str | Path) -> list[Ci
def _build_import_review_payload(session: ReviewSession, import_dir: Path) -> dict[str, Any]:
manifest = _read_json(import_dir / "manifest.json")
resolved_source_root = _resolve_source_root(import_dir, manifest.get("source_root", ""))
bibliography_index = load_bibliography_index(resolved_source_root) if resolved_source_root else {}
resolved_bibliography_root = _resolve_bibliography_root(import_dir, manifest, resolved_source_root)
bibliography_index = load_bibliography_index(resolved_bibliography_root) if resolved_bibliography_root else {}
lint_payload = _read_json(import_dir / "lint_findings.json")
queue_payload = _read_json(import_dir / "review_queue.json")
graph_payload = _read_json(import_dir / "graph_diagnostics.json")
@ -377,6 +391,7 @@ def _build_import_review_payload(session: ReviewSession, import_dir: Path) -> di
artifact_citations, artifact_citation_summary = _artifact_citation_payloads(
artifacts,
source_root=resolved_source_root,
bibliography_root=resolved_bibliography_root,
)
artifact_by_id = {item["artifact_id"]: item for item in artifacts}
queue_by_candidate_id = {
@ -510,7 +525,7 @@ def _build_import_review_payload(session: ReviewSession, import_dir: Path) -> di
],
"concept_reviews": concept_reviews,
"citation_reviews": [entry.model_dump() for entry in session.citation_reviews],
"bibliography": bibliography_summary_payload(resolved_source_root),
"bibliography": bibliography_summary_payload(resolved_bibliography_root),
"graph_diagnostics": graph_payload,
"citations": {
"enabled": True,

37
tests/test_groundrecall_review_workspace.py
View File

@ -139,3 +139,40 @@ def test_review_workspace_surfaces_local_bibliography_support_suggestions(tmp_pa
assert suggestions
assert suggestions[0]["citation_key"] == "kimura1968evolutionary"
assert "abstract" in suggestions[0]["reason"].lower() or "title" in suggestions[0]["reason"].lower()
def test_review_workspace_can_use_separate_bibliography_root(tmp_path: Path) -> None:
root = tmp_path / "pilot"
source_root = root / "source"
bib_root = root / "bibliography"
(source_root / "wiki").mkdir(parents=True)
bib_root.mkdir(parents=True)
(source_root / "wiki" / "drift.md").write_text(
"# Drift\n\n"
"- Random genetic drift can dominate allele-frequency change in small populations.\n",
encoding="utf-8",
)
(bib_root / "refs.bib").write_text(
"@article{kimura1968evolutionary,\n"
" author = {Motoo Kimura},\n"
" title = {Evolutionary Rate at the Molecular Level},\n"
" journal = {Nature},\n"
" year = {1968},\n"
" abstract = {The rate of molecular evolution is compatible with neutral changes driven by random genetic drift in populations.}\n"
"}\n",
encoding="utf-8",
)
import_result = run_groundrecall_import(source_root, out_root=tmp_path / "imports", mode="quick", import_id="separate-bib-root")
manifest_path = import_result.out_dir / "manifest.json"
manifest = json.loads(manifest_path.read_text(encoding="utf-8"))
manifest["bibliography_root"] = str(bib_root)
manifest_path.write_text(json.dumps(manifest, indent=2), encoding="utf-8")
workspace = GroundRecallReviewWorkspace(import_result.out_dir)
payload = workspace.load_review_data()
concept_review = next(item for item in payload["concept_reviews"] if item["concept_id"] == "drift")
suggestions = concept_review["top_claims"][0]["support_suggestions"]
assert payload["bibliography"]["entry_count"] == 1
assert suggestions
assert suggestions[0]["citation_key"] == "kimura1968evolutionary"