Mercurial > repos > shellac > sam_consensus_v3
view env/lib/python3.9/site-packages/planemo/linters/biocontainer_registered.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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"""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 = ["*"] 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) def mulled_container_name(namespace, targets): name = targets_to_mulled_name(targets=targets, hash_func="v2", namespace=namespace) if name: return "quay.io/%s/%s" % (namespace, name)