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Source code for galaxy.tool_util.lint

"""This modules contains the functions that drive the tool linting framework."""

import inspect

from galaxy.tool_util.parser import get_tool_source
from galaxy.util import submodules
from galaxy.util.getargspec import getfullargspec

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.tool_util.linters tool_xml = getattr(tool_source, "xml_tree", None) linter_modules = submodules.import_submodules(galaxy.tool_util.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 = getfullargspec(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:
[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 {}... {}".format(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