view env/lib/python3.9/site-packages/planemo/galaxy/test/structures.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

"""Utilities for reasoning about Galaxy test results."""
from __future__ import absolute_import
from __future__ import print_function

import os
from typing 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 = "./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


class TestId(NamedTuple):
    name: str
    num: int
    id: str

    @property
    def label(self):
        if self.num is not None:
            return "{0}[{1}]".format(self.name, self.num)
        else:
            return self.id