Improvements for mule job handler testing. Ensure that the server

running the job is a mule. Added a test tool that will write Galaxy
app.config attributes to the output dataset.

test/base/driver_util.py

@@ -21,6 +21,7 @@ import nose.core
 import nose.loader
 import nose.plugins.manager
 from paste import httpserver
+from six.moves import shlex_quote
 
 from functional import database_contexts
 from galaxy.app import UniverseApplication as GalaxyUniverseApplication
@@ -657,6 +658,8 @@ def launch_uwsgi(kwargs, tempdir, prefix=DEFAULT_CONFIG_PREFIX, config_object=No
             yaml_config_path,
             "--module",
             "galaxy.webapps.galaxy.buildapp:uwsgi_app_factory()",
+            "--enable-threads",
+            "--die-on-term",
         ]
 
         handle_uwsgi_cli_command = getattr(
@@ -665,6 +668,8 @@ def launch_uwsgi(kwargs, tempdir, prefix=DEFAULT_CONFIG_PREFIX, config_object=No
         if handle_uwsgi_cli_command is not None:
             handle_uwsgi_cli_command(uwsgi_command)
 
+        # we don't want to quote every argument but we don't want to print unquoted ones either, so do this
+        log.info("Starting uwsgi with command line: %s", ' '.join([shlex_quote(x) for x in uwsgi_command]))
         p = subprocess.Popen(
             uwsgi_command,
             cwd=galaxy_root,

test/functional/tools/config_vars.xml

@@ -0,0 +1,25 @@
+<tool id="config_vars" name="config_vars" version="1.0.0">
+    <command>
+        #if str($var) != "__test_key":
+            echo "#echo getattr($__app__.config, str($var))#" > $out_file1
+        #else:
+            echo "__test_value" > $out_file1
+        #end if
+    </command>
+    <inputs>
+        <param name="var" value="__test_key" type="text" />
+    </inputs>
+    <outputs>
+        <data name="out_file1" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="var" value="__test_key" />
+            <output name="out_file1">
+                <assert_contents>
+                    <has_line line="__test_value" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+</tool>

test/functional/tools/samples_tool_conf.xml

@@ -118,6 +118,7 @@
   <tool file="cheetah_problem_unbound_var_input.xml" />
   <tool file="cheetah_problem_syntax_error.xml" />
   <tool file="python_environment_problem.xml" />
+  <tool file="config_vars.xml" />
 
   <tool file="multiple_versions_v01.xml" />
   <tool file="multiple_versions_v02.xml" />

test/integration/test_mules_as_job_handlers.py

@@ -17,13 +17,27 @@ class MulesAsJobHandlersIntegrationTestCase(integration_util.IntegrationTestCase
     @classmethod
     def handle_uwsgi_cli_command(cls, command):
         command.extend([
+            "--py-call-osafterfork",
             "--mule=lib/galaxy/main.py",
             "--farm=job-handlers:1",
         ])
 
     def test_tool_simple_constructs(self):
+        tool_id = 'config_vars'
+        expect_server_name = 'main.mule'
         dataset_populator = DatasetPopulator(self.galaxy_interactor)
         history_id = dataset_populator.new_history()
-        dataset_populator.new_dataset(
-            history_id, contents="test 1 2 3", file_type="txt", wait=True
+        payload = dataset_populator.run_tool(
+            tool_id=tool_id,
+            inputs={'var': 'server_name'},
+            history_id=history_id,
+        )
+        dataset_id = payload['outputs'][0]['id']
+        dataset_populator.wait_for_dataset(history_id, dataset_id, assert_ok=True)
+        output = dataset_populator.get_history_dataset_content(history_id, dataset_id=dataset_id).strip()
+        assert output.startswith(expect_server_name), (
+            "Job handler's server name '{output}' does not start with expected string '{expected}'".format(
+                output=output,
+                expected=expect_server_name,
+            )
         )