def _update_user_data(self):
if 'filesystems' in self.app.ud:
old_fs_list = self.app.ud.get('filesystems') or []
new_fs_list = []
# clear 'services' and replace with the new format
for fs in old_fs_list:
svc_roles = ServiceRole.from_string_array(fs['roles'])
if ServiceRole.GALAXY_TOOLS in svc_roles and ServiceRole.GALAXY_DATA in svc_roles:
# This condition should only occur in new configs, but check
# added so that things work properly even if run against a new config
# Only works for default configs though...
new_fs_list.append(fs)
elif ServiceRole.GALAXY_TOOLS in svc_roles:
pass # skip adding the galaxy tools file system, no longer needed.
else:
if ServiceRole.GALAXY_DATA in ServiceRole.from_string_array(fs['roles']):
fs['roles'] = ServiceRole.to_string_array([ServiceRole.GALAXY_TOOLS,
ServiceRole.GALAXY_DATA])
new_fs_list.append(fs)
else:
new_fs_list.append(fs)
self.app.ud['filesystems'] = new_fs_list
self.app.ud['deployment_version'] = 2
self.app.ud.pop('galaxy_home', None) # TODO: Galaxy home is always reset
# to default. Discuss implications
return True
def _update_user_data(self):
if 'filesystems' in self.app.config.user_data:
old_fs_list = self.app.config.user_data.get('filesystems') or []
new_fs_list = []
# clear 'services' and replace with the new format
for fs in old_fs_list:
svc_roles = ServiceRole.from_string_array(fs['roles'])
if ServiceRole.GALAXY_TOOLS in svc_roles and ServiceRole.GALAXY_DATA in svc_roles:
# This condition should only occur in new configs, but check
# added so that things work properly even if run against a new config
# Only works for default configs though...
new_fs_list.append(fs)
elif ServiceRole.GALAXY_TOOLS in svc_roles:
pass # skip adding the galaxy tools file system, no longer needed.
else:
if ServiceRole.GALAXY_DATA in ServiceRole.from_string_array(fs['roles']):
fs['roles'] = ServiceRole.to_string_array([ServiceRole.GALAXY_TOOLS,
ServiceRole.GALAXY_DATA])
new_fs_list.append(fs)
else:
new_fs_list.append(fs)
self.app.config.user_data['filesystems'] = new_fs_list
self.app.config.user_data['deployment_version'] = 2
self.app.config.user_data.pop('galaxy_home', None) # TODO: Galaxy home is always reset to default. Discuss implications
return True
def __init__(self, app):
super(MigrationService, self).__init__(app)
self.svc_roles = [ServiceRole.MIGRATION]
self.name = ServiceRole.to_string(ServiceRole.MIGRATION)
self.dependencies = []
if 'filesystems' in self.app.ud:
for fs in self.app.ud.get('filesystems') or []:
# Wait for galaxy data, indices and tools to come up before attempting migration
if ServiceRole.GALAXY_DATA in ServiceRole.from_string_array(fs['roles']):
self.dependencies.append(ServiceDependency(self, ServiceRole.GALAXY_DATA))
if ServiceRole.GALAXY_TOOLS in ServiceRole.from_string_array(fs['roles']):
self.dependencies.append(ServiceDependency(self, ServiceRole.GALAXY_TOOLS))
if ServiceRole.GALAXY_INDICES in ServiceRole.from_string_array(fs['roles']):
self.dependencies.append(ServiceDependency(self, ServiceRole.GALAXY_INDICES))
def __init__(self, app):
super(MigrationService, self).__init__(app)
self.svc_roles = [ServiceRole.MIGRATION]
self.name = ServiceRole.to_string(ServiceRole.MIGRATION)
self.svc_type = ServiceType.CM_SERVICE
self.dependencies = []
if 'filesystems' in self.app.config.user_data:
for fs in self.app.config.user_data.get('filesystems') or []:
# Wait for galaxy data, indices and tools to come up before attempting migration
if ServiceRole.GALAXY_DATA in ServiceRole.from_string_array(fs['roles']):
self.dependencies.append(ServiceDependency(self, ServiceRole.GALAXY_DATA))
if ServiceRole.GALAXY_TOOLS in ServiceRole.from_string_array(fs['roles']):
self.dependencies.append(ServiceDependency(self, ServiceRole.GALAXY_TOOLS))
if ServiceRole.GALAXY_INDICES in ServiceRole.from_string_array(fs['roles']):
self.dependencies.append(ServiceDependency(self, ServiceRole.GALAXY_INDICES))