diff env/lib/python3.7/site-packages/galaxy/tool_util/lint.py @ 5:9b1c78e6ba9c draft default tip

"planemo upload commit 6c0a8142489327ece472c84e558c47da711a9142"
author shellac
date Mon, 01 Jun 2020 08:59:25 -0400
parents 79f47841a781
children
line wrap: on
line diff
--- 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