test: add coverage for server/tools/* and index_service pipeline flow

server/tools/*.py had zero tests, and index_service only had a single
parser-failure regression test. Adds tests for search_code, find_symbol,
find_usages (including the path reconstruction in get_code_context and the
limit/self-match interaction in find_usages), admin, index, and history
tools by extracting registered @mcp.tool() functions from a throwaway
FastMCP instance. Also covers index_service's incremental skip, force
override, stale-entry cleanup, no-symbols cleanup, embedding-failure
preservation, and delete-before-upsert ordering.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

Author: GoodbyePlanet

tests/test_pipeline.py

@@ -180,3 +180,213 @@ async def test_parser_failure_preserves_existing_index_entries() -> None:
     store.delete_by_file.assert_not_called()
     store.upsert_chunks.assert_not_called()
     assert result["files"] == 0
+
+
+async def test_unchanged_file_is_skipped_without_fetching_content() -> None:
+    svc = ServiceConfig(name="svc", github_repo="org/repo", exclude=[])
+    github_file = GitHubFile(rel_path="unchanged.py", blob_sha="same-sha")
+
+    store = AsyncMock()
+    store.get_indexed_file_hashes.return_value = {"svc/unchanged.py": "same-sha"}
+
+    pipeline = _make_pipeline(store)
+
+    with (
+        patch.object(
+            type(pipeline_module.settings), "load_services", return_value=[svc]
+        ),
+        patch.object(
+            pipeline_module, "list_github_files", AsyncMock(return_value=[github_file])
+        ),
+        patch.object(pipeline_module, "fetch_blob_content", AsyncMock()) as mock_fetch,
+    ):
+        result = await pipeline.index_service("svc", force=False)
+
+    mock_fetch.assert_not_called()
+    store.delete_by_file.assert_not_called()
+    assert result == {"files": 0, "chunks": 0, "skipped": 1}
+
+
+async def test_force_reindexes_even_when_hash_unchanged() -> None:
+    svc = ServiceConfig(name="svc", github_repo="org/repo", exclude=[])
+    github_file = GitHubFile(rel_path="unchanged.py", blob_sha="same-sha")
+    symbol = CodeSymbol(
+        name="fn",
+        symbol_type="function",
+        language="python",
+        source="def fn(): pass",
+        file_path="svc/unchanged.py",
+        start_line=1,
+        end_line=1,
+    )
+
+    store = AsyncMock()
+    store.get_indexed_file_hashes.return_value = {"svc/unchanged.py": "same-sha"}
+
+    pipeline = _make_pipeline(store)
+
+    with (
+        patch.object(
+            type(pipeline_module.settings), "load_services", return_value=[svc]
+        ),
+        patch.object(
+            pipeline_module, "list_github_files", AsyncMock(return_value=[github_file])
+        ),
+        patch.object(
+            pipeline_module,
+            "fetch_blob_content",
+            AsyncMock(return_value=b"def fn(): pass"),
+        ),
+        patch.object(pipeline_module, "parse_file", return_value=[symbol]),
+    ):
+        result = await pipeline.index_service("svc", force=True)
+
+    store.delete_by_file.assert_called_once_with("svc", "svc/unchanged.py")
+    store.upsert_chunks.assert_called_once()
+    assert result == {"files": 1, "chunks": 1, "skipped": 0}
+
+
+async def test_stale_index_entries_removed_when_file_no_longer_in_repo() -> None:
+    svc = ServiceConfig(name="svc", github_repo="org/repo", exclude=[])
+
+    store = AsyncMock()
+    store.get_indexed_file_hashes.return_value = {
+        "svc/deleted.py": "old-sha",
+        "svc/still-there.py": "sha",
+    }
+
+    pipeline = _make_pipeline(store)
+
+    with (
+        patch.object(
+            type(pipeline_module.settings), "load_services", return_value=[svc]
+        ),
+        patch.object(
+            pipeline_module,
+            "list_github_files",
+            AsyncMock(
+                return_value=[GitHubFile(rel_path="still-there.py", blob_sha="sha")]
+            ),
+        ),
+    ):
+        result = await pipeline.index_service("svc", force=False)
+
+    store.delete_by_file.assert_called_once_with("svc", "svc/deleted.py")
+    assert result["skipped"] == 1
+
+
+async def test_file_with_no_symbols_deletes_stale_entries_and_skips_upsert() -> None:
+    svc = ServiceConfig(name="svc", github_repo="org/repo", exclude=[])
+    github_file = GitHubFile(rel_path="empty.py", blob_sha="sha1")
+
+    store = AsyncMock()
+    store.get_indexed_file_hashes.return_value = {}
+
+    pipeline = _make_pipeline(store)
+
+    with (
+        patch.object(
+            type(pipeline_module.settings), "load_services", return_value=[svc]
+        ),
+        patch.object(
+            pipeline_module, "list_github_files", AsyncMock(return_value=[github_file])
+        ),
+        patch.object(
+            pipeline_module, "fetch_blob_content", AsyncMock(return_value=b"")
+        ),
+        patch.object(pipeline_module, "parse_file", return_value=[]),
+    ):
+        result = await pipeline.index_service("svc", force=True)
+
+    store.delete_by_file.assert_called_once_with("svc", "svc/empty.py")
+    store.upsert_chunks.assert_not_called()
+    assert result["files"] == 0
+
+
+async def test_embedding_failure_preserves_existing_index_entries() -> None:
+    svc = ServiceConfig(name="svc", github_repo="org/repo", exclude=[])
+    github_file = GitHubFile(rel_path="broken.py", blob_sha="sha1")
+    symbol = CodeSymbol(
+        name="fn",
+        symbol_type="function",
+        language="python",
+        source="def fn(): pass",
+        file_path="svc/broken.py",
+        start_line=1,
+        end_line=1,
+    )
+
+    store = AsyncMock()
+    store.get_indexed_file_hashes.return_value = {"svc/broken.py": "old-sha"}
+
+    pipeline = _make_pipeline(store)
+    pipeline._embedder.embed_batch = AsyncMock(side_effect=RuntimeError("503"))
+
+    with (
+        patch.object(
+            type(pipeline_module.settings), "load_services", return_value=[svc]
+        ),
+        patch.object(
+            pipeline_module, "list_github_files", AsyncMock(return_value=[github_file])
+        ),
+        patch.object(
+            pipeline_module,
+            "fetch_blob_content",
+            AsyncMock(return_value=b"def fn(): pass"),
+        ),
+        patch.object(pipeline_module, "parse_file", return_value=[symbol]),
+    ):
+        result = await pipeline.index_service("svc", force=True)
+
+    store.delete_by_file.assert_not_called()
+    store.upsert_chunks.assert_not_called()
+    assert result["files"] == 0
+
+
+async def test_delete_by_file_called_before_upsert_for_changed_file() -> None:
+    svc = ServiceConfig(name="svc", github_repo="org/repo", exclude=[])
+    github_file = GitHubFile(rel_path="mod.py", blob_sha="new-sha")
+    symbol = CodeSymbol(
+        name="fn",
+        symbol_type="function",
+        language="python",
+        source="def fn(): pass",
+        file_path="svc/mod.py",
+        start_line=1,
+        end_line=1,
+    )
+
+    call_order: list[str] = []
+    store = AsyncMock()
+    store.get_indexed_file_hashes.return_value = {"svc/mod.py": "old-sha"}
+    store.delete_by_file.side_effect = lambda *a, **k: call_order.append("delete")
+    store.upsert_chunks.side_effect = lambda *a, **k: call_order.append("upsert")
+
+    pipeline = _make_pipeline(store)
+
+    with (
+        patch.object(
+            type(pipeline_module.settings), "load_services", return_value=[svc]
+        ),
+        patch.object(
+            pipeline_module, "list_github_files", AsyncMock(return_value=[github_file])
+        ),
+        patch.object(
+            pipeline_module,
+            "fetch_blob_content",
+            AsyncMock(return_value=b"def fn(): pass"),
+        ),
+        patch.object(pipeline_module, "parse_file", return_value=[symbol]),
+    ):
+        await pipeline.index_service("svc", force=False)
+
+    assert call_order == ["delete", "upsert"]
+
+
+async def test_unknown_service_returns_error_without_touching_github() -> None:
+    pipeline = _make_pipeline(AsyncMock())
+
+    with patch.object(type(pipeline_module.settings), "load_services", return_value=[]):
+        result = await pipeline.index_service("missing")
+
+    assert result == {"error": 1, "files": 0, "chunks": 0}

tests/tools/__init__.py

@@ -0,0 +1,21 @@
+from __future__ import annotations
+
+from collections.abc import Callable
+from dataclasses import dataclass, field
+from typing import Any
+
+from mcp.server.fastmcp import FastMCP
+
+
+def get_tool(register: Callable[[FastMCP], None], name: str) -> Callable:
+    """Register a tool module against a throwaway FastMCP instance and return
+    the underlying async function, bypassing MCP's request/response plumbing."""
+    mcp = FastMCP("test")
+    register(mcp)
+    return mcp._tool_manager._tools[name].fn
+
+
+@dataclass
+class StubHit:
+    payload: dict[str, Any] = field(default_factory=dict)
+    score: float = 1.0

tests/tools/conftest.py

@@ -0,0 +1,89 @@
+from __future__ import annotations
+
+from unittest.mock import AsyncMock, patch
+
+from server.config import ServiceConfig
+from server.tools.admin import register_admin_tools
+from tests.tools.conftest import get_tool
+
+
+def _tool(name: str):
+    return get_tool(register_admin_tools, name)
+
+
+async def test_list_indexed_services_reports_when_empty() -> None:
+    list_indexed_services = _tool("list_indexed_services")
+    store = AsyncMock()
+    store.get_service_stats.return_value = []
+
+    with patch("server.tools.admin.get_store", return_value=store):
+        result = await list_indexed_services()
+
+    assert "No services indexed yet" in result
+
+
+async def test_list_indexed_services_formats_stats_sorted_by_name() -> None:
+    list_indexed_services = _tool("list_indexed_services")
+    store = AsyncMock()
+    store.get_service_stats.return_value = [
+        {
+            "service": "zebra",
+            "chunk_count": 5,
+            "file_count": 2,
+            "languages": ["python"],
+            "last_indexed": "2026-01-01",
+        },
+        {
+            "service": "alpha",
+            "chunk_count": 10,
+            "file_count": 4,
+            "languages": ["java", "python"],
+            "last_indexed": "2026-01-02",
+        },
+    ]
+
+    with patch("server.tools.admin.get_store", return_value=store):
+        result = await list_indexed_services()
+
+    assert result.index("alpha") < result.index("zebra")
+    assert "Chunks: 10" in result
+
+
+async def test_index_stats_reports_qdrant_error() -> None:
+    index_stats = _tool("index_stats")
+    store = AsyncMock()
+    store.collection_info.side_effect = RuntimeError("connection refused")
+
+    with (
+        patch("server.tools.admin.get_store", return_value=store),
+        patch("server.tools.admin.settings") as mock_settings,
+    ):
+        mock_settings.load_services.return_value = []
+        result = await index_stats()
+
+    assert "Could not reach Qdrant" in result
+    assert "connection refused" in result
+
+
+async def test_index_stats_includes_provider_endpoint() -> None:
+    index_stats = _tool("index_stats")
+    store = AsyncMock()
+    store.collection_info.return_value = {
+        "collection": "code_symbols",
+        "total_vectors": 100,
+        "vector_size": 768,
+        "status": "green",
+    }
+    svc = ServiceConfig(name="orders", github_repo="org/orders", exclude=[])
+
+    with (
+        patch("server.tools.admin.get_store", return_value=store),
+        patch("server.tools.admin.settings") as mock_settings,
+    ):
+        mock_settings.load_services.return_value = [svc]
+        mock_settings.embeddings_provider = "voyage"
+        result = await index_stats()
+
+    assert "**Embeddings provider**: voyage" in result
+    assert "https://api.voyageai.com/v1/embeddings" in result
+    assert "`orders` — `org/orders@main`" in result