From 995a8f621be82c32d97d8be9eb68126530ede6dc Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 4 May 2026 16:26:24 +0200
Subject: [PATCH] Add integration test for tool source storage and LazyToolBox

End-to-end test that boots Galaxy through the composite store +
LazyToolBox path and verifies tools are discoverable via /api/tools,
covering the wiring exercised by all of the preceding commits.
---
 test/integration/test_tool_source_storage.py | 113 +++++++++++++++++++
 1 file changed, 113 insertions(+)
 create mode 100644 test/integration/test_tool_source_storage.py

diff --git a/test/integration/test_tool_source_storage.py b/test/integration/test_tool_source_storage.py
new file mode 100644
index 00000000000..8a2623beb67
--- /dev/null
+++ b/test/integration/test_tool_source_storage.py
@@ -0,0 +1,113 @@
+"""Integration tests for tool source storage backends.
+
+These tests configure Galaxy to use different tool source storage backends
+and verify that the toolbox boots and serves tools through the API.
+Dataset uploads / job execution are exercised by Galaxy's general
+integration suite — these tests focus only on the tool source storage
+plumbing.
+"""
+
+import os
+import tempfile
+
+from galaxy_test.driver import integration_util
+
+
+class BaseToolSourceStorageIntegrationTestCase(integration_util.IntegrationTestCase):
+    """Base class for tool source storage integration tests."""
+
+    framework_tool_and_types = True
+
+    def _test_api_tools_list(self):
+        response = self._get("tools")
+        self._assert_status_code_is(response, 200)
+        tools = response.json()
+        assert len(tools) > 0, "Expected at least one tool to be loaded"
+
+    def _test_api_tools_show(self, tool_id: str = "cat1"):
+        response = self._get(f"tools/{tool_id}")
+        self._assert_status_code_is(response, 200)
+        tool_info = response.json()
+        assert tool_info["id"] == tool_id
+
+
+class TestDatabaseToolSourceStorage(BaseToolSourceStorageIntegrationTestCase):
+    """Integration tests with database tool source storage backend."""
+
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        super().handle_galaxy_config_kwds(config)
+        config["tool_source_store"] = "database"
+
+    def test_api_tools_list(self):
+        self._test_api_tools_list()
+
+    def test_api_tools_show(self):
+        self._test_api_tools_show()
+
+    def test_default_store_is_database_backend(self):
+        from galaxy.tool_source_store.database import DatabaseToolSourceStore
+
+        assert isinstance(self._app.tool_source_store, DatabaseToolSourceStore)
+
+
+class TestCompositeToolSourceStorage(BaseToolSourceStorageIntegrationTestCase):
+    """Galaxy boots with a default DB store + a per-conf read-only sqlite store.
+
+    Verifies the composite wiring: a tool_conf carrying ``store="cvmfs_main"``
+    plus ``use_lazy_toolbox: true`` causes ``build_tool_source_store`` to wrap
+    the default backend in a composite store.
+    """
+
+    _sqlite_path: str
+    _conf_path: str
+    _tmpdir: str
+
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        super().handle_galaxy_config_kwds(config)
+        cls._tmpdir = tempfile.mkdtemp(prefix="composite_tss_")
+        cls._sqlite_path = os.path.join(cls._tmpdir, "sources.sqlite")
+
+        from galaxy.tool_source_store.sqlalchemy import SqlAlchemyToolSourceStore
+
+        SqlAlchemyToolSourceStore(path=cls._sqlite_path).count()
+
+        cls._conf_path = os.path.join(cls._tmpdir, "extra_tool_conf.xml")
+        with open(cls._conf_path, "w") as f:
+            f.write('<?xml version="1.0"?>\n<toolbox store="cvmfs_main"/>\n')
+
+        config["tool_source_store"] = "database"
+        config["use_lazy_toolbox"] = True
+        existing_confs = config.get("tool_config_file") or "config/tool_conf.xml.sample"
+        if isinstance(existing_confs, str):
+            config["tool_config_file"] = f"{existing_confs},{cls._conf_path}"
+        else:
+            config["tool_config_file"] = list(existing_confs) + [cls._conf_path]
+        config["tool_source_stores"] = {
+            "cvmfs_main": {
+                "backend": "sqlalchemy",
+                "path": cls._sqlite_path,
+                "read_only": True,
+            }
+        }
+
+    def test_composite_store_is_wired(self):
+        # The boot path must produce a CompositeToolSourceStore when a
+        # tool_conf opts into a named per-conf store and use_lazy_toolbox
+        # is enabled. Verifying the live app's store directly is more
+        # robust than relying on /api/tools, which depends on whether the
+        # store was populated in advance.
+        from galaxy.tool_source_store.composite import CompositeToolSourceStore
+
+        assert isinstance(self._app.tool_source_store, CompositeToolSourceStore)
+
+    def test_api_tools_list_populated_via_bootstrap(self):
+        # With use_lazy_toolbox=true and an empty store, LazyToolBox
+        # auto-bootstraps from the configured tool confs on first boot;
+        # /api/tools must therefore return a non-empty tool list.
+        response = self._get("tools")
+        self._assert_status_code_is(response, 200)
+        tools = response.json()
+        assert isinstance(tools, list)
+        assert len(tools) > 0, "Bootstrap should have populated the store with framework tools"