Fix the dataset controller's stderr method and add one for stdout. Link to

both from the dataset info page.  The functional tests will now provide output
of these on tool test failure.  The functional tests can now use
tool_dependency_dir as well.

lib/galaxy/web/controllers/dataset.py

@@ -154,10 +154,24 @@ class DatasetInterface( BaseUIController, UsesAnnotations, UsesHistory, UsesHist
         hda = trans.sa_session.query( model.HistoryDatasetAssociation ).get( id )
         return trans.fill_template( "dataset/errors.mako", hda=hda )
     @web.expose
-    def stderr( self, trans, id ):
-        dataset = trans.sa_session.query( model.HistoryDatasetAssociation ).get( id )
-        job = dataset.creating_job_associations[0].job
+    def stdout( self, trans, dataset_id=None, **kwargs ):
         trans.response.set_content_type( 'text/plain' )
+        try:
+            hda = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.security.decode_id( dataset_id ) )
+            assert hda and trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset )
+            job = hda.creating_job_associations[0].job
+        except:
+            return "Invalid dataset ID or you are not allowed to access this dataset"
+        return job.stdout
+    @web.expose
+    def stderr( self, trans, dataset_id=None, **kwargs ):
+        trans.response.set_content_type( 'text/plain' )
+        try:
+            hda = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.security.decode_id( dataset_id ) )
+            assert hda and trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset )
+            job = hda.creating_job_associations[0].job
+        except:
+            return "Invalid dataset ID or you are not allowed to access this dataset"
         return job.stderr
     @web.expose
     def report_error( self, trans, id, email='', message="" ):

scripts/functional_tests.py

@@ -58,6 +58,7 @@ def main():
     tool_path = os.environ.get( 'GALAXY_TEST_TOOL_PATH', 'tools' )
     tool_config_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', 'tool_conf.xml.sample' )
     tool_data_table_config_path = 'tool_data_table_conf.xml'
+    tool_dependency_dir = os.environ.get( 'GALAXY_TOOL_DEPENDENCY_DIR', None )
     if os.path.exists( 'tool_data_table_conf.test.xml' ):
         tool_data_table_config_path = 'tool_data_table_conf.test.xml'
     if start_server:
@@ -149,6 +150,9 @@ def main():
         if not database_connection.startswith( 'sqlite://' ):
             kwargs['database_engine_option_max_overflow'] = '20'
 
+        if tool_dependency_dir is not None:
+            kwargs['tool_dependency_dir'] = tool_dependency_dir
+
         # Build the Universe Application
         app = UniverseApplication( job_queue_workers = 5,
                                    id_secret = 'changethisinproductiontoo',

test/base/twilltestcase.py

@@ -624,6 +624,14 @@ class TwillTestCase( unittest.TestCase ):
         fd,temp_prefix = tempfile.mkstemp(prefix='tmp',suffix=suffix)
         return temp_prefix
 
+    def get_history_dataset_stdout( self, hda_id ):
+        self.visit_page( "/datasets/%s/stdout" % hda_id )
+        return self.last_page()
+
+    def get_history_dataset_stderr( self, hda_id ):
+        self.visit_page( "/datasets/%s/stderr" % hda_id )
+        return self.last_page()
+
     def verify_dataset_correctness( self, filename, hid=None, wait=True, maxseconds=120, attributes=None ):
         """Verifies that the attributes and contents of a history item meet expectations"""
         if wait:

test/functional/test_toolbox.py

@@ -93,7 +93,19 @@ class ToolTestCase( TwillTestCase ):
             self.assertTrue( elem is not None )
             elem_hid = elem.get( 'hid' )
             elem_index += 1
-            self.verify_dataset_correctness( outfile, hid=elem_hid, maxseconds=testdef.maxseconds, attributes=attributes )
+            try:
+                self.verify_dataset_correctness( outfile, hid=elem_hid, maxseconds=testdef.maxseconds, attributes=attributes )
+            except Exception, e:
+                print '-----------'
+                print 'Job STDOUT:'
+                print '-----------'
+                print self.get_history_dataset_stdout( elem.get( 'id' ) )
+                print '-----------'
+                print 'Job STDERR:'
+                print '-----------'
+                print self.get_history_dataset_stderr( elem.get( 'id' ) )
+                print '-----------'
+                raise
         self.delete_history( id=self.security.encode_id( latest_history.id ) )
 
     def __expand_grouping( self, tool_inputs, declared_inputs, prefix='' ):