def pull(self, container):
if self.cli_available:
cmds = container.build_mulled_singularity_pull_command(
cache_directory=self.cache_directory.path,
namespace=self.namespace)
shell(cmds=cmds)
self.cache_directory.invalidate_cache()
def resolve(self, enabled_container_types, tool_info, install=False, **kwds):
"""Find a container explicitly mentioned in tool description.
This ignores the tool requirements and assumes the tool author crafted
a correct container. We use singularity here to fetch docker containers,
hence the container_description hack here.
"""
for container_description in tool_info.container_descriptions: # type: ContainerDescription
if container_description.type == 'docker':
desc_dict = container_description.to_dict()
desc_dict['type'] = self.container_type
desc_dict['identifier'] = f"docker://{container_description.identifier}"
container_description = container_description.from_dict(desc_dict)
if not self._container_type_enabled(container_description, enabled_container_types):
return None
if not self.cli_available:
return container_description
image_id = container_description.identifier
cache_path = os.path.normpath(os.path.join(self.cache_directory_path, image_id))
if install and not os.path.exists(cache_path):
destination_info = {}
destination_for_container_type = kwds.get(
'destination_for_container_type')
if destination_for_container_type:
destination_info = destination_for_container_type(
self.container_type)
container = SingularityContainer(
container_description.identifier,
self.app_info,
tool_info,
destination_info,
{},
container_description)
command = container.build_singularity_pull_command(cache_path=cache_path)
shell(command)
# Point to container in the cache in stead.
container_description.identifier = cache_path
return container_description
else: # No container descriptions found
return None
def pull(self, container):
cmds = container.build_mulled_singularity_pull_command(
cache_directory=self.cache_directory, namespace=self.namespace)
shell(cmds=cmds)
def pull(self, container):
command = container.build_pull_command()
shell(command)
def pull(self, container):
if self.cli_available:
command = container.build_pull_command()
shell(command)
def shell(cmds, **kwds):
"""Print and execute shell command."""
cmd_string = args_to_str(cmds)
info(cmd_string)
return commands.shell(cmds, **kwds)
def shell(cmds, **kwds):
cmd_string = args_to_str(cmds)
info(cmd_string)
return commands.shell(cmds, **kwds)
