Merge branch 'dev' of git://github.com/galaxyproject/galaxy into ts_a…

…pi_backbone

config/openid_conf.xml.sample

@@ -1,8 +1,7 @@
 <?xml version="1.0"?>
 <openid>
-    <provider file="google.xml" />
+    <provider file="genomespace.xml" />
     <provider file="yahoo.xml" />
     <provider file="aol.xml" />
     <provider file="launchpad.xml" />
-    <provider file="genomespace.xml" />
 </openid>

lib/galaxy/datatypes/data.py

@@ -129,7 +129,7 @@ def get_raw_data( self, dataset ):
         try:
             return open(dataset.file_name, 'rb').read(-1)
         except OSError:
-            log.exception('%s reading a file that does not exist %s' % (self.__class__.__name__, dataset.file_name))
+            log.exception('%s reading a file that does not exist %s', self.__class__.__name__, dataset.file_name)
             return ''
 
     def dataset_content_needs_grooming( self, file_name ):
@@ -229,7 +229,7 @@ def _archive_main_file(self, archive, display_name, data_filename):
             archive.add(data_filename, archname)
         except IOError:
             error = True
-            log.exception("Unable to add composite parent %s to temporary library download archive" % data_filename)
+            log.exception("Unable to add composite parent %s to temporary library download archive", data_filename)
             msg = "Unable to create archive for download, please report this error"
             messagetype = "error"
         return error, msg, messagetype
@@ -284,7 +284,7 @@ def _archive_composite_dataset( self, trans, data=None, **kwd ):
                                 archive.add( fpath, rpath )
                             except IOError:
                                 error = True
-                                log.exception( "Unable to add %s to temporary library download archive" % rpath)
+                                log.exception( "Unable to add %s to temporary library download archive", rpath)
                                 msg = "Unable to create archive for download, please report this error"
                                 continue
                 if not error:
@@ -439,7 +439,7 @@ def remove_display_app(self, app_id):
         try:
             del self.supported_display_apps[app_id]
         except:
-            log.exception('Tried to remove display app %s from datatype %s, but this display app is not declared.' % ( type, self.__class__.__name__ ) )
+            log.exception('Tried to remove display app %s from datatype %s, but this display app is not declared.', type, self.__class__.__name__ )
 
     def clear_display_apps( self ):
         self.supported_display_apps = {}
@@ -477,7 +477,7 @@ def as_display_type(self, dataset, type, **kwd):
             if type in self.get_display_types():
                 return getattr(self, self.supported_display_apps[type]['file_function'])(dataset, **kwd)
         except:
-            log.exception('Function %s is referred to in datatype %s for displaying as type %s, but is not accessible' % (self.supported_display_apps[type]['file_function'], self.__class__.__name__, type) )
+            log.exception('Function %s is referred to in datatype %s for displaying as type %s, but is not accessible', self.supported_display_apps[type]['file_function'], self.__class__.__name__, type )
         return "This display type (%s) is not implemented for this datatype (%s)." % ( type, dataset.ext)
 
     def get_display_links( self, dataset, type, app, base_url, target_frame='_blank', **kwd ):
@@ -491,8 +491,8 @@ def get_display_links( self, dataset, type, app, base_url, target_frame='_blank'
             if app.config.enable_old_display_applications and type in self.get_display_types():
                 return target_frame, getattr( self, self.supported_display_apps[type]['links_function'] )( dataset, type, app, base_url, **kwd )
         except:
-            log.exception( 'Function %s is referred to in datatype %s for generating links for type %s, but is not accessible'
-                           % ( self.supported_display_apps[type]['links_function'], self.__class__.__name__, type ) )
+            log.exception( 'Function %s is referred to in datatype %s for generating links for type %s, but is not accessible',
+                           self.supported_display_apps[type]['links_function'], self.__class__.__name__, type )
         return target_frame, []
 
     def get_converter_types(self, original_dataset, datatypes_registry):

lib/galaxy/datatypes/registry.py

@@ -187,7 +187,7 @@ def __import_module( full_path, datatype_module, datatype_class_name ):
                                 datatype_module = fields[ 0 ]
                                 datatype_class_name = fields[ 1 ]
                             except Exception as e:
-                                self.log.exception( 'Error parsing datatype definition for dtype %s: %s' % ( str( dtype ), str( e ) ) )
+                                self.log.exception( 'Error parsing datatype definition for dtype %s', str( dtype ) )
                                 ok = False
                             if ok:
                                 datatype_class = None
@@ -217,13 +217,13 @@ def __import_module( full_path, datatype_module, datatype_class_name ):
                                         datatype_class = getattr( module, datatype_class_name )
                                         self.log.debug( 'Retrieved datatype module %s:%s from the datatype registry.' % ( str( datatype_module ), datatype_class_name ) )
                                     except Exception as e:
-                                        self.log.exception( 'Error importing datatype module %s: %s' % ( str( datatype_module ), str( e ) ) )
+                                        self.log.exception( 'Error importing datatype module %s', str( datatype_module ) )
                                         ok = False
                         elif type_extension is not None:
                             try:
                                 datatype_class = self.datatypes_by_extension[ type_extension ].__class__
                             except Exception as e:
-                                self.log.exception( 'Error determining datatype_class for type_extension %s: %s' % ( str( type_extension ), str( e ) ) )
+                                self.log.exception( 'Error determining datatype_class for type_extension %s', str( type_extension ) )
                                 ok = False
                         if ok:
                             if not deactivate:
@@ -324,7 +324,7 @@ def _load_build_sites( self, root ):
         def load_build_site( build_site_config ):
             # Take in either an XML element or simple dictionary from YAML and add build site for this.
             if not (build_site_config.get( 'type' ) and build_site_config.get( 'file' )):
-                self.log.exception( "Site is missing required 'type' and 'file' attributes: %s" )
+                self.log.exception( "Site is missing required 'type' and 'file' attributes" )
                 return
 
             site_type = build_site_config.get( 'type' )
@@ -397,7 +397,7 @@ def load_datatype_sniffers( self, root, deactivate=False, handling_proprietary_d
                         datatype_class_name = fields[ 1 ]
                         module = None
                     except Exception as e:
-                        self.log.exception( 'Error determining datatype class or module for dtype %s: %s' % ( str( dtype ), str( e ) ) )
+                        self.log.exception( 'Error determining datatype class or module for dtype %s', str( dtype ) )
                         ok = False
                     if ok:
                         if handling_proprietary_datatypes:
@@ -413,13 +413,13 @@ def load_datatype_sniffers( self, root, deactivate=False, handling_proprietary_d
                                 for comp in datatype_module.split( '.' )[ 1: ]:
                                     module = getattr( module, comp )
                             except Exception as e:
-                                self.log.exception( "Error importing datatype class for '%s': %s" % ( str( dtype ), str( e ) ) )
+                                self.log.exception( "Error importing datatype class for '%s'", str( dtype ) )
                                 ok = False
                         if ok:
                             try:
                                 aclass = getattr( module, datatype_class_name )()
                             except Exception as e:
-                                self.log.exception( 'Error calling method %s from class %s: %s', str( datatype_class_name ), str( module ), str( e ) )
+                                self.log.exception( 'Error calling method %s from class %s', str( datatype_class_name ), str( module ) )
                                 ok = False
                             if ok:
                                 if deactivate:
@@ -560,11 +560,11 @@ def load_datatype_converters( self, toolbox, installed_repository_dict=None, dea
                         self.datatype_converters[ source_datatype ] = odict()
                     self.datatype_converters[ source_datatype ][ target_datatype ] = converter
                     self.log.debug( "Loaded converter: %s", converter.id )
-            except Exception as e:
+            except Exception:
                 if deactivate:
-                    self.log.exception( "Error deactivating converter from (%s): %s" % ( converter_path, str( e ) ) )
+                    self.log.exception( "Error deactivating converter from (%s)" % converter_path )
                 else:
-                    self.log.exception( "Error loading converter (%s): %s" % ( converter_path, str( e ) ) )
+                    self.log.exception( "Error loading converter (%s)" % converter_path )
 
     def load_display_applications( self, app, installed_repository_dict=None, deactivate=False ):
         """
@@ -628,11 +628,11 @@ def load_display_applications( self, app, installed_repository_dict=None, deacti
                             if inherit and ( self.datatypes_by_extension[ extension ], display_app ) not in self.inherit_display_application_by_class:
                                 self.inherit_display_application_by_class.append( ( self.datatypes_by_extension[ extension ], display_app ) )
                             self.log.debug( "Loaded display application '%s' for datatype '%s', inherit=%s." % ( display_app.id, extension, inherit ) )
-                except Exception as e:
+                except Exception:
                     if deactivate:
-                        self.log.exception( "Error deactivating display application (%s): %s" % ( config_path, str( e ) ) )
+                        self.log.exception( "Error deactivating display application (%s)" % config_path )
                     else:
-                        self.log.exception( "Error loading display application (%s): %s" % ( config_path, str( e ) ) )
+                        self.log.exception( "Error loading display application (%s)" % config_path )
         # Handle display_application subclass inheritance.
         for extension, d_type1 in self.datatypes_by_extension.iteritems():
             for d_type2, display_app in self.inherit_display_application_by_class:

lib/galaxy/datatypes/tabular.py

@@ -167,7 +167,7 @@ def make_html_peek_header( self, dataset, skipchars=None, column_names=None, col
                 out.append( '</th>' )
             out.append( '</tr>' )
         except Exception as exc:
-            log.exception( 'make_html_peek_header failed on HDA %s' % dataset.id )
+            log.exception( 'make_html_peek_header failed on HDA %s', dataset.id )
             raise Exception( "Can't create peek header %s" % str( exc ) )
         return "".join( out )
 
@@ -198,7 +198,7 @@ def make_html_peek_rows( self, dataset, skipchars=None, **kwargs ):
                             out.append( '<td>%s</td>' % escape( elem ) )
                         out.append( '</tr>' )
         except Exception as exc:
-            log.exception( 'make_html_peek_rows failed on HDA %s' % dataset.id )
+            log.exception( 'make_html_peek_rows failed on HDA %s', dataset.id )
             raise Exception( "Can't create peek rows %s" % str( exc ) )
         return "".join( out )
 

lib/galaxy/datatypes/text.py

@@ -150,7 +150,7 @@ def _display_data_trusted(self, trans, dataset, preview=False, filename=None, to
                 ofilename = '%s.html' % ofilename
             except:
                 ofilename = dataset.file_name
-                log.exception( 'Command "%s" failed. Could not convert the Jupyter Notebook to HTML, defaulting to plain text.' % cmd )
+                log.exception( 'Command "%s" failed. Could not convert the Jupyter Notebook to HTML, defaulting to plain text.', cmd )
             return open( ofilename )
 
     def set_meta( self, dataset, **kwd ):

lib/galaxy/jobs/__init__.py

@@ -631,8 +631,8 @@ def get_job_runner_plugins(self, handler_id):
                 try:
                     rval[id] = runner_class( self.app, runner[ 'workers' ], **runner.get( 'kwds', {} ) )
                 except TypeError:
-                    log.exception( "Job runner '%s:%s' has not been converted to a new-style runner or encountered TypeError on load"
-                                   % ( module_name, class_name ) )
+                    log.exception( "Job runner '%s:%s' has not been converted to a new-style runner or encountered TypeError on load",
+                                   module_name, class_name )
                     rval[id] = runner_class( self.app )
                 log.debug( "Loaded job runner '%s:%s' as '%s'" % ( module_name, class_name, id ) )
         return rval
@@ -1443,7 +1443,7 @@ def cleanup( self, delete_files=True ):
             if delete_files:
                 self.app.object_store.delete(self.get_job(), base_dir='job_work', entire_dir=True, dir_only=True, obj_dir=True)
         except:
-            log.exception( "Unable to cleanup job %d" % self.job_id )
+            log.exception( "Unable to cleanup job %d", self.job_id )
 
     def _collect_extra_files(self, dataset, job_working_directory):
         temp_file_path = os.path.join( job_working_directory, "dataset_%s_files" % ( dataset.id ) )

lib/galaxy/jobs/deferred/__init__.py

@@ -40,7 +40,7 @@ def _load_plugins( self ):
                 try:
                     module = __import__( module_name )
                 except:
-                    log.exception( 'Deferred job plugin appears to exist but is not loadable: %s' % module_name )
+                    log.exception( 'Deferred job plugin appears to exist but is not loadable: %s', module_name )
                     continue
                 for comp in module_name.split( "." )[1:]:
                     module = getattr( module, comp )
@@ -105,16 +105,16 @@ def __monitor_step( self ):
             if job.is_check_time:
                 try:
                     job_state = self.plugins[job.plugin].check_job( job )
-                except Exception as e:
+                except Exception:
                     self.__fail_job( job )
-                    log.exception( 'Set deferred job %s to error because of an exception in check_job(): %s' % ( job.id, str( e ) ) )
+                    log.exception( 'Set deferred job %s to error because of an exception in check_job()' % job.id )
                     continue
                 if job_state == self.job_states.READY:
                     try:
                         self.plugins[job.plugin].run_job( job )
-                    except Exception as e:
+                    except Exception:
                         self.__fail_job( job )
-                        log.exception( 'Set deferred job %s to error because of an exception in run_job(): %s' % ( job.id, str( e ) ) )
+                        log.exception( 'Set deferred job %s to error because of an exception in run_job()' % job.id )
                         continue
                 elif job_state == self.job_states.INVALID:
                     self.__fail_job( job )

lib/galaxy/jobs/handler.py

@@ -309,7 +309,7 @@ def __monitor_step( self ):
                     log.error( "(%d) Job in unknown state '%s'" % ( job.id, job_state ) )
                     new_waiting_jobs.append( job.id )
             except Exception:
-                log.exception( "failure running job %d" % job.id )
+                log.exception( "failure running job %d", job.id )
         # Update the waiting list
         if not self.track_jobs_in_database:
             self.waiting_jobs = new_waiting_jobs
@@ -784,8 +784,8 @@ def url_to_destination( self, url ):
         runner_name = url.split(':', 1)[0]
         try:
             return self.job_runners[runner_name].url_to_destination(url)
-        except Exception as e:
-            log.exception("Unable to convert legacy job runner URL '%s' to job destination, destination will be the '%s' runner with no params: %s" % (url, runner_name, e))
+        except Exception:
+            log.exception("Unable to convert legacy job runner URL '%s' to job destination, destination will be the '%s' runner with no params", url, runner_name)
             return JobDestination(runner=runner_name)
 
     def put( self, job_wrapper ):

lib/galaxy/jobs/metrics/__init__.py

@@ -94,7 +94,7 @@ def pre_execute_commands(self, job_directory):
                 if plugin_commands:
                     commands.extend(util.listify(plugin_commands))
             except Exception:
-                log.exception("Failed to generate pre-execute commands for plugin %s" % plugin)
+                log.exception("Failed to generate pre-execute commands for plugin %s", plugin)
         return "\n".join([ c for c in commands if c ])
 
     def post_execute_commands(self, job_directory):
@@ -105,7 +105,7 @@ def post_execute_commands(self, job_directory):
                 if plugin_commands:
                     commands.extend(util.listify(plugin_commands))
             except Exception:
-                log.exception("Failed to generate post-execute commands for plugin %s" % plugin)
+                log.exception("Failed to generate post-execute commands for plugin %s", plugin)
         return "\n".join([ c for c in commands if c ])
 
     def collect_properties(self, job_id, job_directory):
@@ -116,7 +116,7 @@ def collect_properties(self, job_id, job_directory):
                 if properties:
                     per_plugin_properites[ plugin.plugin_type ] = properties
             except Exception:
-                log.exception("Failed to collect job properties for plugin %s" % plugin)
+                log.exception("Failed to collect job properties for plugin %s", plugin)
         return per_plugin_properites
 
     def __plugins_from_source(self, plugins_source):

lib/galaxy/jobs/runners/__init__.py

@@ -247,7 +247,7 @@ def get_work_dir_outputs( self, job_wrapper, job_working_directory=None, tool_wo
                         output_pairs.append( ( source_file, destination ) )
                     else:
                         # Security violation.
-                        log.exception( "from_work_dir specified a location not in the working directory: %s, %s" % ( source_file, job_wrapper.working_directory ) )
+                        log.exception( "from_work_dir specified a location not in the working directory: %s, %s", source_file, job_wrapper.working_directory )
         return output_pairs
 
     def _walk_dataset_outputs( self, job ):

lib/galaxy/jobs/runners/local.py

@@ -120,7 +120,7 @@ def queue_job( self, job_wrapper ):
             stderr_file.close()
             log.debug('execution finished: %s' % command_line)
         except Exception:
-            log.exception("failure running job %d" % job_wrapper.job_id)
+            log.exception("failure running job %d", job_wrapper.job_id)
             self._fail_job_local(job_wrapper, "failure running job")
             return