Automated merge

lib/tool_shed/util/shed_util_common.py

@@ -148,7 +148,8 @@ def build_tool_dependencies_select_field( trans, tool_shed_repository, name, mul
     """Method called from Galaxy to generate the current list of tool dependency ids for an installed tool shed repository."""
     tool_dependencies_select_field = SelectField( name=name, multiple=multiple, display=display )
     for tool_dependency in tool_shed_repository.tool_dependencies:
-        if uninstalled and tool_dependency.status != trans.model.ToolDependency.installation_status.UNINSTALLED:
+        if uninstalled and tool_dependency.status not in [ trans.model.ToolDependency.installation_status.NEVER_INSTALLED,
+                                                           trans.model.ToolDependency.installation_status.UNINSTALLED ]:
             continue
         option_label = '%s version %s' % ( str( tool_dependency.name ), str( tool_dependency.version ) )
         option_value = trans.security.encode_id( tool_dependency.id )

templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako

@@ -35,7 +35,8 @@ ${render_galaxy_repository_actions( repository )}
                     else:
                         error_message = ''
                     if not can_install:
-                        if tool_dependency.status in [ trans.model.ToolDependency.installation_status.UNINSTALLED ]:
+                        if tool_dependency.status in [ trans.model.ToolDependency.installation_status.NEVER_INSTALLED,
+                                                       trans.model.ToolDependency.installation_status.UNINSTALLED ]:
                             can_install = True
                     if not can_uninstall:
                         if tool_dependency.status not in [ trans.model.ToolDependency.installation_status.UNINSTALLED ]:

test/install_and_test_tool_shed_repositories/functional_tests.py

@@ -275,6 +275,7 @@ def execute_uninstall_method( app, deactivate_only=False ):
 
 def extract_log_data( test_result, from_tool_test=True ):
     '''Extract any useful data from the test_result.failures and test_result.errors attributes.'''
+    log_data = []
     for failure in test_result.failures + test_result.errors:
         # Record the twill test identifier and information about the tool, so the repository owner can discover which test is failing.
         test_id = str( failure[0] )
@@ -314,7 +315,8 @@ def extract_log_data( test_result, from_tool_test=True ):
         for output_type in [ 'stderr', 'traceback' ]:
             if output_type in tmp_output:
                 test_status[ output_type ] = '\n'.join( tmp_output[ output_type ] )
-        return test_status
+        log_data.append( test_status )
+    return log_data
 
 def get_api_url( base, parts=[], params=None, key=None ):
     if 'api' in parts and parts.index( 'api' ) != 0: