From 44344fe2e0baf7e58665609e2a3f9e0a3ed82a0f Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Tue, 6 Dec 2011 11:29:02 -0500
Subject: [PATCH] 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 | 20 +++++++++++++++++---
 scripts/functional_tests.py           |  4 ++++
 test/base/twilltestcase.py            |  8 ++++++++
 test/functional/test_toolbox.py       | 14 +++++++++++++-
 4 files changed, 42 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/web/controllers/dataset.py b/lib/galaxy/web/controllers/dataset.py
index 449bf06dd00..c7e86d166ff 100644
--- a/lib/galaxy/web/controllers/dataset.py
+++ b/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="" ):
diff --git a/scripts/functional_tests.py b/scripts/functional_tests.py
index dc8fa1a754d..66f2ad682f6 100644
--- a/scripts/functional_tests.py
+++ b/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',
diff --git a/test/base/twilltestcase.py b/test/base/twilltestcase.py
index fff6c754f7e..c12654c5eb8 100644
--- a/test/base/twilltestcase.py
+++ b/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:
diff --git a/test/functional/test_toolbox.py b/test/functional/test_toolbox.py
index 1843ada7ede..4a2b53eae07 100644
--- a/test/functional/test_toolbox.py
+++ b/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='' ):