Mercurial > repos > guerler > springsuite
view planemo/lib/python3.7/site-packages/galaxy/tool_util/linters/general.py @ 1:56ad4e20f292 draft
"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
| author | guerler |
|---|---|
| date | Fri, 31 Jul 2020 00:32:28 -0400 |
| parents | |
| children |
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"""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 = ["*"] def lint_general(tool_source, lint_ctx): """Check tool version, name, and id.""" version = tool_source.parse_version() or '' 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.")
