Source code for galaxy.tool_util.deps.container_resolvers.explicit

"""This module describes the :class:`ExplicitContainerResolver` ContainerResolver plugin."""
import logging

from ..container_resolvers import (
    ContainerResolver,
)

log = logging.getLogger(__name__)


[docs]class ExplicitContainerResolver(ContainerResolver):
    """Find explicit containers referenced in the tool description (e.g. tool XML file) if present."""

    resolver_type = "explicit"

[docs]    def resolve(self, enabled_container_types, tool_info, **kwds):
        """Find a container explicitly mentioned in tool description.

        This ignores the tool requirements and assumes the tool author crafted
        a correct container.
        """
        for container_description in tool_info.container_descriptions:
            if self._container_type_enabled(container_description, enabled_container_types):
                return container_description

        return None


[docs]class ExplicitSingularityContainerResolver(ExplicitContainerResolver):

    resolver_type = 'explicit_singularity'
    container_type = 'singularity'

[docs]    def resolve(self, enabled_container_types, tool_info, **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:
            if container_description.type == 'docker':
                desc_dict = container_description.to_dict()
                desc_dict['type'] = self.container_type
                desc_dict['identifier'] = "docker://%s" % container_description.identifier
                container_description = container_description.from_dict(desc_dict)
            if self._container_type_enabled(container_description, enabled_container_types):
                return container_description

        return None


__all__ = ("ExplicitContainerResolver", "ExplicitSingularityContainerResolver")