def reset_metadata_on_selected_installed_repositories(self, trans, **kwd):
repository_ids = util.listify(kwd.get("repository_ids"))
if repository_ids:
irmm = InstalledRepositoryMetadataManager(self.app)
failed = []
successful = []
for repository_id in repository_ids:
try:
repository = repository_util.get_installed_tool_shed_repository(
self.app, repository_id)
irmm.set_repository(repository)
irmm.reset_all_metadata_on_installed_repository()
if irmm.invalid_file_tups:
failed.append(repository_id)
else:
successful.append(repository_id)
except Exception:
failed.append(repository_id)
if successful:
message = "Successful reset of metadata for %s." % len(
successful)
if failed:
message += " Failed for %s." % len(failed)
elif failed:
message = "Failed to reset metadata for %s." % len(failed)
return dict(message=message, successful=successful, failed=failed)
else:
raise exceptions.MessageException(
"Please specify repository ids [repository_ids].")
def reset_all_metadata_on_installed_repository( self, id ):
"""Reset all metadata on a single tool shed repository installed into a Galaxy instance."""
invalid_file_tups = []
metadata_dict = {}
repository = repository_util.get_installed_tool_shed_repository( self.app, id )
repository_clone_url = common_util.generate_clone_url_for_installed_repository( self.app, repository )
tool_path, relative_install_dir = repository.get_tool_relative_path( self.app )
if relative_install_dir:
original_metadata_dict = repository.metadata
metadata_dict, invalid_file_tups = \
self.generate_metadata_for_changeset_revision( repository=repository,
changeset_revision=repository.changeset_revision,
repository_clone_url=repository_clone_url,
shed_config_dict = repository.get_shed_config_dict( self.app ),
relative_install_dir=relative_install_dir,
repository_files_dir=None,
resetting_all_metadata_on_repository=False,
updating_installed_repository=False,
persist=False )
repository.metadata = metadata_dict
if metadata_dict != original_metadata_dict:
self.update_in_shed_tool_config( repository )
self.app.install_model.context.add( repository )
self.app.install_model.context.flush()
log.debug( 'Metadata has been reset on repository %s.' % repository.name )
else:
log.debug( 'Metadata did not need to be reset on repository %s.' % repository.name )
else:
log.debug( 'Error locating installation directory for repository %s.' % repository.name )
return invalid_file_tups, metadata_dict
def reset_metadata_on_selected_repositories(self, user, **kwd):
"""
Inspect the repository changelog to reset metadata for all appropriate changeset revisions.
This method is called from both Galaxy and the Tool Shed.
"""
repository_ids = util.listify(kwd.get('repository_ids', None))
message = ''
status = 'done'
if repository_ids:
successful_count = 0
unsuccessful_count = 0
for repository_id in repository_ids:
try:
repository = repository_util.get_installed_tool_shed_repository(
self.app, repository_id)
self.set_repository(repository)
self.reset_all_metadata_on_installed_repository()
if self.invalid_file_tups:
message = tool_util.generate_message_for_invalid_tools(
self.app,
self.invalid_file_tups,
repository,
None,
as_html=False)
log.debug(message)
unsuccessful_count += 1
else:
log.debug(
"Successfully reset metadata on repository %s owned by %s"
% (str(repository.name), str(repository.owner)))
successful_count += 1
except:
log.exception(
"Error attempting to reset metadata on repository %s",
str(repository.name))
unsuccessful_count += 1
message = "Successfully reset metadata on %d %s. " % \
( successful_count, inflector.cond_plural( successful_count, "repository" ) )
if unsuccessful_count:
message += "Error setting metadata on %d %s - see the paster log for details. " % \
( unsuccessful_count, inflector.cond_plural( unsuccessful_count, "repository" ) )
else:
message = 'Select at least one repository to on which to reset all metadata.'
status = 'error'
return message, status
def reset_metadata_on_selected_repositories( self, user, **kwd ):
"""
Inspect the repository changelog to reset metadata for all appropriate changeset revisions.
This method is called from both Galaxy and the Tool Shed.
"""
repository_ids = util.listify( kwd.get( 'repository_ids', None ) )
message = ''
status = 'done'
if repository_ids:
successful_count = 0
unsuccessful_count = 0
for repository_id in repository_ids:
try:
repository = repository_util.get_installed_tool_shed_repository( self.app, repository_id )
self.set_repository( repository )
self.reset_all_metadata_on_installed_repository()
if self.invalid_file_tups:
message = tool_util.generate_message_for_invalid_tools( self.app,
self.invalid_file_tups,
repository,
None,
as_html=False )
log.debug( message )
unsuccessful_count += 1
else:
log.debug( "Successfully reset metadata on repository %s owned by %s" %
( str( repository.name ), str( repository.owner ) ) )
successful_count += 1
except:
log.exception( "Error attempting to reset metadata on repository %s", str( repository.name ) )
unsuccessful_count += 1
message = "Successfully reset metadata on %d %s. " % \
( successful_count, inflector.cond_plural( successful_count, "repository" ) )
if unsuccessful_count:
message += "Error setting metadata on %d %s - see the paster log for details. " % \
( unsuccessful_count, inflector.cond_plural( unsuccessful_count, "repository" ) )
else:
message = 'Select at least one repository to on which to reset all metadata.'
status = 'error'
return message, status
