def _find_container(
self,
job_wrapper,
compute_working_directory=None,
compute_tool_directory=None,
compute_job_directory=None,
compute_tmp_directory=None,
):
job_directory_type = "galaxy" if compute_working_directory is None else "pulsar"
if not compute_working_directory:
compute_working_directory = job_wrapper.tool_working_directory
if not compute_job_directory:
compute_job_directory = job_wrapper.working_directory
if not compute_tool_directory:
compute_tool_directory = job_wrapper.tool.tool_dir
if not compute_tmp_directory:
compute_tmp_directory = job_wrapper.tmp_directory()
tool = job_wrapper.tool
guest_ports = job_wrapper.guest_ports
tool_info = ToolInfo(
tool.containers,
tool.requirements,
tool.requires_galaxy_python_environment,
tool.docker_env_pass_through,
guest_ports=guest_ports,
tool_id=tool.id,
tool_version=tool.version,
profile=tool.profile,
)
job_info = JobInfo(
working_directory=compute_working_directory,
tool_directory=compute_tool_directory,
job_directory=compute_job_directory,
tmp_directory=compute_tmp_directory,
home_directory=job_wrapper.home_directory(),
job_directory_type=job_directory_type,
)
destination_info = job_wrapper.job_destination.params
container = self.app.container_finder.find_container(
tool_info,
destination_info,
job_info
)
if container:
job_wrapper.set_container(container)
return container
def _find_container(
self,
job_wrapper,
compute_working_directory=None,
compute_tool_directory=None,
compute_job_directory=None,
compute_tmp_directory=None,
):
job_directory_type = "galaxy" if compute_working_directory is None else "pulsar"
if not compute_working_directory:
compute_working_directory = job_wrapper.tool_working_directory
if not compute_job_directory:
compute_job_directory = job_wrapper.working_directory
if not compute_tool_directory:
compute_tool_directory = job_wrapper.tool.tool_dir
if not compute_tmp_directory:
compute_tmp_directory = job_wrapper.tmp_directory()
tool = job_wrapper.tool
guest_ports = [
ep.get('port')
for ep in getattr(job_wrapper, 'interactivetools', [])
]
tool_info = ToolInfo(tool.containers,
tool.requirements,
tool.requires_galaxy_python_environment,
tool.docker_env_pass_through,
guest_ports=guest_ports)
job_info = JobInfo(
compute_working_directory,
compute_tool_directory,
compute_job_directory,
compute_tmp_directory,
job_directory_type,
)
destination_info = job_wrapper.job_destination.params
container = self.app.container_finder.find_container(
tool_info, destination_info, job_info)
if container:
job_wrapper.set_container(container)
return container