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Source code for galaxy.tools.deps.containers

import logging
import os

from galaxy.util import (
    asbool,
    plugin_config
)
from .container_classes import (
    CONTAINER_CLASSES,
    DOCKER_CONTAINER_TYPE,
    NULL_CONTAINER,
    SINGULARITY_CONTAINER_TYPE,
)
from .container_resolvers.explicit import (
    ExplicitContainerResolver,
    ExplicitSingularityContainerResolver,
)
from .container_resolvers.mulled import (
    BuildMulledDockerContainerResolver,
    BuildMulledSingularityContainerResolver,
    CachedMulledDockerContainerResolver,
    CachedMulledSingularityContainerResolver,
    MulledDockerContainerResolver,
    MulledSingularityContainerResolver,
)
from .requirements import (
    ContainerDescription,
)

log = logging.getLogger(__name__)


DEFAULT_CONTAINER_TYPE = DOCKER_CONTAINER_TYPE
ALL_CONTAINER_TYPES = [DOCKER_CONTAINER_TYPE, SINGULARITY_CONTAINER_TYPE]


[docs]class ContainerFinder(object):
[docs] def __init__(self, app_info): self.app_info = app_info self.container_registry = ContainerRegistry(app_info)
def _enabled_container_types(self, destination_info): return [t for t in ALL_CONTAINER_TYPES if self.__container_type_enabled(t, destination_info)]
[docs] def find_best_container_description(self, enabled_container_types, tool_info): """Regardless of destination properties - find best container for tool. Given container types and container.ToolInfo description of the tool.""" container_description = self.container_registry.find_best_container_description(enabled_container_types, tool_info) return container_description
[docs] def find_container(self, tool_info, destination_info, job_info): enabled_container_types = self._enabled_container_types(destination_info) # Short-cut everything else and just skip checks if no container type is enabled. if not enabled_container_types: return NULL_CONTAINER def __destination_container(container_description=None, container_id=None, container_type=None): if container_description: container_id = container_description.identifier container_type = container_description.type container = self.__destination_container( container_id, container_type, tool_info, destination_info, job_info, container_description, ) return container def container_from_description_from_dicts(destination_container_dicts): for destination_container_dict in destination_container_dicts: container_description = ContainerDescription.from_dict(destination_container_dict) if container_description: container = __destination_container(container_description) if container: return container if "container_override" in destination_info: container = container_from_description_from_dicts(destination_info["container_override"]) if container: return container # If destination forcing Galaxy to use a particular container do it, # this is likely kind of a corner case. For instance if deployers # do not trust the containers annotated in tools. for container_type in CONTAINER_CLASSES.keys(): container_id = self.__overridden_container_id(container_type, destination_info) if container_id: container = __destination_container(container_type=container_type, container_id=container_id) if container: return container # Otherwise lets see if we can find container for the tool. container_description = self.find_best_container_description(enabled_container_types, tool_info) container = __destination_container(container_description) if container: return container # If we still don't have a container, check to see if any container # types define a default container id and use that. if "container" in destination_info: container = container_from_description_from_dicts(destination_info["container"]) if container: return container for container_type in CONTAINER_CLASSES.keys(): container_id = self.__default_container_id(container_type, destination_info) if container_id: container = __destination_container(container_type=container_type, container_id=container_id) if container: return container return NULL_CONTAINER
def __overridden_container_id(self, container_type, destination_info): if not self.__container_type_enabled(container_type, destination_info): return None if "%s_container_id_override" % container_type in destination_info: return destination_info.get("%s_container_id_override" % container_type) if "%s_image_override" % container_type in destination_info: return self.__build_container_id_from_parts(container_type, destination_info, mode="override") def __build_container_id_from_parts(self, container_type, destination_info, mode): repo = "" owner = "" repo_key = "%s_repo_%s" % (container_type, mode) owner_key = "%s_owner_%s" % (container_type, mode) if repo_key in destination_info: repo = destination_info[repo_key] + "/" if owner_key in destination_info: owner = destination_info[owner_key] + "/" cont_id = repo + owner + destination_info["%s_image_%s" % (container_type, mode)] tag_key = "%s_tag_%s" % (container_type, mode) if tag_key in destination_info: cont_id += ":" + destination_info[tag_key] return cont_id def __default_container_id(self, container_type, destination_info): if not self.__container_type_enabled(container_type, destination_info): return None key = "%s_default_container_id" % container_type # Also allow docker_image... if key not in destination_info: key = "%s_image" % container_type if key in destination_info: return destination_info.get(key) elif "%s_image_default" in destination_info: return self.__build_container_id_from_parts(container_type, destination_info, mode="default") return None def __destination_container(self, container_id, container_type, tool_info, destination_info, job_info, container_description=None): # TODO: ensure destination_info is dict-like if not self.__container_type_enabled(container_type, destination_info): return NULL_CONTAINER # TODO: Right now this assumes all containers available when a # container type is - there should be more thought put into this. # Checking which are availalbe - settings policies for what can be # auto-fetched, etc.... return CONTAINER_CLASSES[container_type](container_id, self.app_info, tool_info, destination_info, job_info, container_description) def __container_type_enabled(self, container_type, destination_info): return asbool(destination_info.get("%s_enabled" % container_type, False))
[docs]class NullContainerFinder(object):
[docs] def find_container(self, tool_info, destination_info, job_info): return []
[docs]class ContainerRegistry(object): """Loop through enabled ContainerResolver plugins and find first match."""
[docs] def __init__(self, app_info): self.resolver_classes = self.__resolvers_dict() self.enable_beta_mulled_containers = app_info.enable_beta_mulled_containers self.app_info = app_info self.container_resolvers = self.__build_container_resolvers(app_info)
def __build_container_resolvers(self, app_info): conf_file = getattr(app_info, 'containers_resolvers_config_file', None) if not conf_file: return self.__default_containers_resolvers() if not os.path.exists(conf_file): log.debug("Unable to find config file '%s'", conf_file) return self.__default_containers_resolvers() plugin_source = plugin_config.plugin_source_from_path(conf_file) return self.__parse_resolver_conf_xml(plugin_source) def __parse_resolver_conf_xml(self, plugin_source): extra_kwds = { 'app_info': self.app_info } return plugin_config.load_plugins(self.resolver_classes, plugin_source, extra_kwds) def __default_containers_resolvers(self): default_resolvers = [ ExplicitContainerResolver(self.app_info), ExplicitSingularityContainerResolver(self.app_info), ] if self.enable_beta_mulled_containers: default_resolvers.extend([ CachedMulledDockerContainerResolver(self.app_info, namespace="biocontainers"), CachedMulledSingularityContainerResolver(self.app_info, namespace="biocontainers"), MulledDockerContainerResolver(self.app_info, namespace="biocontainers"), MulledSingularityContainerResolver(self.app_info, namespace="biocontainers"), BuildMulledDockerContainerResolver(self.app_info), BuildMulledSingularityContainerResolver(self.app_info), ]) return default_resolvers def __resolvers_dict(self): import galaxy.tools.deps.container_resolvers return plugin_config.plugins_dict(galaxy.tools.deps.container_resolvers, 'resolver_type')
[docs] def find_best_container_description(self, enabled_container_types, tool_info): """Yield best container description of supplied types matching tool info.""" for container_resolver in self.container_resolvers: if hasattr(container_resolver, "container_type"): if container_resolver.container_type not in enabled_container_types: continue container_description = container_resolver.resolve(enabled_container_types, tool_info) log.info("Checking with container resolver [%s] found description [%s]" % (container_resolver, container_description)) if container_description: assert container_description.type in enabled_container_types return container_description return None