codex/cli.py

@@ -188,6 +188,24 @@ def discover_leads(
         typer.echo(f"{item['pull']:>4}×  {item['cited_id']}")
 
 
+@discover_app.command("recommend")
+def discover_recommend(
+    paper_id: str = typer.Argument(
+        ..., help="Semantic Scholar paper ID (or arXiv:/DOI: prefixed)."
+    ),
+    limit: int = typer.Option(20, "--limit", "-n", help="Number of recommendations."),
+) -> None:
+    """Recommended papers for PAPER_ID via Semantic Scholar."""
+    from codex.sources.semanticscholar import fetch_recommendations
+
+    rec = fetch_recommendations(paper_id, limit=limit)
+    if not rec:
+        typer.echo(f"No recommendations found for {paper_id}.")
+        return
+    for pid in rec:
+        typer.echo(pid)
+
+
 @discover_app.command("citing")
 def discover_citing(paper_id: str = typer.Argument(...)) -> None:
     """List papers that cite PAPER_ID."""
@@ -582,7 +600,9 @@ def graph_report(
     settings = get_settings()
     with get_conn() as conn:
         graph = build_citation_graph(conn)
-        known_ids = {row["id"] for row in conn.execute("SELECT id FROM papers").fetchall()}
+        paper_rows = conn.execute("SELECT id, title FROM papers").fetchall()
+    known_ids = {row["id"] for row in paper_rows}
+    titles = {row["id"]: row["title"] for row in paper_rows}
 
     if graph.number_of_nodes() == 0:
         typer.echo("Citation graph is empty — ingest some papers first.")
@@ -592,6 +612,13 @@ def graph_report(
     pr = citation_pagerank(graph)
     hubs = sorted(pr.items(), key=lambda x: -x[1])[:top_n]
     dangling = sorted(dangling_citations(graph, known_ids))
+    small_corpus = n_papers < settings.graph_min_corpus_size
+    warning = (
+        f"only {n_papers} ingested papers; recommended >= {settings.graph_min_corpus_size} "
+        "for meaningful ranking"
+        if small_corpus
+        else None
+    )
 
     if output_json:
         typer.echo(
@@ -599,7 +626,11 @@ def graph_report(
                 {
                     "nodes": graph.number_of_nodes(),
                     "edges": graph.number_of_edges(),
-                    "hubs": [{"paper_id": pid, "pagerank": score} for pid, score in hubs],
+                    "small_corpus_warning": warning,  # null unless below threshold (audit U-3)
+                    "hubs": [
+                        {"paper_id": pid, "title": titles.get(pid), "pagerank": score}
+                        for pid, score in hubs
+                    ],
                     "dangling_count": len(dangling),
                     "dangling": dangling,
                 },
@@ -608,18 +639,16 @@ def graph_report(
         )
         return
 
-    if n_papers < settings.graph_min_corpus_size:
+    if warning:
-        typer.echo(
+        typer.echo(f"Warning: {warning}.", err=True)
-            f"Warning: only {n_papers} ingested papers "
-            f"(recommended ≥ {settings.graph_min_corpus_size} for meaningful ranking).",
-            err=True,
-        )
     typer.echo(f"Graph: {graph.number_of_nodes()} nodes, {graph.number_of_edges()} edges")
     typer.echo("")
     typer.echo(f"TOP-{top_n} HUB PAPERS (PageRank)")
     typer.echo("-" * 48)
     for pid, score in hubs:
-        typer.echo(f"  {score:.4f}  {pid}")
+        # in-KB hubs show their title; dangling (OpenAlex-id) hubs are flagged (U-1)
+        label = titles.get(pid) or "(dangling — not ingested)"
+        typer.echo(f"  {score:.4f}  {pid}  {label}")
     typer.echo("")
     typer.echo(f"DANGLING CITATIONS ({len(dangling)} cited but not ingested)")
     typer.echo("-" * 48)
@@ -652,3 +681,23 @@ def graph_related(
     )
     for pid in related:
         typer.echo(f"  {pid}")
+
+
+@graph_app.command("cocited")
+def graph_cocited(
+    paper_id: str = typer.Argument(..., help="Paper ID to find co-cited papers for."),
+) -> None:
+    """List papers frequently co-cited with PAPER_ID (graph co-citation)."""
+    from codex.db import get_conn
+    from codex.graph import build_citation_graph, find_co_cited
+
+    with get_conn() as conn:
+        graph = build_citation_graph(conn)
+
+    results = find_co_cited(paper_id, graph)
+    if not results:
+        typer.echo(f"No papers co-cited with {paper_id}.")
+        return
+    typer.echo(f"Papers co-cited with {paper_id} (count desc):")
+    for pid, count in results:
+        typer.echo(f"  {count:>3}×  {pid}")

tests/graph/test_cli.py

@@ -28,9 +28,11 @@ def _make_conn_cm(conn: MagicMock):
 
 
 def _make_conn_with_paper_ids(*paper_ids: str) -> MagicMock:
-    """Mock conn that returns paper rows for SELECT id FROM papers."""
+    """Mock conn that returns paper rows for SELECT id, title FROM papers."""
     conn = MagicMock()
-    conn.execute.return_value.fetchall.return_value = [{"id": pid} for pid in paper_ids]
+    conn.execute.return_value.fetchall.return_value = [
+        {"id": pid, "title": f"Title of {pid}"} for pid in paper_ids
+    ]
     return conn