Mercurial > repos > shellac > guppy_basecaller
view env/lib/python3.7/site-packages/planemo/galaxy/test/structures.py @ 0:26e78fe6e8c4 draft
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author | shellac |
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date | Sat, 02 May 2020 07:14:21 -0400 |
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"""Utilities for reasoning about Galaxy test results.""" from __future__ import absolute_import from __future__ import print_function import os from collections import namedtuple from xml.etree import ElementTree as ET from six.moves import shlex_quote from planemo.io import error from planemo.test.results import StructuredData as BaseStructuredData NO_STRUCTURED_FILE = ( "Warning: Problem with target Galaxy, it did not " "produce a structured test results file [%s] - summary " "information and planemo reports will be incorrect." ) class GalaxyTestCommand(object): """Abstraction around building a ``run_tests.sh`` command for Galaxy tests.""" def __init__( self, html_report_file, xunit_report_file, structured_report_file, failed=False, installed=False, ): self.html_report_file = html_report_file self.xunit_report_file = xunit_report_file self.structured_report_file = structured_report_file self.failed = failed self.installed = installed def build(self): xunit_report_file = self.xunit_report_file sd_report_file = self.structured_report_file cmd = "sh run_tests.sh $COMMON_STARTUP_ARGS --report_file %s" % shlex_quote(self.html_report_file) if xunit_report_file: cmd += " --xunit_report_file %s" % shlex_quote(xunit_report_file) if sd_report_file: cmd += " --structured_data_report_file %s" % shlex_quote(sd_report_file) if self.installed: cmd += ' -installed' elif self.failed: sd = StructuredData(sd_report_file) tests = " ".join(sd.failed_ids) cmd += " %s" % tests else: cmd += ' functional.test_toolbox' return cmd class StructuredData(BaseStructuredData): """Abstraction around Galaxy's structured test data output.""" def __init__(self, json_path): if not json_path or not os.path.exists(json_path): error(NO_STRUCTURED_FILE % json_path) super(StructuredData, self).__init__(json_path) def merge_xunit(self, xunit_root): self.has_details = True xunit_attrib = xunit_root.attrib num_tests = int(xunit_attrib.get("tests", 0)) num_failures = int(xunit_attrib.get("failures", 0)) num_errors = int(xunit_attrib.get("errors", 0)) num_skips = int(xunit_attrib.get("skips", 0)) summary = dict( num_tests=num_tests, num_failures=num_failures, num_errors=num_errors, num_skips=num_skips, ) self.structured_data["summary"] = summary for testcase_el in xunit_t_elements_from_root(xunit_root): test = case_id(testcase_el) test_data = self.structured_data_by_id.get(test.id) if not test_data: continue problem_el = None for problem_type in ["skip", "failure", "error"]: problem_el = testcase_el.find(problem_type) if problem_el is not None: break if problem_el is not None: status = problem_el.tag test_data["problem_type"] = problem_el.attrib["type"] test_data["problem_log"] = problem_el.text else: status = "success" test_data["status"] = status class GalaxyTestResults(object): """ Class that combine the test-centric xunit output with the Galaxy centric structured data output - and abstracts away the difference (someday). """ def __init__( self, output_json_path, output_xml_path, output_html_path, exit_code, ): self.output_html_path = output_html_path sd = StructuredData(output_json_path) self.sd = sd self.structured_data = sd.structured_data self.structured_data_tests = sd.structured_data_tests self.structured_data_by_id = sd.structured_data_by_id self.xunit_tree = parse_xunit_report(output_xml_path) sd.merge_xunit(self._xunit_root) self.sd.set_exit_code(exit_code) self.sd.read_summary() self.sd.update() @property def exit_code(self): return self.sd.exit_code @property def has_details(self): return self.sd.has_details @property def num_tests(self): return self.sd.num_tests @property def num_problems(self): return self.sd.num_problems @property def _xunit_root(self): return self.xunit_tree.getroot() @property def all_tests_passed(self): return self.sd.num_problems == 0 @property def xunit_testcase_elements(self): return xunit_t_elements_from_root(self._xunit_root) def xunit_t_elements_from_root(xunit_root): for testcase_el in find_cases(xunit_root): yield testcase_el def parse_xunit_report(xunit_report_path): return ET.parse(xunit_report_path) def find_cases(xunit_root): return xunit_root.findall("testcase") def case_id(testcase_el=None, raw_id=None): if raw_id is None: assert testcase_el is not None name_raw = testcase_el.attrib["name"] if "TestForTool_" in name_raw: raw_id = name_raw else: class_name = testcase_el.attrib["classname"] raw_id = "{0}.{1}".format(class_name, name_raw) name = None num = None if "TestForTool_" in raw_id: tool_and_num = raw_id.split("TestForTool_")[-1] if ".test_tool_" in tool_and_num: name, num_str = tool_and_num.split(".test_tool_", 1) num = _parse_num(num_str) # Tempted to but something human friendly in here like # num + 1 - but then it doesn't match HTML report. else: name = tool_and_num else: name = raw_id return TestId(name, num, raw_id) def _parse_num(num_str): try: num = int(num_str) except ValueError: num = None return num TestId = namedtuple("TestId", ["name", "num", "id"]) @property def _label(self): if self.num is not None: return "{0}[{1}]".format(self.name, self.num) else: return self.id TestId.label = _label