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Source code for galaxy.tool_util.linters.general

"""This module contains 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]."

WARN_WHITESPACE_MSG = "%s contains whitespace, this may cause errors: [%s]."
WARN_WHITESPACE_PRESUFFIX = "%s is pre/suffixed by whitespace, this may cause errors: [%s]."
WARN_ID_WHITESPACE_MSG = "Tool ID contains whitespace - this is discouraged: [%s]."

lint_tool_types = ["*"]

[docs]def lint_general(tool_source, lint_ctx): """Check tool version, name, and id.""" # determine line to report for general problems with outputs tool_xml = getattr(tool_source, "xml_tree", None) if tool_xml: tool_node = tool_xml.getroot() else: tool_node = None version = tool_source.parse_version() or "" parsed_version = packaging.version.parse(version) if not version: lint_ctx.error(ERROR_VERSION_MSG, node=tool_node) elif isinstance(parsed_version, packaging.version.LegacyVersion): lint_ctx.warn(WARN_VERSION_MSG % version, node=tool_node) elif version != version.strip(): lint_ctx.warn(WARN_WHITESPACE_PRESUFFIX % ("Tool version", version), node=tool_node) else: lint_ctx.valid(VALID_VERSION_MSG % version, node=tool_node) name = tool_source.parse_name() if not name: lint_ctx.error(ERROR_NAME_MSG, node=tool_node) elif name != name.strip(): lint_ctx.warn(WARN_WHITESPACE_PRESUFFIX % ("Tool name", name), node=tool_node) else: lint_ctx.valid(VALID_NAME_MSG % name, node=tool_node) tool_id = tool_source.parse_id() if not tool_id: lint_ctx.error(ERROR_ID_MSG, node=tool_node) elif re.search(r"\s", tool_id): lint_ctx.warn(WARN_ID_WHITESPACE_MSG % tool_id, node=tool_node) else: lint_ctx.valid(VALID_ID_MSG % tool_id, node=tool_node) profile = tool_source.parse_profile() profile_valid = PROFILE_PATTERN.match(profile) is not None if not profile_valid: lint_ctx.error(PROFILE_INVALID_MSG % profile, node=tool_node) elif profile == "16.01": lint_ctx.valid(PROFILE_INFO_DEFAULT_MSG, node=tool_node) else: lint_ctx.valid(PROFILE_INFO_SPECIFIED_MSG % profile, node=tool_node) requirements, containers, resource_requirements = tool_source.parse_requirements_and_containers() for r in requirements: if r.type == "package": if not r.name: lint_ctx.error("Requirement without name found") if not r.version: lint_ctx.warn(f"Requirement {r.name} defines no version") # Warn requirement attributes with leading/trailing whitespace: elif r.version != r.version.strip(): lint_ctx.warn(WARN_WHITESPACE_MSG % ("Requirement version", r.version)) for rr in resource_requirements: if rr.runtime_required: lint_ctx.warn("Expressions in resource requirement not supported yet")