This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

Source code for galaxy.tools.lint

"""This modules contains the functions that drive the tool linting framework."""
from __future__ import print_function

import inspect

from galaxy.util import submodules
from .parser import get_tool_source

LEVEL_ALL = "all"
LEVEL_WARN = "warn"
LEVEL_ERROR = "error"

[docs]def lint_tool_source(tool_source, level=LEVEL_ALL, fail_level=LEVEL_WARN, extra_modules=[], skip_types=[], name=None): lint_context = LintContext(level=level, skip_types=skip_types, object_name=name) lint_tool_source_with(lint_context, tool_source, extra_modules) return not lint_context.failed(fail_level)
[docs]def lint_xml(tool_xml, level=LEVEL_ALL, fail_level=LEVEL_WARN, extra_modules=[], skip_types=[], name=None): lint_context = LintContext(level=level, skip_types=skip_types, object_name=name) lint_xml_with(lint_context, tool_xml, extra_modules) return not lint_context.failed(fail_level)
[docs]def lint_tool_source_with(lint_context, tool_source, extra_modules=[]): import galaxy.tools.linters tool_xml = getattr(tool_source, "xml_tree", None) linter_modules = submodules.import_submodules(galaxy.tools.linters, ordered=True) linter_modules.extend(extra_modules) for module in linter_modules: tool_type = tool_source.parse_tool_type() or "default" lint_tool_types = getattr(module, "lint_tool_types", ["default"]) if not ("*" in lint_tool_types or tool_type in lint_tool_types): continue for (name, value) in inspect.getmembers(module): if callable(value) and name.startswith("lint_"): # Look at the first argument to the linter to decide # if we should lint the XML description or the abstract # tool parser object. first_arg = inspect.getargspec(value).args[0] if first_arg == "tool_xml": if tool_xml is None: # XML linter and non-XML tool, skip for now continue else: lint_context.lint(name, value, tool_xml) else: lint_context.lint(name, value, tool_source)
[docs]def lint_xml_with(lint_context, tool_xml, extra_modules=[]): tool_source = get_tool_source(xml_tree=tool_xml) return lint_tool_source_with(lint_context, tool_source, extra_modules=extra_modules)
# TODO: Nothing inherently tool-y about LintContext and in fact # it is reused for repositories in planemo. Therefore, it should probably # be moved to galaxy.util.lint.
[docs]class LintContext(object):
[docs] def __init__(self, level, skip_types=[], object_name=None): self.skip_types = skip_types self.level = level self.object_name = object_name self.found_errors = False self.found_warns = False
[docs] def lint(self, name, lint_func, lint_target): name = name.replace("tsts", "tests")[len("lint_"):] if name in self.skip_types: return self.printed_linter_info = False self.valid_messages = [] self.info_messages = [] self.warn_messages = [] self.error_messages = [] lint_func(lint_target, self) # TODO: colorful emoji if in click CLI. if self.error_messages: status = "FAIL" elif self.warn_messages: status = "WARNING" else: status = "CHECK" def print_linter_info(): if self.printed_linter_info: return self.printed_linter_info = True print("Applying linter %s... %s" % (name, status)) for message in self.error_messages: self.found_errors = True print_linter_info() print(".. ERROR: %s" % message) if self.level != LEVEL_ERROR: for message in self.warn_messages: self.found_warns = True print_linter_info() print(".. WARNING: %s" % message) if self.level == LEVEL_ALL: for message in self.info_messages: print_linter_info() print(".. INFO: %s" % message) for message in self.valid_messages: print_linter_info() print(".. CHECK: %s" % message)
def __handle_message(self, message_list, message, *args): if args: message = message % args message_list.append(message)
[docs] def valid(self, message, *args): self.__handle_message(self.valid_messages, message, *args)
[docs] def info(self, message, *args): self.__handle_message(self.info_messages, message, *args)
[docs] def error(self, message, *args): self.__handle_message(self.error_messages, message, *args)
[docs] def warn(self, message, *args): self.__handle_message(self.warn_messages, message, *args)
[docs] def failed(self, fail_level): found_warns = self.found_warns found_errors = self.found_errors if fail_level == LEVEL_WARN: lint_fail = (found_warns or found_errors) else: lint_fail = found_errors return lint_fail