When running functional tests, display the tool's stderr when a job ends in error.

lib/galaxy/web/controllers/dataset.py

@@ -50,6 +50,13 @@ class DatasetInterface( BaseController ):
         dataset = model.Dataset.get( id )
         return trans.fill_template( "dataset/errors.tmpl", dataset=dataset )
     
+    @web.expose
+    def stderr( self, trans, id ):
+        dataset = model.Dataset.get( id )
+        job = dataset.creating_job_associations[0].job
+        trans.response.set_content_type( 'text/plain' )
+        return job.stderr
+
     @web.expose
     def report_error( self, trans, id, email="no email provided", message="" ):
         smtp_server = trans.app.config.smtp_server

test/base/twilltestcase.py

@@ -210,9 +210,17 @@ class TwillTestCase( unittest.TestCase ):
         self.visit_page( "history_available" )
 
     """Functions associated with datasets (history items) and meta data"""
+    def get_job_stderr( self, id ):
+        self.visit_page( "dataset/stderr?id=%s" % id )
+        return self.last_page()
+
     def _assert_dataset_state( self, elem, state ):
-        assert elem.get( 'state' ) == state, \
-            "Expecting dataset state '%s' but is '%s'. Dataset blurb: %s" % ( state, elem.get('state'), elem.text.strip() )
+        if elem.get( 'state' ) != state:
+            errmsg = "Expecting dataset state '%s' but is '%s'. Dataset blurb: %s\n\n" % ( state, elem.get('state'), elem.text.strip() )
+            errmsg += "---------------------- >> begin tool stderr << -----------------------\n"
+            errmsg += self.get_job_stderr( elem.get( 'id' ) ) + "\n"
+            errmsg += "----------------------- >> end tool stderr << ------------------------\n"
+            raise AssertionError( errmsg )
 
     def check_metadata_for_string( self, patt, hid=None ):
         """Looks for 'patt' in the edit page when editing a dataset"""

test/functional/__init__.py

@@ -52,9 +52,18 @@ def setup():
             database_connection = os.environ['GALAXY_TEST_DBURI']
         else:
             database_connection = 'sqlite:///' + os.path.join( db_path, 'universe.sqlite' )
+        if 'GALAXY_TEST_RUNNERS' in os.environ:
+            start_job_runners = os.environ['GALAXY_TEST_RUNNERS']
+        else:
+            start_job_runners = None
+        if 'GALAXY_TEST_DEF_RUNNER' in os.environ:
+            default_cluster_job_runner = os.environ['GALAXY_TEST_DEF_RUNNER']
+        else:
+            default_cluster_job_runner = 'local:///'
     
         app = UniverseApplication( job_queue_workers = 5,
-                                   use_pbs = ( 'GALAXY_TEST_USE_PBS' in os.environ ),
+                                   start_job_runners = start_job_runners,
+                                   default_cluster_job_runner = default_cluster_job_runner,
                                    template_path = "templates",
                                    database_connection = database_connection,
                                    file_path = file_path,