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

"planemo upload commit 6c0a8142489327ece472c84e558c47da711a9142"

--- a/env/lib/python3.7/site-packages/planemo/galaxy/test/structures.py	Thu May 14 16:47:39 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,216 +0,0 @@
-"""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