diff env/lib/python3.9/site-packages/planemo/galaxy/test/structures.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/planemo/galaxy/test/structures.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,215 @@
+"""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