def supports_container(self, job_or_tool, container_type):
"""
Job rules can pass this function a job, job_wrapper, or tool and
determine if the underlying tool believes it can be run with a specific container type.
:param job_or_tool:
:param container_type: either "docker" or "singularity" currently
:return: true if the tool supports the specified container type.
"""
# Not a ton of logic in this method - but the idea is to shield rule
# developers from the details and they shouldn't have to know how to
# interrogate tool or job to figure out if it can be run in a
# container.
if hasattr(job_or_tool, 'containers'):
tool = job_or_tool
elif hasattr(job_or_tool, 'tool'):
# Have a JobWrapper-like
tool = job_or_tool.tool
else:
# Have a Job object.
tool = self.app.toolbox.get_tool(
job_or_tool.tool_id, tool_version=job_or_tool.tool_version)
tool_info = ToolInfo(tool.containers, tool.requirements,
tool.requires_galaxy_python_environment,
tool.docker_env_pass_through)
container_description = self.app.container_finder.find_best_container_description(
[container_type], tool_info)
return container_description is not None
def get_container_from_software_requirements(
use_biocontainers: bool, builder: "HasReqsHints") -> Optional[str]:
if use_biocontainers:
ensure_galaxy_lib_available()
from galaxy.tool_util.deps.containers import (
DOCKER_CONTAINER_TYPE,
ContainerRegistry,
)
from galaxy.tool_util.deps.dependencies import AppInfo, ToolInfo
app_info = AppInfo(
involucro_auto_init=True,
enable_mulled_containers=True,
container_image_cache_path=".",
) # type: AppInfo
container_registry = ContainerRegistry(
app_info) # type: ContainerRegistry
requirements = get_dependencies(builder)
tool_info = ToolInfo(requirements=requirements) # type: ToolInfo
container_description = container_registry.find_best_container_description(
[DOCKER_CONTAINER_TYPE], tool_info)
if container_description:
return container_description.identifier
return None
def test_docker_container_docker_cli_absent_resolve(mocker):
mocker.patch('galaxy.tool_util.deps.container_resolvers.mulled.which', return_value=None)
resolver = MulledDockerContainerResolver()
assert resolver.cli_available is False
requirement = ToolRequirement(name="samtools", version="1.10", type="package")
tool_info = ToolInfo(requirements=[requirement])
mocker.patch('galaxy.tool_util.deps.container_resolvers.mulled.targets_to_mulled_name', return_value='samtools:1.10--h2e538c0_3')
container_description = resolver.resolve(enabled_container_types=['docker'], tool_info=tool_info)
assert container_description.type == 'docker'
assert container_description.identifier == 'quay.io/biocontainers/samtools:1.10--h2e538c0_3'
def test_docker_container_docker_cli_exception_resolve(mocker):
mocker.patch('galaxy.tool_util.deps.container_resolvers.mulled.which', return_value='/bin/docker')
resolver = MulledDockerContainerResolver()
assert resolver.cli_available is True
requirement = ToolRequirement(name="samtools", version="1.10", type="package")
tool_info = ToolInfo(requirements=[requirement])
mocker.patch('galaxy.tool_util.deps.container_resolvers.mulled.targets_to_mulled_name', return_value='samtools:1.10--h2e538c0_3')
mocker.patch('galaxy.tool_util.deps.container_resolvers.mulled.docker_cached_container_description', side_effect=CalledProcessError(1, 'bla'))
container_description = resolver.resolve(enabled_container_types=['docker'], tool_info=tool_info, install=True)
assert resolver.cli_available is True
assert container_description.type == 'docker'
assert container_description.identifier == 'quay.io/biocontainers/samtools:1.10--h2e538c0_3'
def test_cached_singularity_container_resolver_uncached(mocker):
mocker.patch('os.listdir', return_value=SINGULARITY_IMAGES)
mocker.patch('os.path.exists', return_value=True)
mocker.patch(
'galaxy.tool_util.deps.container_resolvers.mulled.safe_makedirs')
resolver = CachedMulledSingularityContainerResolver(app_info=mocker.Mock(
container_image_cache_path='/'))
requirement = ToolRequirement(name="foo", version="1.0", type="package")
tool_info = ToolInfo(requirements=[requirement])
container_description = resolver.resolve(
enabled_container_types=['singularity'], tool_info=tool_info)
assert container_description.type == 'singularity'
assert container_description.identifier == '/singularity/mulled/foo:1.0--bar'
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
def test_cached_singularity_container_resolver_dir_mtime_cached(mocker):
mocker.patch('os.listdir', return_value=SINGULARITY_IMAGES)
mocker.patch('os.path.exists', return_value=True)
mocker.patch(
'galaxy.tool_util.deps.container_resolvers.mulled.safe_makedirs')
mocker.patch('os.stat', return_value=mocker.Mock(st_mtime=42))
resolver = CachedMulledSingularityContainerResolver(
app_info=mocker.Mock(container_image_cache_path='/'),
cache_directory_cacher_type='dir_mtime')
requirement = ToolRequirement(name="baz", version="2.22", type="package")
tool_info = ToolInfo(requirements=[requirement])
container_description = resolver.resolve(
enabled_container_types=['singularity'], tool_info=tool_info)
assert container_description.type == 'singularity'
assert container_description.identifier == '/singularity/mulled/baz:2.22'
requirement = ToolRequirement(name="foo", version="1.0", type="package")
tool_info.requirements.append(requirement)
container_description = resolver.resolve(
enabled_container_types=['singularity'], tool_info=tool_info)
assert container_description.type == 'singularity'
assert container_description.identifier == '/singularity/mulled/mulled-v2-fe8a3b846bc50d24e5df78fa0b562c43477fe9ce:9f946d13f673ab2903cb0da849ad42916d619d18-0'
