Mercurial > repos > bcclaywell > argo_navis
diff venv/lib/python2.7/site-packages/planemo/tool_lint.py @ 0:d67268158946 draft
planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
author | bcclaywell |
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date | Mon, 12 Oct 2015 17:43:33 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/venv/lib/python2.7/site-packages/planemo/tool_lint.py Mon Oct 12 17:43:33 2015 -0400 @@ -0,0 +1,97 @@ +import os + +from planemo.io import info +from planemo.io import error + +import planemo.linters.xsd + +from planemo.tools import load_tool_elements_from_path, is_tool_load_error +from galaxy.tools.lint import lint_xml + +SKIP_XML_MESSAGE = "Skipping XML file - does not appear to be a tool %s." +LINTING_TOOL_MESSAGE = "Linting tool %s" +SHED_FILES = ["tool_dependencies.xml", "repository_dependencies.xml"] + + +def lint_tools_on_path(ctx, paths, lint_args, **kwds): + assert_tools = kwds.get("assert_tools", True) + recursive = kwds.get("recursive", False) + exit = 0 + valid_tools = 0 + for path in paths: + for (tool_path, tool_xml) in yield_tool_xmls(ctx, path, recursive): + if handle_tool_load_error(tool_path, tool_xml): + exit = 1 + continue + info("Linting tool %s" % tool_path) + if not lint_xml(tool_xml, **lint_args): + error("Failed linting") + exit = 1 + else: + valid_tools += 1 + if exit == 0 and valid_tools == 0 and assert_tools: + exit = 2 + return exit + + +def handle_tool_load_error(tool_path, tool_xml): + """ Return True if tool_xml is tool load error (invalid XML), and + print a helpful error message. + """ + is_error = False + if is_tool_load_error(tool_xml): + info("Could not lint %s due to malformed xml." % tool_path) + is_error = True + return is_error + + +def yield_tool_xmls(ctx, path, recursive=False): + tools = load_tool_elements_from_path( + path, + recursive, + register_load_errors=True, + ) + for (tool_path, tool_xml) in tools: + if is_tool_load_error(tool_xml): + yield (tool_path, tool_xml) + continue + if not _is_tool_xml(ctx, tool_path, tool_xml): + continue + yield (tool_path, tool_xml) + + +def build_lint_args(ctx, **kwds): + report_level = kwds.get("report_level", "all") + fail_level = kwds.get("fail_level", "warn") + skip = kwds.get("skip", None) + if skip is None: + skip = ctx.global_config.get("lint_skip", "") + if isinstance(skip, list): + skip = ",".join(skip) + + skip_types = [s.strip() for s in skip.split(",")] + lint_args = dict( + level=report_level, + fail_level=fail_level, + extra_modules=_lint_extra_modules(**kwds), + skip_types=skip_types, + ) + return lint_args + + +def _lint_extra_modules(**kwds): + xsd = kwds.get("xsd", False) + if xsd: + return [planemo.linters.xsd] + else: + return [] + + +def _is_tool_xml(ctx, tool_path, tool_xml): + if os.path.basename(tool_path) in SHED_FILES: + return False + if tool_xml.getroot().tag != "tool": + if ctx.verbose: + info(SKIP_XML_MESSAGE % tool_path) + return False + return True