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Source code for galaxy.tools.linters.general

"""This module contains a linting functions for general aspects of the tool."""
import re

import packaging.version

ERROR_VERSION_MSG = "Tool version is missing or empty."
WARN_VERSION_MSG = "Tool version [%s] is not compliant with PEP 440."
VALID_VERSION_MSG = "Tool defines a version [%s]."

ERROR_NAME_MSG = "Tool name is missing or empty."
VALID_NAME_MSG = "Tool defines a name [%s]."

ERROR_ID_MSG = "Tool does not define an id attribute."
VALID_ID_MSG = "Tool defines an id [%s]."

PROFILE_PATTERN = re.compile(r"^[1,2]\d\.[0,1]\d$")
PROFILE_INFO_DEFAULT_MSG = "Tool targets 16.01 Galaxy profile."
PROFILE_INFO_SPECIFIED_MSG = "Tool specifies profile version [%s]."
PROFILE_INVALID_MSG = "Tool specifies an invalid profile version [%s]."

lint_tool_types = ["*"]

[docs]def lint_general(tool_source, lint_ctx): """Check tool version, name, and id.""" version = tool_source.parse_version() parsed_version = packaging.version.parse(version) if not version: lint_ctx.error(ERROR_VERSION_MSG) elif isinstance(parsed_version, packaging.version.LegacyVersion): lint_ctx.warn(WARN_VERSION_MSG % version) else: lint_ctx.valid(VALID_VERSION_MSG % version) name = tool_source.parse_name() if not name: lint_ctx.error(ERROR_NAME_MSG) else: lint_ctx.valid(VALID_NAME_MSG % name) tool_id = tool_source.parse_id() if not tool_id: lint_ctx.error(ERROR_ID_MSG) else: lint_ctx.valid(VALID_ID_MSG % tool_id) profile = tool_source.parse_profile() profile_valid = PROFILE_PATTERN.match(profile) is not None if not profile_valid: lint_ctx.warn(PROFILE_INVALID_MSG) elif profile == "16.01": lint_ctx.valid(PROFILE_INFO_DEFAULT_MSG) else: lint_ctx.valid(PROFILE_INFO_SPECIFIED_MSG % profile) if re.search(r"\s", tool_id): lint_ctx.warn("Tool id contains a space - this is discouraged.")