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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")