/
mulled.py
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/
mulled.py
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"""This module describes the :class:`MulledContainerResolver` ContainerResolver plugin."""
import collections
import logging
import six
from ..container_resolvers import (
ContainerResolver,
)
from ..docker_util import build_docker_images_command
from ..mulled.mulled_build import (
check_output,
DEFAULT_CHANNELS,
ensure_installed,
InvolucroContext,
mull_targets,
)
from ..mulled.mulled_build_tool import requirements_to_mulled_targets
from ..mulled.util import (
mulled_tags_for,
split_tag,
v1_image_name,
v2_image_name,
)
from ..requirements import ContainerDescription
log = logging.getLogger(__name__)
CachedMulledImageSingleTarget = collections.namedtuple("CachedMulledImageSingleTarget", ["package_name", "version", "build", "image_identifier"])
CachedV1MulledImageMultiTarget = collections.namedtuple("CachedV1MulledImageMultiTarget", ["hash", "build", "image_identifier"])
CachedV2MulledImageMultiTarget = collections.namedtuple("CachedV2MulledImageMultiTarget", ["package_hash", "version_hash", "build", "image_identifier"])
CachedMulledImageSingleTarget.multi_target = False
CachedV1MulledImageMultiTarget.multi_target = "v1"
CachedV2MulledImageMultiTarget.multi_target = "v2"
def list_cached_mulled_images(namespace=None, hash_func="v2"):
command = build_docker_images_command(truncate=True, sudo=False)
command = "%s | tail -n +2 | tr -s ' ' | cut -d' ' -f1,2" % command
images_and_versions = check_output(command)
name_filter = get_filter(namespace)
def output_line_to_image(line):
image_name, version = line.split(" ", 1)
identifier = "%s:%s" % (image_name, version)
url, namespace, package_description = image_name.split("/")
if not version or version == "latest":
version = None
image = None
if package_description.startswith("mulled-v1-"):
if hash_func == "v2":
return None
hash = package_description
build = None
if version and version.isdigit():
build = version
image = CachedV1MulledImageMultiTarget(hash, build, identifier)
elif package_description.startswith("mulled-v2-"):
if hash_func == "v1":
return None
version_hash = None
build = None
if version and "-" in version:
version_hash, build = version.rsplit("-", 1)
elif version.isdigit():
version_hash, build = None, version
elif version:
log.debug("Unparsable mulled image tag encountered [%s]" % version)
image = CachedV2MulledImageMultiTarget(package_description, version_hash, build, identifier)
else:
build = None
if version and "--" in version:
version, build = split_tag(version)
image = CachedMulledImageSingleTarget(image_name, version, build, identifier)
return image
# TODO: Sort on build ...
raw_images = [output_line_to_image(_) for _ in filter(name_filter, images_and_versions.splitlines())]
return [i for i in raw_images if i is not None]
def get_filter(namespace):
prefix = "quay.io/" if namespace is None else "quay.io/%s" % namespace
return lambda name: name.startswith(prefix) and name.count("/") == 2
def cached_container_description(targets, namespace, hash_func="v2"):
if len(targets) == 0:
return None
cached_images = list_cached_mulled_images(namespace, hash_func=hash_func)
image = None
if len(targets) == 1:
target = targets[0]
for cached_image in cached_images:
if cached_image.multi_target:
continue
if not cached_image.package_name == target.package_name:
continue
if not target.version or target.version == cached_image.version:
image = cached_image
break
elif hash_func == "v2":
name = v2_image_name(targets)
if ":" in name:
package_hash, version_hash = name.split(":", 2)
else:
package_hash, version_hash = name, None
for cached_image in cached_images:
if cached_image.multi_target != "v2":
continue
if version_hash is None:
# Just match on package hash...
if package_hash == cached_image.package_hash:
image = cached_image
break
else:
# Match on package and version hash...
if package_hash == cached_image.package_hash and version_hash == cached_image.version_hash:
image = cached_image
break
elif hash_func == "v1":
name = v1_image_name(targets)
for cached_image in cached_images:
if cached_image.multi_target != "v1":
continue
if name == cached_image.hash:
image = cached_image
break
container = None
if image:
container = ContainerDescription(
image.image_identifier,
type="docker",
)
return container
@six.python_2_unicode_compatible
class CachedMulledContainerResolver(ContainerResolver):
resolver_type = "cached_mulled"
def __init__(self, app_info=None, namespace=None, hash_func="v2"):
super(CachedMulledContainerResolver, self).__init__(app_info)
self.namespace = namespace
self.hash_func = hash_func
def resolve(self, enabled_container_types, tool_info):
if tool_info.requires_galaxy_python_environment:
return None
targets = mulled_targets(tool_info)
return cached_container_description(targets, self.namespace, hash_func=self.hash_func)
def __str__(self):
return "CachedMulledContainerResolver[namespace=%s]" % self.namespace
@six.python_2_unicode_compatible
class MulledContainerResolver(ContainerResolver):
"""Look for mulled images matching tool dependencies."""
resolver_type = "mulled"
def __init__(self, app_info=None, namespace="biocontainers", hash_func="v2"):
super(MulledContainerResolver, self).__init__(app_info)
self.namespace = namespace
self.hash_func = hash_func
def resolve(self, enabled_container_types, tool_info):
if tool_info.requires_galaxy_python_environment:
return None
targets = mulled_targets(tool_info)
if len(targets) == 0:
return None
name = None
if len(targets) == 1:
target = targets[0]
target_version = target.version
tags = mulled_tags_for(self.namespace, target.package_name)
if not tags:
return None
if target_version:
for tag in tags:
version, build = split_tag(tag)
if version == target_version:
name = "%s:%s--%s" % (target.package_name, version, build)
break
else:
version, build = split_tag(tags[0])
name = "%s:%s--%s" % (target.package_name, version, build)
else:
def tags_if_available(image_name):
if ":" in image_name:
repo_name, tag_prefix = image_name.split(":", 2)
else:
repo_name = image_name
tag_prefix = None
tags = mulled_tags_for(self.namespace, repo_name, tag_prefix=tag_prefix)
return tags
if self.hash_func == "v2":
base_image_name = v2_image_name(targets)
tags = tags_if_available(base_image_name)
if tags:
name = "%s:%s" % (base_image_name, tags[0])
elif self.hash_func == "v1":
base_image_name = v1_image_name(targets)
tags = tags_if_available(base_image_name)
if tags:
name = "%s:%s" % (base_image_name, tags[0])
if name:
return ContainerDescription(
"quay.io/%s/%s" % (self.namespace, name),
type="docker",
)
def __str__(self):
return "MulledContainerResolver[namespace=%s]" % self.namespace
@six.python_2_unicode_compatible
class BuildMulledContainerResolver(ContainerResolver):
"""Look for mulled images matching tool dependencies."""
resolver_type = "build_mulled"
def __init__(self, app_info=None, namespace="local", hash_func="v2", **kwds):
super(BuildMulledContainerResolver, self).__init__(app_info)
self._involucro_context_kwds = {
'involucro_bin': self._get_config_option("involucro_path", None)
}
self.namespace = namespace
self.hash_func = hash_func
self._mulled_kwds = {
'namespace': namespace,
'channels': self._get_config_option("channels", DEFAULT_CHANNELS, prefix="mulled"),
}
self.auto_init = self._get_config_option("auto_init", DEFAULT_CHANNELS, prefix="involucro")
def resolve(self, enabled_container_types, tool_info):
if tool_info.requires_galaxy_python_environment:
return None
targets = mulled_targets(tool_info)
if len(targets) == 0:
return None
mull_targets(
targets,
involucro_context=self._get_involucro_context(),
hash_func=self.hash_func,
**self._mulled_kwds
)
return cached_container_description(targets, self.namespace, hash_func=self.hash_func)
def _get_involucro_context(self):
involucro_context = InvolucroContext(**self._involucro_context_kwds)
self.enabled = ensure_installed(involucro_context, self.auto_init)
return involucro_context
def __str__(self):
return "BuildContainerResolver[namespace=%s]" % self.namespace
def mulled_targets(tool_info):
return requirements_to_mulled_targets(tool_info.requirements)
__all__ = (
"CachedMulledContainerResolver",
"MulledContainerResolver",
"BuildMulledContainerResolver",
)