Replace remaining print statements with log.*

lib/galaxy/app.py

@@ -30,7 +30,7 @@
 class UniverseApplication( object, config.ConfiguresGalaxyMixin ):
     """Encapsulates the state of a Universe application"""
     def __init__( self, **kwargs ):
-        print >> sys.stderr, "python path is: " + ", ".join( sys.path )
+        log.debug( "python path is: %s", ", ".join( sys.path ) )
         self.name = 'galaxy'
         self.new_installation = False
         # Read config file and check for errors

lib/galaxy/config.py

@@ -201,7 +201,7 @@ def __init__( self, **kwargs ):
                 with open( self.blacklist_file ) as blacklist:
                     self.blacklist_content = [ line.rstrip() for line in blacklist.readlines() ]
             except IOError:
-                print ( "CONFIGURATION ERROR: Can't open supplied blacklist file from path: " + str( self.blacklist_file ) )
+                log.error( "CONFIGURATION ERROR: Can't open supplied blacklist file from path: " + str( self.blacklist_file ) )
         self.smtp_server = kwargs.get( 'smtp_server', None )
         self.smtp_username = kwargs.get( 'smtp_username', None )
         self.smtp_password = kwargs.get( 'smtp_password', None )

lib/galaxy/model/__init__.py

@@ -2927,7 +2927,7 @@ def clear( self, purge=False, delete_dataset=True ):
             try:
                 os.unlink( self.file_name )
             except Exception, e:
-                print "Failed to purge associated file (%s) from disk: %s" % ( self.file_name, e )
+                log.error( "Failed to purge associated file (%s) from disk: %s" % ( self.file_name, e ) )
 
 
 DEFAULT_COLLECTION_NAME = "Unnamed Collection"

lib/galaxy/util/__init__.py

@@ -950,7 +950,7 @@ class DBNames( list ):
         man_builds = [(build, name) for name, build in man_builds]
         db_names = DBNames( db_names + man_builds )
     except Exception, e:
-        print "ERROR: Unable to read builds file:", e
+        log.error( "ERROR: Unable to read builds file: %s", str( e ) )
     if len(db_names) < 1:
         db_names = DBNames( [( db_names.default_value, db_names.default_name )] )
     return db_names
@@ -976,7 +976,7 @@ def read_build_sites( filename, check_builds=True ):
             except:
                 continue
     except:
-        print "ERROR: Unable to read builds for site file %s" % filename
+        log.error( "ERROR: Unable to read builds for site file %s", filename )
     return build_sites
 
 

lib/galaxy/webapps/galaxy/api/library_contents.py

@@ -400,7 +400,7 @@ def delete( self, trans, library_id, id, **kwd ):
             ld = self.get_library_dataset( trans, id, check_ownership=False, check_accessible=True )
             user_is_admin = trans.user_is_admin()
             can_modify = trans.app.security_agent.can_modify_library_item( trans.user.all_roles(), ld )
-            print 'is_admin: %s, can_modify: %s' % ( user_is_admin, can_modify )
+            log.debug( 'is_admin: %s, can_modify: %s',  user_is_admin, can_modify )
             if not ( user_is_admin or can_modify ):
                 trans.response.status = 403
                 rval.update({ 'error': 'Unauthorized to delete or purge this library dataset' })

lib/galaxy/webapps/galaxy/controllers/requests_common.py

@@ -1212,8 +1212,8 @@ def __save_samples( self, trans, cntrller, request, sample_widgets, saving_new_s
             redirect_action = 'edit_samples'
         # Check for duplicate sample names within the request
         self.__validate_sample_names( trans, cntrller, request, sample_widgets, **kwd )
-        print "SAVING SAMPLES!"
-        print "saving_new_samples is %s" % saving_new_samples
+        log.debug( "SAVING SAMPLES!" )
+        log.debug( "saving_new_samples is %s" % saving_new_samples )
         if not saving_new_samples:
             library = None
             folder = None
@@ -1874,8 +1874,8 @@ def __validate_request( self, trans, cntrller, request ):
         empty_sample_fields = []
         for s in request.samples:
             for field in request.type.sample_form.fields:
-                print "field:", field
-                print "svc:", s.values.content
+                log.debug("field: %s", field)
+                log.debug("svc: %s", s.values.content)
                 if field['required'] == 'required' and s.values.content[field['name']] in ['', None]:
                     empty_sample_fields.append((s.name, field['label']))
         if empty_fields or empty_sample_fields:

lib/galaxy/webapps/reports/app.py

@@ -4,12 +4,14 @@
 
 import galaxy.model
 from galaxy.web import security
+import logging
+log = logging.getLogger( __name__ )
 
 
 class UniverseApplication( object ):
     """Encapsulates the state of a Universe application"""
     def __init__( self, **kwargs ):
-        print >> sys.stderr, "python path is: " + ", ".join( sys.path )
+        log.debug( "python path is: %s", ", ".join( sys.path ) )
         self.name = "reports"
         # Read config file and check for errors
         self.config = config.Configuration( **kwargs )

lib/galaxy/webapps/tool_shed/app.py

@@ -13,13 +13,16 @@
 import tool_shed.repository_registry
 import tool_shed.repository_types.registry
 from tool_shed.grids.repository_grid_filter_manager import RepositoryGridFilterManager
+import logging
+log = logging.getLogger( __name__ )
+
 
 
 class UniverseApplication( object ):
     """Encapsulates the state of a Universe application"""
 
     def __init__( self, **kwd ):
-        print >> sys.stderr, "python path is: " + ", ".join( sys.path )
+        log.debug( "python path is: %s", ", ".join( sys.path ) )
         self.name = "tool_shed"
         # Read the tool_shed.ini configuration file and check for errors.
         self.config = config.Configuration( **kwd )
@@ -75,7 +78,7 @@ def __init__( self, **kwd ):
         self.repository_registry = tool_shed.repository_registry.Registry( self )
         #  used for cachebusting -- refactor this into a *SINGLE* UniverseApplication base.
         self.server_starttime = int(time.time())
-        print >> sys.stderr, "Tool shed hgweb.config file is: ", self.hgweb_config_manager.hgweb_config
+        log.debug( "Tool shed hgweb.config file is: %s", self.hgweb_config_manager.hgweb_config )
 
     def shutdown( self ):
         pass

lib/galaxy/webapps/tool_shed/framework/middleware/hg.py

@@ -25,7 +25,7 @@
 class Hg( object ):
 
     def __init__( self, app, config ):
-        print "mercurial version is:", mercurial.__version__.version
+        log.debug( "mercurial version is: %s", mercurial.__version__.version )
         self.app = app
         self.config = config
         # Authenticate this mercurial request using basic authentication

lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py

@@ -293,7 +293,7 @@ def get_repository_dependencies_for_installed_tool_shed_repository( self, app, r
         try:
             raw_text = common_util.tool_shed_get( app, tool_shed_url, pathspec=pathspec, params=params )
         except Exception, e:
-            print "The URL\n%s\nraised the exception:\n%s\n" % ( common_util.url_join( tool_shed_url, pathspec=pathspec, params=params ), str( e ) )
+            log.error("The URL\n%s\nraised the exception:\n%s\n", common_util.url_join( tool_shed_url, pathspec=pathspec, params=params ), str( e ) )
             return ''
         if len( raw_text ) > 2:
             encoded_text = json.loads( raw_text )

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

@@ -96,7 +96,7 @@ def sync_database_with_file_system( self, app, tool_shed_repository, tool_depend
                       str( basic_util.INSTALLATION_LOG ) )
                 error_message += ' is missing.  This indicates an installation error so the tool dependency is being'
                 error_message += ' prepared for re-installation.'
-                print error_message
+                log.error( error_message )
                 tool_dependency.status = app.install_model.ToolDependency.installation_status.NEVER_INSTALLED
                 basic_util.remove_dir( tool_dependency_install_dir )
                 can_install_tool_dependency = True
@@ -464,7 +464,7 @@ def handle_complex_repository_dependency_for_package( self, elem, package_name,
                 # required_repository.
                 if required_repository.is_deactivated_or_installed:
                     if not os.path.exists( required_repository_package_install_dir ):
-                        print 'Missing required tool dependency directory %s' % str( required_repository_package_install_dir )
+                        log.error( 'Missing required tool dependency directory %s' % str( required_repository_package_install_dir ) )
                     repo_files_dir = required_repository.repo_files_directory( self.app )
                     tool_dependencies_config = suc.get_absolute_path_to_file_in_repository( repo_files_dir, 'tool_dependencies.xml' )
                     if tool_dependencies_config:
@@ -518,7 +518,7 @@ def process_tag_set( self, tool_shed_repository, tool_dependency, package_elem,
         for rd_tool_dependency in rd_tool_dependencies:
             if rd_tool_dependency.status == self.app.install_model.ToolDependency.installation_status.ERROR:
                 # We'll log the error here, but continue installing packages since some may not require this dependency.
-                print "Error installing tool dependency for required repository: %s" % str( rd_tool_dependency.error_message )
+                log.error( "Error installing tool dependency for required repository: %s" % str( rd_tool_dependency.error_message ) )
         return tool_dependency, proceed_with_install, action_elem_tuples
 
     def remove_file( self, file_name ):

lib/tool_shed/galaxy_install/tool_migration_manager.py

@@ -62,16 +62,16 @@ def __init__( self, app, latest_migration_script_number, tool_shed_install_confi
         # setting from migrated_tools_config.
         tree, error_message = xml_util.parse_xml( migrated_tools_config )
         if tree is None:
-            print error_message
+            log.error( error_message )
         else:
             root = tree.getroot()
             self.tool_path = root.get( 'tool_path' )
-            print "Repositories will be installed into configured tool_path location ", str( self.tool_path )
+            log.debug( "Repositories will be installed into configured tool_path location ", str( self.tool_path ) )
             # Parse tool_shed_install_config to check each of the tools.
             self.tool_shed_install_config = tool_shed_install_config
             tree, error_message = xml_util.parse_xml( tool_shed_install_config )
             if tree is None:
-                print error_message
+                log.error( error_message )
             else:
                 root = tree.getroot()
                 defined_tool_shed_url = root.get( 'name' )
@@ -157,12 +157,12 @@ def __init__( self, app, latest_migration_script_number, tool_shed_install_confi
                             str( latest_migration_script_number )
                         message += "file%s named %s,\nso no repositories will be installed on disk.\n" % \
                             ( plural, file_names )
-                        print message
+                        log.info( message )
                 else:
                     message = "\nThe main Galaxy tool shed is not currently available, so skipped migration stage %s.\n" % \
                         str( latest_migration_script_number )
                     message += "Try again later.\n"
-                    print message
+                    log.error( message )
 
     def create_or_update_tool_shed_repository_record( self, name, owner, changeset_revision, description=None ):
 
@@ -403,8 +403,8 @@ def handle_repository_contents( self, tool_shed_repository, repository_clone_url
                             if tool_config not in tool_configs_to_filter:
                                 tool_configs_to_filter.append( tool_config )
                 else:
-                    print 'The tool "%s" (%s) has not been enabled because it is not defined in a proprietary tool config (%s).' \
-                        % ( guid, tool_config, ", ".join( self.proprietary_tool_confs or [] ) )
+                    log.error( 'The tool "%s" (%s) has not been enabled because it is not defined in a proprietary tool config (%s).' \
+                        % ( guid, tool_config, ", ".join( self.proprietary_tool_confs or [] ) ) )
             if tool_configs_to_filter:
                 lock = threading.Lock()
                 lock.acquire( True )
@@ -489,8 +489,9 @@ def handle_repository_contents( self, tool_shed_repository, repository_clone_url
                                                                                     from_tool_migration_manager=True )
             for installed_tool_dependency in installed_tool_dependencies:
                 if installed_tool_dependency.status == self.app.install_model.ToolDependency.installation_status.ERROR:
-                    print '\nThe ToolMigrationManager returned the following error while installing tool dependency ', installed_tool_dependency.name, ':'
-                    print installed_tool_dependency.error_message, '\n\n'
+                    log.error(
+                        'The ToolMigrationManager returned the following error while installing tool dependency %s: %s',
+                        installed_tool_dependency.name, installed_tool_dependency.error_message )
         if 'datatypes' in irmm_metadata_dict:
             cdl = custom_datatype_manager.CustomDatatypeLoader( self.app )
             tool_shed_repository.status = self.app.install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES
@@ -544,7 +545,8 @@ def install_repository( self, repository_elem, tool_shed_repository, install_dep
                                             self.app.install_model.ToolShedRepository.installation_status.DEACTIVATED ]:
             is_installed = True
         if cloned_ok and is_installed:
-            print "Skipping automatic install of repository '", tool_shed_repository.name, "' because it has already been installed in location ", clone_dir
+            log.info( "Skipping automatic install of repository '%s' because it has already been installed in location %s",
+                     tool_shed_repository.name, clone_dir )
         else:
             irm = install_manager.InstallRepositoryManager( self.app, self.tpm )
             repository_clone_url = os.path.join( self.tool_shed_url, 'repos', tool_shed_repository.owner, tool_shed_repository.name )
@@ -614,7 +616,7 @@ def install_repository( self, repository_elem, tool_shed_repository, install_dep
                 irm.update_tool_shed_repository_status( tool_shed_repository,
                                                         self.app.install_model.ToolShedRepository.installation_status.INSTALLED )
             else:
-                print 'Error attempting to clone repository %s: %s' % ( str( tool_shed_repository.name ), str( error_message ) )
+                log.error('Error attempting to clone repository %s: %s', str( tool_shed_repository.name ), str( error_message ) )
                 irm.update_tool_shed_repository_status( tool_shed_repository,
                                                         self.app.install_model.ToolShedRepository.installation_status.ERROR,
                                                         error_message=error_message )

lib/tool_shed/util/common_util.py

@@ -163,7 +163,7 @@ def get_repository_dependencies( app, tool_shed_url, repository_name, repository
         tool_shed_accessible = True
     except Exception, e:
         tool_shed_accessible = False
-        print "The URL\n%s\nraised the exception:\n%s\n" % ( url_join( tool_shed_url, pathspec=pathspec, params=params ), str( e ) )
+        log.warn( "The URL\n%s\nraised the exception:\n%s\n" % ( url_join( tool_shed_url, pathspec=pathspec, params=params ), str( e ) ) )
     if tool_shed_accessible:
         if len( raw_text ) > 2:
             encoded_text = json.loads( raw_text )
@@ -195,7 +195,7 @@ def get_tool_dependencies( app, tool_shed_url, repository_name, repository_owner
         tool_shed_accessible = True
     except Exception, e:
         tool_shed_accessible = False
-        print "The URL\n%s\nraised the exception:\n%s\n" % ( url_join( tool_shed_url, pathspec=pathspec, params=params ), str( e ) )
+        log.warn( "The URL\n%s\nraised the exception:\n%s\n" % ( url_join( tool_shed_url, pathspec=pathspec, params=params ), str( e ) ) )
     if tool_shed_accessible:
         if text:
             tool_dependencies_dict = encoding_util.tool_shed_decode( text )

lib/tool_shed/util/hg_util.py

@@ -436,7 +436,7 @@ def unpack_patches( hg_unbundle10_obj, remaining ):
                 'blocklen': blocklen,
                 'block': block.encode( 'string_escape' ) }
     if remaining > 0:
-        print remaining
+        log.error("Unexpected end of patch stream, %s remaining", remaining)
         raise Exception( "unexpected end of patch stream" )