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

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

tests/discover/test_discover.py

@@ -0,0 +1,145 @@
+"""Tests for codex.discover — graph-based discovery queries.
+
+All DB access is mocked; no real PostgreSQL server required.
+"""
+
+from __future__ import annotations
+
+from contextlib import contextmanager
+from typing import Any
+from unittest.mock import MagicMock, patch
+
+# ---------------------------------------------------------------------------
+# 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_discovery_leads_returns_correct_format
+# ---------------------------------------------------------------------------
+
+
+def test_discovery_leads_returns_correct_format() -> None:
+    """Mock conn returns rows; verify output has correct shape and ordering."""
+    from codex.discover import discovery_leads
+
+    mock_conn = MagicMock()
+    mock_conn.execute.return_value.fetchall.return_value = [
+        _dict_row(cited_id="W111", pull=5),
+        _dict_row(cited_id="W222", pull=3),
+        _dict_row(cited_id="W333", pull=1),
+    ]
+
+    with patch("codex.discover.get_conn", side_effect=_make_conn_cm(mock_conn)):
+        result = discovery_leads(limit=10)
+
+    assert len(result) == 3
+    assert result[0] == {"cited_id": "W111", "pull": 5}
+    assert result[1] == {"cited_id": "W222", "pull": 3}
+    assert result[2] == {"cited_id": "W333", "pull": 1}
+
+    # Verify the SQL and limit param were passed
+    call_args = mock_conn.execute.call_args
+    sql: str = call_args[0][0]
+    params: dict[str, Any] = call_args[0][1]
+    assert "cited_id NOT IN" in sql
+    assert "pull DESC" in sql
+    assert params["limit"] == 10
+
+
+# ---------------------------------------------------------------------------
+# 2. test_citing_papers
+# ---------------------------------------------------------------------------
+
+
+def test_citing_papers() -> None:
+    """Mock returns citing_id list; verify flat list of IDs is returned."""
+    from codex.discover import citing_papers
+
+    mock_conn = MagicMock()
+    mock_conn.execute.return_value.fetchall.return_value = [
+        _dict_row(citing_id="2301.00001"),
+        _dict_row(citing_id="2302.00002"),
+    ]
+
+    with patch("codex.discover.get_conn", side_effect=_make_conn_cm(mock_conn)):
+        result = citing_papers("W999")
+
+    assert result == ["2301.00001", "2302.00002"]
+
+    call_args = mock_conn.execute.call_args
+    sql: str = call_args[0][0]
+    params: dict[str, Any] = call_args[0][1]
+    assert "cited_id" in sql
+    assert params["paper_id"] == "W999"
+
+
+# ---------------------------------------------------------------------------
+# 3. test_cited_by
+# ---------------------------------------------------------------------------
+
+
+def test_cited_by() -> None:
+    """Mock returns cited_id list; verify flat list of IDs is returned."""
+    from codex.discover import cited_by
+
+    mock_conn = MagicMock()
+    mock_conn.execute.return_value.fetchall.return_value = [
+        _dict_row(cited_id="10.1000/ref_a"),
+        _dict_row(cited_id="10.1000/ref_b"),
+    ]
+
+    with patch("codex.discover.get_conn", side_effect=_make_conn_cm(mock_conn)):
+        result = cited_by("2301.00001")
+
+    assert result == ["10.1000/ref_a", "10.1000/ref_b"]
+
+    call_args = mock_conn.execute.call_args
+    sql: str = call_args[0][0]
+    params: dict[str, Any] = call_args[0][1]
+    assert "citing_id" in sql
+    assert params["paper_id"] == "2301.00001"
+
+
+# ---------------------------------------------------------------------------
+# 4. test_cocited_papers
+# ---------------------------------------------------------------------------
+
+
+def test_cocited_papers() -> None:
+    """Mock returns co-citation list; verify shape and ordering."""
+    from codex.discover import cocited_papers
+
+    mock_conn = MagicMock()
+    mock_conn.execute.return_value.fetchall.return_value = [
+        _dict_row(paper_id="W444", co_citations=7),
+        _dict_row(paper_id="W555", co_citations=2),
+    ]
+
+    with patch("codex.discover.get_conn", side_effect=_make_conn_cm(mock_conn)):
+        result = cocited_papers("W111", limit=5)
+
+    assert len(result) == 2
+    assert result[0] == {"paper_id": "W444", "co_citations": 7}
+    assert result[1] == {"paper_id": "W555", "co_citations": 2}
+
+    call_args = mock_conn.execute.call_args
+    sql: str = call_args[0][0]
+    params: dict[str, Any] = call_args[0][1]
+    assert "co_citations DESC" in sql
+    assert params["paper_id"] == "W111"
+    assert params["limit"] == 5