feat(discover,provenance): graph discovery queries + @cite scan + code_links + bib export

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

tests/provenance/test_provenance.py

@@ -0,0 +1,209 @@
+"""Tests for codex.provenance — @cite scan, code_links CRUD, bib export.
+
+All DB access is mocked; no real PostgreSQL server required.
+"""
+
+from __future__ import annotations
+
+from contextlib import contextmanager
+from datetime import UTC, datetime
+from pathlib import Path
+from typing import Any
+from unittest.mock import MagicMock, patch
+
+from codex.models import CodeLink
+
+# ---------------------------------------------------------------------------
+# Helpers
+# ---------------------------------------------------------------------------
+
+
+def _make_conn_cm(mock_conn: MagicMock) -> Any:
+    """Return a context-manager factory that yields *mock_conn*."""
+
+    @contextmanager  # type: ignore[arg-type]
+    def _cm() -> Any:
+        yield mock_conn
+
+    return _cm
+
+
+def _dict_row(**kwargs: Any) -> dict[str, Any]:
+    return dict(kwargs)
+
+
+# ---------------------------------------------------------------------------
+# 1. test_scan_cite_tags
+# ---------------------------------------------------------------------------
+
+
+def test_scan_cite_tags(tmp_path: Path) -> None:
+    """A .cpp file with @cite produces correct dict entries."""
+    from codex.provenance import scan_cite_tags
+
+    src_file = tmp_path / "algo.cpp"
+    src_file.write_text(
+        "// Helper function\n"
+        "void compute_hodge() {\n"
+        "    // @cite somepaper2023\n"
+        "    do_stuff();\n"
+        "}\n",
+        encoding="utf-8",
+    )
+
+    results = scan_cite_tags(str(tmp_path))
+
+    assert len(results) == 1
+    hit = results[0]
+    assert hit["bibkey"] == "somepaper2023"
+    assert hit["line"] == "3"
+    assert hit["file"] == "algo.cpp"
+    # symbol extracted from "compute_hodge()" on the line above
+    assert hit["symbol"] == "compute_hodge"
+
+
+# ---------------------------------------------------------------------------
+# 2. test_scan_cite_tags_no_files
+# ---------------------------------------------------------------------------
+
+
+def test_scan_cite_tags_no_files(tmp_path: Path) -> None:
+    """Empty directory returns an empty list."""
+    from codex.provenance import scan_cite_tags
+
+    result = scan_cite_tags(str(tmp_path))
+    assert result == []
+
+
+# ---------------------------------------------------------------------------
+# 3. test_add_code_link
+# ---------------------------------------------------------------------------
+
+
+def test_add_code_link() -> None:
+    """Mock conn, verify INSERT is issued and returned CodeLink has id from RETURNING."""
+    from codex.provenance import add_code_link
+
+    now = datetime(2026, 6, 5, tzinfo=UTC)
+    mock_conn = MagicMock()
+    mock_conn.execute.return_value.fetchone.return_value = _dict_row(id=42, added_at=now)
+
+    with patch("codex.provenance.get_conn", side_effect=_make_conn_cm(mock_conn)):
+        link = add_code_link(
+            symbol="dec::hodge_star",
+            paper_id="2301.07041",
+            role="implements Thm 3.2",
+            note="core algorithm",
+        )
+
+    assert isinstance(link, CodeLink)
+    assert link.id == 42
+    assert link.added_at == now
+    assert link.symbol == "dec::hodge_star"
+    assert link.paper_id == "2301.07041"
+    assert link.role == "implements Thm 3.2"
+    assert link.note == "core algorithm"
+
+    call_args = mock_conn.execute.call_args
+    sql: str = call_args[0][0]
+    assert "INSERT INTO code_links" in sql
+    assert "RETURNING" in sql
+
+    mock_conn.commit.assert_called_once()
+
+
+# ---------------------------------------------------------------------------
+# 4. test_list_code_links_all
+# ---------------------------------------------------------------------------
+
+
+def test_list_code_links_all() -> None:
+    """No filter → all rows returned as CodeLink list."""
+    from codex.provenance import list_code_links
+
+    now = datetime(2026, 6, 5, tzinfo=UTC)
+    mock_conn = MagicMock()
+    mock_conn.execute.return_value.fetchall.return_value = [
+        _dict_row(id=1, symbol="foo::bar", paper_id="W111", role="uses", note=None, added_at=now),
+        _dict_row(id=2, symbol="baz::qux", paper_id=None, role=None, note="ref", added_at=now),
+    ]
+
+    with patch("codex.provenance.get_conn", side_effect=_make_conn_cm(mock_conn)):
+        links = list_code_links()
+
+    assert len(links) == 2
+    assert all(isinstance(lnk, CodeLink) for lnk in links)
+    assert links[0].symbol == "foo::bar"
+    assert links[0].id == 1
+    assert links[1].symbol == "baz::qux"
+    assert links[1].paper_id is None
+
+    # No WHERE clause in the SQL
+    call_args = mock_conn.execute.call_args
+    sql: str = call_args[0][0]
+    assert "WHERE" not in sql
+
+
+# ---------------------------------------------------------------------------
+# 5. test_list_code_links_filtered
+# ---------------------------------------------------------------------------
+
+
+def test_list_code_links_filtered() -> None:
+    """Filter by paper_id → WHERE clause applied and only matching rows returned."""
+    from codex.provenance import list_code_links
+
+    now = datetime(2026, 6, 5, tzinfo=UTC)
+    mock_conn = MagicMock()
+    mock_conn.execute.return_value.fetchall.return_value = [
+        _dict_row(
+            id=3,
+            symbol="some::func",
+            paper_id="2301.07041",
+            role=None,
+            note=None,
+            added_at=now,
+        ),
+    ]
+
+    with patch("codex.provenance.get_conn", side_effect=_make_conn_cm(mock_conn)):
+        links = list_code_links(paper_id="2301.07041")
+
+    assert len(links) == 1
+    assert links[0].paper_id == "2301.07041"
+
+    call_args = mock_conn.execute.call_args
+    sql: str = call_args[0][0]
+    params: dict[str, Any] = call_args[0][1]
+    assert "WHERE paper_id" in sql
+    assert params["paper_id"] == "2301.07041"
+
+
+# ---------------------------------------------------------------------------
+# 6. test_export_bib_format
+# ---------------------------------------------------------------------------
+
+
+def test_export_bib_format() -> None:
+    """Mock returns one paper row; verify valid BibTeX string output."""
+    from codex.provenance import export_bib
+
+    mock_conn = MagicMock()
+    mock_conn.execute.return_value.fetchall.return_value = [
+        _dict_row(
+            id="2301.07041",
+            bibkey="smith2023conformal",
+            title="Conformal Approaches to Laplacian Eigenmaps",
+            authors=["Alice Smith", "Bob Jones"],
+            year=2023,
+        ),
+    ]
+
+    with patch("codex.provenance.get_conn", side_effect=_make_conn_cm(mock_conn)):
+        bib = export_bib()
+
+    assert "@article{smith2023conformal," in bib
+    assert "title  = {Conformal Approaches to Laplacian Eigenmaps}" in bib
+    assert "author = {Alice Smith and Bob Jones}" in bib
+    assert "year   = {2023}" in bib
+    assert "note   = {2301.07041}" in bib