Mercurial > repos > shellac > guppy_basecaller
diff env/lib/python3.7/site-packages/galaxy/tool_util/lint.py @ 5:9b1c78e6ba9c draft default tip
"planemo upload commit 6c0a8142489327ece472c84e558c47da711a9142"
author | shellac |
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date | Mon, 01 Jun 2020 08:59:25 -0400 |
parents | 79f47841a781 |
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--- a/env/lib/python3.7/site-packages/galaxy/tool_util/lint.py Thu May 14 16:47:39 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,141 +0,0 @@ -"""This modules contains the functions that drive the tool linting framework.""" -from __future__ import print_function - -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" - - -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) - - -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) - - -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) - - -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. -class LintContext(object): - - 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 - - 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) - - def valid(self, message, *args): - self.__handle_message(self.valid_messages, message, *args) - - def info(self, message, *args): - self.__handle_message(self.info_messages, message, *args) - - def error(self, message, *args): - self.__handle_message(self.error_messages, message, *args) - - def warn(self, message, *args): - self.__handle_message(self.warn_messages, message, *args) - - 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