Merge pull request #1299 from mvdbeek/test_log_fixes

Fix printing planemo test logs
galaxyproject · Oct 20, 2022 · 75cbd3a · 75cbd3a
2 parents 2de34aa + ad9253f
commit 75cbd3a
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Showing 4 changed files with 24 additions and 26 deletions.
diff --git a/planemo/commands/cmd_serve.py b/planemo/commands/cmd_serve.py
@@ -40,4 +40,5 @@ def cli(ctx, uris, **kwds):
     paths = uris_to_paths(ctx, uris)
     runnables = for_paths(paths)
     kwds["galaxy_skip_client_build"] = kwds.pop("skip_client_build", False)
-    galaxy_serve(ctx, runnables, **kwds)
+    with galaxy_serve(ctx, runnables, **kwds):
+        pass
diff --git a/planemo/galaxy/config.py b/planemo/galaxy/config.py
@@ -44,7 +44,6 @@
 )
 from planemo.mulled import build_involucro_context
 from planemo.shed import tool_shed_url
-from planemo.virtualenv import DEFAULT_PYTHON_VERSION
 from .api import (
     DEFAULT_ADMIN_API_KEY,
     gi,
@@ -336,12 +335,7 @@ def config_join(*args):
         if not os.path.isdir(galaxy_root):
             _install_galaxy(ctx, galaxy_root, install_env, kwds)
 
-        if parse_version(kwds.get("galaxy_python_version") or DEFAULT_PYTHON_VERSION) >= parse_version("3"):
-            # on python 3 we use gunicorn,
-            # which requires 'main' as server name
-            server_name = "main"
-        else:
-            server_name = f"planemo{random.randint(0, 100000)}"
+        server_name = "main"
         # Once we don't have to support earlier than 18.01 - try putting these files
         # somewhere better than with Galaxy.
         log_file = f"{server_name}.log"
@@ -634,7 +628,7 @@ def _config_directory(ctx, **kwds):
     finally:
         cleanup = not kwds.get("no_cleanup", False)
         if created_config_directory and cleanup:
-            shutil.rmtree(config_directory)
+            shutil.rmtree(config_directory, ignore_errors=True)
 
 
 class GalaxyInterface(metaclass=abc.ABCMeta):

diff --git a/planemo/galaxy/serve.py b/planemo/galaxy/serve.py
@@ -13,17 +13,20 @@
 from .run import run_galaxy_command
 
 
+@contextlib.contextmanager
 def serve(ctx, runnables=None, **kwds):
     if runnables is None:
         runnables = []
     """Serve a Galaxy instance with artifacts defined by paths."""
     try:
-        return _serve(ctx, runnables, **kwds)
+        with _serve(ctx, runnables, **kwds) as config:
+            yield config
     except Exception as e:
         ctx.vlog("Problem serving Galaxy", exception=e)
         raise
 
 
+@contextlib.contextmanager
 def _serve(ctx, runnables, **kwds):
     engine = kwds.get("engine", "galaxy")
     if engine == "docker_galaxy":
@@ -67,7 +70,7 @@ def _serve(ctx, runnables, **kwds):
                 os.symlink(real_pid_file, kwds["pid_file"])
             else:
                 io.warn("Can't find Galaxy pid file [%s] to link" % real_pid_file)
-        return config
+        yield config
 
 
 @contextlib.contextmanager
@@ -76,10 +79,10 @@ def serve_daemon(ctx, runnables=None, **kwds):
     if runnables is None:
         runnables = []
     config = None
+    kwds["daemon"] = True
     try:
-        kwds["daemon"] = True
-        config = serve(ctx, runnables, **kwds)
-        yield config
+        with serve(ctx, runnables, **kwds) as config:
+            yield config
     finally:
         if config:
             if ctx.verbose:

diff --git a/tests/test_galaxy_serve.py b/tests/test_galaxy_serve.py
@@ -29,17 +29,17 @@ def test_serve_daemon(self):
         """Test serving a galaxy tool via a daemon Galaxy process."""
         port = network_util.get_free_port()
         cat_path = os.path.join(TEST_REPOS_DIR, "single_tool", "cat.xml")
-        config = galaxy_serve(
+        with galaxy_serve(
             self.test_context,
             [for_path(cat_path)],
             install_galaxy=True,
             galaxy_branch=target_galaxy_branch(),
             port=port,
             daemon=True,
             no_dependency_resolution=True,
-        )
-        _assert_service_up(config)
-        config.kill()
+        ) as config:
+            _assert_service_up(config)
+            config.kill()
         _assert_service_down(config)
 
     @skip_if_environ("PLANEMO_SKIP_REDUNDANT_TESTS")  # redundant with test_cmd_serve -> test_serve_workflow
@@ -52,7 +52,7 @@ def test_serve_workflow(self):
         cat = os.path.join(PROJECT_TEMPLATES_DIR, "demo", "cat.xml")
         workflow = os.path.join(TEST_DATA_DIR, "wf1.gxwf.yml")
         extra_tools = [random_lines, cat]
-        config = galaxy_serve(
+        with galaxy_serve(
             self.test_context,
             [for_path(workflow)],
             install_galaxy=True,
@@ -61,13 +61,13 @@ def test_serve_workflow(self):
             daemon=True,
             extra_tools=extra_tools,
             no_dependency_resolution=True,
-        )
-        _assert_service_up(config)
-        user_gi = config.user_gi
-        assert user_gi.tools.show_tool("random_lines1")
-        assert len(user_gi.workflows.get_workflows()) == 1
-        config.kill()
-        _assert_service_down(config)
+        ) as config:
+            _assert_service_up(config)
+            user_gi = config.user_gi
+            assert user_gi.tools.show_tool("random_lines1")
+            assert len(user_gi.workflows.get_workflows()) == 1
+            config.kill()
+            _assert_service_down(config)
 
 
 def _assert_service_up(config):