Merge pull request #99 from jmchilton/travis_enhance_1

TraivsCI: More comprehensive checks for *very* broken stuff.

.ci/flake8_wrapper.sh

@@ -2,6 +2,11 @@
 
 set -e
 
+# Run broad range of checks over specific white-listed files, this uses
+# the default checks defined in setup.cfg.
 while read p; do
     flake8 $(eval echo "$p")
 done <.ci/pep8_sources.txt
+
+# Look for obviously broken stuff lots more places.
+flake8 --select=E901,E902,F821,F822,F823,F831 --exclude lib/galaxy/util/pastescript/serve.py lib/{galaxy,tool_shed} test/{api,unit}

lib/galaxy/external_services/service.py

@@ -210,19 +210,5 @@ class PopulatedExternalService( object ):
         assert action, 'Action not found: %s' % actions_list
         return action
 
-    def get_action_links( self ):
-        rval = []
-        param_dict = {}
-        param_dict['fields'] = Bunch( **self.service_instance.form_values.content )
-        param_dict['item'] = self.item
-        for item in self.service.items:
-            if isinstance( item, ExternalServiceParameter ):
-                param_dict[ item.name ] = item.get_value( param_dict )
-            elif isinstance( item, ExternalServiceAction ):
-                rval.append( item.get_action_access_link( self.item, trans, param_dict ) )
-            elif isinstance( item, ExternalServiceActionsGroup ):
-                rval.extend( item.populate( self.service_instance, item, param_dict ).get_action_links() )
-            else:
-                raise 'unknown item type found'
     def __nonzero__( self ):
         return self.actions.has_action()

lib/galaxy/webapps/galaxy/controllers/library_common.py

@@ -1432,7 +1432,6 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
                 message = 'Select at least one dataset from the list of active datasets in your current history'
                 status = 'error'
                 upload_option = kwd.get( 'upload_option', 'import_from_history' )
-                widgets = self._get_populated_widgets( folder )
                 # Send list of data formats to the upload form so the "extension" select list can be populated dynamically
                 file_formats = trans.app.datatypes_registry.upload_file_formats
                 # Send list of genome builds to the form so the "dbkey" select list can be populated dynamically
@@ -1459,7 +1458,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
                                             last_used_build=last_used_build,
                                             roles_select_list=roles_select_list,
                                             history=history,
-                                            widgets=widgets,
+                                            widgets=[],
                                             template_id=template_id,
                                             space_to_tab=space_to_tab,
                                             link_data_only=link_data_only,
@@ -1515,16 +1514,6 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
                 upload_option_select_list.add_option( option_label, option_value, selected=option_value==upload_option )
         return upload_option_select_list
 
-    def _get_populated_widgets( self, folder ):
-        # See if we have any inherited templates.
-        info_association, inherited = folder.get_info_association( inherited=True )
-        if info_association and info_association.inheritable:
-            widgets = folder.get_template_widgets( trans, get_contents=True )
-            # Retain contents of widget fields when form was submitted via refresh_on_change.
-            return self.populate_widgets_from_kwd( trans, widgets, **kwd )
-        else:
-            return []
-
     @web.expose
     def download_dataset_from_folder( self, trans, cntrller, id, library_id=None, **kwd ):
         """Catches the dataset id and displays file contents as directed"""
@@ -2584,8 +2573,8 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
             # Deny access if the user is not an admin and does not have the LIBRARY_MANAGE and DATASET_MANAGE_PERMISSIONS permissions.
             if not ( is_admin or \
                      ( trans.app.security_agent.can_manage_library_item( current_user_roles, item ) and
-                       trans.app.security_agent.can_manage_dataset( current_user_roles, library_dataset.library_dataset_dataset_association.dataset ) ) ):
-                message = "You are not authorized to manage permissions on library dataset (%s)." % escape( library_dataset.name )
+                       trans.app.security_agent.can_manage_dataset( current_user_roles, item.library_dataset_dataset_association.dataset ) ) ):
+                message = "You are not authorized to manage permissions on library dataset (%s)." % escape( item.name )
                 if cntrller == 'api':
                     return 403, message
                 return trans.response.send_redirect( web.url_for( controller='library_common',

lib/galaxy/webapps/tool_shed/api/repositories.py

@@ -12,6 +12,7 @@ from galaxy import util
 from galaxy import web
 from galaxy.exceptions import RequestParameterMissingException
 from galaxy.exceptions import RequestParameterInvalidException
+from galaxy.exceptions import InsufficientPermissionsException
 from galaxy.exceptions import ActionInputError
 from galaxy.exceptions import ObjectNotFound
 from galaxy.exceptions import MalformedId

lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py

@@ -46,11 +46,6 @@ class InstallEnvironment( object ):
         self.install_dir = install_dir
         self.tool_shed_repository_install_dir = tool_shed_repository_install_dir
 
-    def __call__( self ):
-        with settings( warn_only=True, **basic_util.get_env_var_values( self ) ):
-            with prefix( self.__setup_environment() ):
-                yield
-
     def add_env_shell_file_paths( self, paths ):
         for path in paths:
             self.env_shell_file_paths.append( str( path ) )

lib/tool_shed/scripts/api/export.py

@@ -25,7 +25,7 @@ def generate_repository_archive_filename( tool_shed_url, name, owner, changeset_
                                           export_repository_dependencies, use_tmp_archive_dir=False ):
     tool_shed = remove_protocol_from_tool_shed_url( tool_shed_url )
     file_type_str = basic_util.get_file_type_str( changeset_revision, file_type )
-    if self.export_repository_dependencies:
+    if export_repository_dependencies:
         repositories_archive_filename = '%s_%s_%s_%s_%s' % ( CAPSULE_WITH_DEPENDENCIES_FILENAME,
                                                              tool_shed,
                                                              name,

lib/tool_shed/scripts/api/import_capsule.py

@@ -14,7 +14,8 @@ method (they'll have to be created manually, which can be done after the import)
 Here is a working example of how to use this script to install a repository from the test tool shed.
 ./import_capsule.py -a <api key> -u http://localhost:9009 -c capsule_localhost_colon_9009_filter_test1_8923f52d5c6d.tar.gz
 """
-
+import logging
+log = logging.getLogger(__name__)
 import os
 import sys
 import argparse

lib/tool_shed/scripts/api/remove_repository_registry_entry.py

@@ -26,7 +26,7 @@ def main( options ):
             response_dict = submit( url, data, api_key=api_key, return_formatted=False )
             print response_dict
         else:
-            print "Invalid tool_shed: ", base_tool_shed_url, " name: ", name, " or owner: ", owner, "."
+            print "Invalid tool_shed: ", base_tool_shed_url, " name: ", options.name, " or owner: ", options.owner, "."
     else:
         print "An API key for an admin user in the Tool Shed is required to remove entries from the Tool Shed's repository registry."
 

lib/tool_shed/scripts/api/reset_metadata_on_repositories.py

@@ -11,7 +11,8 @@ usage: reset_metadata_on_repositories.py key <my_writable>
 Here is a working example of how to use this script to reset metadata on certain repositories in a specified Tool Shed.
 python ./reset_metadata_on_repositories.py -a 22be3b -m True -u http://localhost:9009/
 """
-
+import logging
+log = logging.getLogger(__name__)
 import argparse
 import os
 import sys

test/api/yaml_to_workflow.py

@@ -17,7 +17,7 @@ STEP_TYPE_ALIASES = {
 
 def yaml_to_workflow(has_yaml):
     as_python = yaml.load(has_yaml)
-    return python_to_workflow(as_path)
+    return python_to_workflow(as_python)
 
 
 def python_to_workflow(as_python):