Source code for planemo.linters.biocontainer_registered

"""Ensure best-practice biocontainer registered for this tool."""

from galaxy.tool_util.deps.container_resolvers.mulled import targets_to_mulled_name
from galaxy.tool_util.deps.mulled.util import build_target

from planemo.conda import tool_source_conda_targets

MESSAGE_WARN_NO_REQUIREMENTS = "No valid package requirement tags found to infer BioContainer from."
MESSAGE_WARN_NO_CONTAINER = "Failed to find a BioContainer registered for these requirements."
MESSAGE_INFO_FOUND_BIOCONTAINER = "BioContainer best-practice container found [%s]."

lint_tool_types = ["*"]


[docs]def lint_biocontainer_registered(tool_source, lint_ctx): conda_targets = tool_source_conda_targets(tool_source) if not conda_targets: lint_ctx.warn(MESSAGE_WARN_NO_REQUIREMENTS) return mulled_targets = [build_target(c.package, c.version) for c in conda_targets] name = mulled_container_name("biocontainers", mulled_targets) if name: lint_ctx.info(MESSAGE_INFO_FOUND_BIOCONTAINER % name) else: lint_ctx.warn(MESSAGE_WARN_NO_CONTAINER)
[docs]def mulled_container_name(namespace, targets): name = targets_to_mulled_name(targets=targets, hash_func="v2", namespace=namespace) if name: return f"quay.io/{namespace}/{name}"