diff env/lib/python3.9/site-packages/galaxy/tool_util/lint.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.9/site-packages/galaxy/tool_util/lint.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,146 @@
+"""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"
+
+
+def lint_tool_source(tool_source, level=LEVEL_ALL, fail_level=LEVEL_WARN, extra_modules=None, skip_types=None, name=None):
+    extra_modules = extra_modules or []
+    skip_types = skip_types or []
+    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=None, skip_types=None, name=None):
+    extra_modules = extra_modules or []
+    skip_types = skip_types or []
+    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=None):
+    extra_modules = extra_modules or []
+    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=None):
+    extra_modules = extra_modules or []
+    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:
+
+    def __init__(self, level, skip_types=None, object_name=None):
+        self.skip_types = skip_types or []
+        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(f"Applying linter {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