"""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"^[12]\d\.\d{1,2}$")
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")