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wrap bare str raises with generic Exception()

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as Pyton 2.7 does not support bare str
This commit is contained in:
Martin Cech
2016-05-26 13:14:22 -04:00
parent 4eeb73ec8c
commit d72eee3d4a
15 changed files with 62 additions and 63 deletions
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lib/galaxy/external_services/actions.py
+2 -2
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@@ -80,7 +80,7 @@ class ExternalServiceAction( object ):
return handled_results
def perform_action( self, param_dict ):
raise 'Abstract Method'
raise Exception( 'Abstract Method' )
class ExternalServiceResult( object ):
@@ -90,7 +90,7 @@ class ExternalServiceResult( object ):
@property
def content( self ):
raise 'Abstract Method'
raise Exception( 'Abstract Method' )
class ExternalServiceWebAPIActionResult( ExternalServiceResult ):
lib/galaxy/external_services/parameters.py
+1 -1
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@@ -21,7 +21,7 @@ class ExternalServiceParameter( object ):
self.parent = parent
def get_value( self, param_dict ):
raise 'Abstract Method'
raise Exception( 'Abstract Method' )
class ExternalServiceTemplateParameter( ExternalServiceParameter ):
lib/galaxy/external_services/service.py
+1 -1
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@@ -218,7 +218,7 @@ class PopulatedExternalService( object ):
elif isinstance( item, ExternalServiceActionsGroup ):
item.prepare_actions( param_dict, param_dict, action_list )
else:
raise 'unknown item type found'
raise Exception( 'unknown item type found' )
self.param_dict = param_dict
self.actions = action_list
lib/galaxy/forms/forms.py
+1 -1
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@@ -69,7 +69,7 @@ class FormDefinitionFieldFactory( object ):
type = None
def __get_stored_field_type( self, **kwds ):
raise 'not implemented'
raise Exception( 'not implemented' )
def new( self, name=None, label=None, required=False, helptext=None, default=None, visible=True, layout=None ):
"""
lib/galaxy/model/__init__.py
+5 -5
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@@ -1572,7 +1572,7 @@ class LibraryPermissions( object ):
if isinstance( library_item, Library ):
self.library = library_item
else:
raise "Invalid Library specified: %s" % library_item.__class__.__name__
raise Exception( "Invalid Library specified: %s" % library_item.__class__.__name__ )
self.role = role
@@ -1582,7 +1582,7 @@ class LibraryFolderPermissions( object ):
if isinstance( library_item, LibraryFolder ):
self.folder = library_item
else:
raise "Invalid LibraryFolder specified: %s" % library_item.__class__.__name__
raise Exception( "Invalid LibraryFolder specified: %s" % library_item.__class__.__name__ )
self.role = role
@@ -1592,7 +1592,7 @@ class LibraryDatasetPermissions( object ):
if isinstance( library_item, LibraryDataset ):
self.library_dataset = library_item
else:
raise "Invalid LibraryDataset specified: %s" % library_item.__class__.__name__
raise Exception( "Invalid LibraryDataset specified: %s" % library_item.__class__.__name__ )
self.role = role
@@ -1602,7 +1602,7 @@ class LibraryDatasetDatasetAssociationPermissions( object ):
if isinstance( library_item, LibraryDatasetDatasetAssociation ):
self.library_dataset_dataset_association = library_item
else:
raise "Invalid LibraryDatasetDatasetAssociation specified: %s" % library_item.__class__.__name__
raise Exception( "Invalid LibraryDatasetDatasetAssociation specified: %s" % library_item.__class__.__name__ )
self.role = role
@@ -2079,7 +2079,7 @@ class DatasetInstance( object ):
return fake_hda
def clear_associated_files( self, metadata_safe=False, purge=False ):
raise 'Unimplemented'
raise Exception( "Unimplemented" )
def get_child_by_designation(self, designation):
for child in self.children:
lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py
+1 -1
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@@ -274,7 +274,7 @@ class DatasetInstance( object ):
return valid
def clear_associated_files( self, metadata_safe=False, purge=False ):
raise 'Unimplemented'
raise Exception( 'Unimplemented' )
def get_child_by_designation(self, designation):
for child in self.children:
lib/galaxy/security/__init__.py
+35 -35
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@@ -48,97 +48,97 @@ class RBACAgent:
return self.permitted_actions.__dict__.values()
def get_item_actions( self, action, item ):
raise 'No valid method of retrieving action (%s) for item %s.' % ( action, item )
raise Exception( 'No valid method of retrieving action (%s) for item %s.' % ( action, item ) )
def guess_derived_permissions_for_datasets( self, datasets=[] ):
raise "Unimplemented Method"
raise Exception( "Unimplemented Method" )
def can_access_dataset( self, roles, dataset ):
raise "Unimplemented Method"
raise Exception( "Unimplemented Method" )
def can_manage_dataset( self, roles, dataset ):
raise "Unimplemented Method"
raise Exception( "Unimplemented Method" )
def can_access_library( self, roles, library ):
raise "Unimplemented Method"
raise Exception( "Unimplemented Method" )
def can_add_library_item( self, roles, item ):
raise "Unimplemented Method"
raise Exception( "Unimplemented Method" )
def can_modify_library_item( self, roles, item ):
raise "Unimplemented Method"
raise Exception( "Unimplemented Method" )
def can_manage_library_item( self, roles, item ):
raise "Unimplemented Method"
raise Exception( "Unimplemented Method" )
def associate_components( self, **kwd ):
raise 'No valid method of associating provided components: %s' % kwd
raise Exception( 'No valid method of associating provided components: %s' % kwd )
def create_private_user_role( self, user ):
raise "Unimplemented Method"
raise Exception( "Unimplemented Method" )
def get_private_user_role( self, user ):
raise "Unimplemented Method"
raise Exception( "Unimplemented Method" )
def get_accessible_request_types( self, trans, user ):
raise "Unimplemented Method"
raise Exception( "Unimplemented Method" )
def user_set_default_permissions( self, user, permissions={}, history=False, dataset=False ):
raise "Unimplemented Method"
raise Exception( "Unimplemented Method" )
def history_set_default_permissions( self, history, permissions=None, dataset=False, bypass_manage_permission=False ):
raise "Unimplemented Method"
raise Exception( "Unimplemented Method" )
def set_all_dataset_permissions( self, dataset, permissions, new=False ):
raise "Unimplemented Method"
raise Exception( "Unimplemented Method" )
def set_dataset_permission( self, dataset, permission ):
raise "Unimplemented Method"
raise Exception( "Unimplemented Method" )
def set_all_library_permissions( self, trans, dataset, permissions ):
raise "Unimplemented Method"
raise Exception( "Unimplemented Method" )
def set_library_item_permission( self, library_item, permission ):
raise "Unimplemented Method"
raise Exception( "Unimplemented Method" )
def library_is_public( self, library ):
raise "Unimplemented Method"
raise Exception( "Unimplemented Method" )
def make_library_public( self, library ):
raise "Unimplemented Method"
raise Exception( "Unimplemented Method" )
def get_accessible_libraries( self, trans, user ):
raise "Unimplemented Method"
raise Exception( "Unimplemented Method" )
def get_permitted_libraries( self, trans, user, actions ):
raise "Unimplemented Method"
raise Exception( "Unimplemented Method" )
def folder_is_public( self, library ):
raise "Unimplemented Method"
raise Exception( "Unimplemented Method" )
def make_folder_public( self, folder, count=0 ):
raise "Unimplemented Method"
raise Exception( "Unimplemented Method" )
def dataset_is_public( self, dataset ):
raise "Unimplemented Method"
raise Exception( "Unimplemented Method" )
def make_dataset_public( self, dataset ):
raise "Unimplemented Method"
raise Exception( "Unimplemented Method" )
def get_permissions( self, library_dataset ):
raise "Unimplemented Method"
raise Exception( "Unimplemented Method" )
def get_all_roles( self, trans, cntrller ):
raise "Unimplemented Method"
raise Exception( "Unimplemented Method" )
def get_legitimate_roles( self, trans, item, cntrller ):
raise "Unimplemented Method"
raise Exception( "Unimplemented Method" )
def derive_roles_from_access( self, trans, item_id, cntrller, library=False, **kwd ):
raise "Unimplemented Method"
raise Exception( "Unimplemented Method" )
def get_component_associations( self, **kwd ):
raise "Unimplemented Method"
raise Exception( "Unimplemented Method" )
def components_are_associated( self, **kwd ):
return bool( self.get_component_associations( **kwd ) )
@@ -736,7 +736,7 @@ class GalaxyRBACAgent( RBACAgent ):
if 'action' in kwd:
if 'dataset' in kwd and 'role' in kwd:
return self.associate_action_dataset_role( kwd['action'], kwd['dataset'], kwd['role'] )
raise 'No valid method of associating provided components: %s' % kwd
raise Exception( 'No valid method of associating provided components: %s' % kwd )
def associate_user_group( self, user, group ):
assoc = self.model.UserGroupAssociation( user, group )
@@ -1300,7 +1300,7 @@ class GalaxyRBACAgent( RBACAgent ):
self.sa_session.add( lp )
self.sa_session.flush()
else:
raise 'Invalid class (%s) specified for target_library_item (%s)' % \
raise Exception( 'Invalid class (%s) specified for target_library_item (%s)' % \ )
( target_library_item.__class__, target_library_item.__class__.__name__ )
def get_permitted_libraries( self, trans, user, actions ):
@@ -1435,7 +1435,7 @@ class GalaxyRBACAgent( RBACAgent ):
elif 'group' in kwd:
if 'role' in kwd:
return self.sa_session.query( self.model.GroupRoleAssociation ).filter_by( role_id=kwd['role'].id, group_id=kwd['group'].id ).first()
raise 'No valid method of associating provided components: %s' % kwd
raise Exception( 'No valid method of associating provided components: %s' % kwd )
def check_folder_contents( self, user, roles, folder, hidden_folder_ids='' ):
"""
@@ -1567,7 +1567,7 @@ class HostAgent( RBACAgent ):
log.debug( 'Allowing access to private dataset with hda: %i. Remote server is: %s.' % ( hda.id, server ) )
return True
else:
raise 'The dataset access permission is the only valid permission in the host security agent.'
raise Exception( 'The dataset access permission is the only valid permission in the host security agent.' )
def set_dataset_permissions( self, hda, user, site ):
hdadaa = self.sa_session.query( self.model.HistoryDatasetAssociationDisplayAtAuthorization ) \
lib/galaxy/tools/actions/__init__.py
+1 -1
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@@ -78,7 +78,7 @@ class DefaultToolAction( object ):
data = new_data
if not trans.app.security_agent.can_access_dataset( current_user_roles, data.dataset ):
raise "User does not have permission to use a dataset (%s) provided for input." % data.id
raise Exception( "User does not have permission to use a dataset (%s) provided for input." % data.id )
return data
if isinstance( input, DataToolParameter ):
if isinstance( value, list ):
lib/galaxy/visualization/data_providers/genome.py
+1 -1
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@@ -1483,7 +1483,7 @@ class ENCODEPeakDataProvider( GenomeDataProvider ):
"""
def get_iterator( self, data_file, chrom, start, end, **kwargs ):
raise "Unimplemented Method"
raise Exception( "Unimplemented Method" )
def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ):
"""
lib/galaxy/webapps/galaxy/controllers/external_services.py
+1 -1
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@@ -24,4 +24,4 @@ class ExternalServiceController( BaseUIController ):
results = populated_action.handle_results( trans )
return results
else:
raise 'unknown item class type'
raise Exception( 'unknown item class type' )
lib/galaxy/webapps/tool_shed/security/__init__.py
+6 -6
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@@ -22,10 +22,10 @@ class RBACAgent:
permitted_actions = Bunch()
def associate_components( self, **kwd ):
raise 'No valid method of associating provided components: %s' % kwd
raise Exception( 'No valid method of associating provided components: %s' % kwd )
def associate_user_role( self, user, role ):
raise 'No valid method of associating a user with a role'
raise Exception( 'No valid method of associating a user with a role' )
def convert_permitted_action_strings( self, permitted_action_strings ):
"""
@@ -35,7 +35,7 @@ class RBACAgent:
return filter( lambda x: x is not None, [ self.permitted_actions.get( action_string ) for action_string in permitted_action_strings ] )
def create_private_user_role( self, user ):
raise "Unimplemented Method"
raise Exception( "Unimplemented Method" )
def get_action( self, name, default=None ):
"""Get a permitted action by its dict key or action name"""
@@ -49,10 +49,10 @@ class RBACAgent:
return self.permitted_actions.__dict__.values()
def get_item_actions( self, action, item ):
raise 'No valid method of retrieving action (%s) for item %s.' % ( action, item )
raise Exception( 'No valid method of retrieving action (%s) for item %s.' % ( action, item ) )
def get_private_user_role( self, user ):
raise "Unimplemented Method"
raise Exception( "Unimplemented Method" )
class CommunityRBACAgent( RBACAgent ):
@@ -93,7 +93,7 @@ class CommunityRBACAgent( RBACAgent ):
return self.associate_group_role( kwd['group'], kwd['role'] )
elif 'repository' in kwd:
return self.associate_repository_category( kwd[ 'repository' ], kwd[ 'category' ] )
raise 'No valid method of associating provided components: %s' % kwd
raise Exception( 'No valid method of associating provided components: %s' % kwd )
def associate_group_role( self, group, role ):
assoc = self.model.GroupRoleAssociation( group, role )
lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
+2 -2
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@@ -239,10 +239,10 @@ class RecipeStep( object ):
def execute_step( self, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
install_environment, work_dir, current_dir=None, initial_download=False ):
raise "Unimplemented Method"
raise Exception( "Unimplemented Method")
def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
raise "Unimplemented Method"
raise Exception( "Unimplemented Method" )
class AssertDirectoryExecutable( RecipeStep ):
lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
+1 -1
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@@ -22,7 +22,7 @@ class RecipeTag( object ):
def process_tag_set( self, tool_shed_repository, tool_dependency, package_elem, package_name, package_version,
from_tool_migration_manager=False, tool_dependency_db_records=None ):
raise "Unimplemented Method"
raise Exception( "Unimplemented Method" )
class SyncDatabase( object ):
lib/tool_shed/repository_types/metadata.py
+1 -1
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@@ -16,7 +16,7 @@ class Metadata( object ):
return repo.changelog
def is_valid_for_type( self, app, repository, revisions_to_check=None ):
raise "Unimplemented Method"
raise Exception( "Unimplemented Method" )
class TipOnly( Metadata ):
tools/filters/axt_to_lav.py
+3 -4
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@@ -156,17 +156,16 @@ def read_lengths(fileName):
fields = line.split()
if len(fields) != 2:
raise "bad lengths line (%s:%d): %s" % (fileName, lineNumber, line)
raise Exception( "bad lengths line (%s:%d): %s" % (fileName, lineNumber, line) )
chrom = fields[0]
try:
length = int(fields[1])
except:
raise "bad lengths line (%s:%d): %s" % (fileName, lineNumber, line)
raise Exception( "bad lengths line (%s:%d): %s" % (fileName, lineNumber, line) )
if chrom in chromToLength:
raise "%s appears more than once (%s:%d): %s" \
% (chrom, fileName, lineNumber)
raise Exception( "%s appears more than once (%s:%d): %s" % (chrom, fileName, lineNumber) )
chromToLength[chrom] = length