Fix galaxy testing for xunit reports in newer nose versions.

Fixes planemo for galaxyproject/galaxy#172.

planemo/commands/cmd_test.py

@@ -256,32 +256,20 @@ def __summarize_tests_full(
 
 def __summarize_test_case(structured_data, testcase_el, **kwds):
     summary_style = kwds.get("summary")
-    name_raw = testcase_el.attrib["name"]
-    tool_and_num = name_raw.split("TestForTool_", 1)[-1]
-    if "test_tool_" in tool_and_num:
-        tool, num = tool_and_num.split(".test_tool_", 1)
-        try:
-            num = int(num)
-        except ValueError:
-            pass
-        # Tempted to but something human friendly in here like
-        # num + 1 - but then it doesn't match HTML report.
-        label = "%s[%s]" % (tool, num)
-    else:
-        label = tool_and_num
+    test_id = galaxy_test.test_id(testcase_el)
     passed = len(list(testcase_el)) == 0
     if not passed:
         state = click.style("failed", bold=True, fg='red')
     else:
         state = click.style("passed", bold=True, fg='green')
-    click.echo(label + ": " + state)
+    click.echo(test_id.label + ": " + state)
     if summary_style != "minimal":
-        __print_command_line(structured_data, name_raw)
+        __print_command_line(structured_data, test_id)
 
 
 def __print_command_line(structured_data, test_id):
     try:
-        test = [d for d in structured_data if d["id"] == test_id][0]["data"]
+        test = [d for d in structured_data if d["id"] == test_id.id][0]["data"]
     except (KeyError, IndexError):
         # Failed to find structured data for this test - likely targetting
         # and older Galaxy version.

planemo/galaxy_test.py

@@ -1,6 +1,8 @@
 """ Utilities for reasoning about Galaxy test results.
 """
 from __future__ import absolute_import
+
+from collections import namedtuple
 import json
 import xml.etree.ElementTree as ET
 
@@ -37,7 +39,7 @@ def __init__(
         self.structured_data_by_id = structured_data_by_id
 
         if output_xml_path:
-            self.xunit_tree = ET.parse(output_xml_path)
+            self.xunit_tree = parse_xunit_report(output_xml_path)
             self.__merge_xunit()
             self.has_details = True
         else:
@@ -70,8 +72,8 @@ def __merge_xunit(self):
         self.num_problems = num_skips + num_errors + num_failures
 
         for testcase_el in self.xunit_testcase_elements:
-            id = testcase_el.get("name")
-            test_data = self.structured_data_by_id.get(id)
+            test = test_id(testcase_el)
+            test_data = self.structured_data_by_id.get(test.id)
             if not test_data:
                 continue
             problem_el = None
@@ -93,5 +95,60 @@ def all_tests_passed(self):
 
     @property
     def xunit_testcase_elements(self):
-        for testcase_el in self._xunit_root.findall("testcase"):
+        for testcase_el in find_testcases(self._xunit_root):
             yield testcase_el
+
+
+def parse_xunit_report(xunit_report_path):
+    return ET.parse(xunit_report_path)
+
+
+def find_testcases(xunit_root):
+    return xunit_root.findall("testcase")
+
+
+def test_id(testcase_el):
+    name_raw = testcase_el.attrib["name"]
+    if "TestForTool_" in name_raw:
+        raw_id = name_raw
+    else:
+        class_name = testcase_el.attrib["classname"]
+        raw_id = "{}.{}".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 "{}[{}]".format(self.name, self.num)
+    else:
+        return self.id
+
+
+TestId.label = _label

tests/data/xunit_nose_0_11.xml

@@ -0,0 +1 @@
+<?xml version="1.0" encoding="UTF-8"?><testsuite name="nosetests" tests="1" errors="0" failures="0" skip="0"><testcase classname="functional.test_toolbox.TestForTool_cat" name="functional.test_toolbox.TestForTool_cat.test_tool_000000" time="13" /></testsuite>

tests/data/xunit_nose_1_3.xml

@@ -0,0 +1 @@
+<?xml version="1.0" encoding="UTF-8"?><testsuite name="nosetests" tests="3" errors="0" failures="0" skip="0"><testcase classname="functional.test_toolbox.TestForTool_cat" name="test_tool_000000" time="12.190"></testcase></testsuite>

tests/test_galaxy_test.py

@@ -0,0 +1,29 @@
+""" Tests for the galaxy_test module :) """
+
+import os
+
+from .test_utils import TEST_DATA_DIR
+
+from planemo import galaxy_test
+
+nose_1_3_report = os.path.join(TEST_DATA_DIR, "xunit_nose_1_3.xml")
+nose_0_11_report = os.path.join(TEST_DATA_DIR, "xunit_nose_0_11.xml")
+
+
+def get_test_id_new():
+    _get_test_id(nose_1_3_report)
+
+
+def get_test_id_old():
+    _get_test_id(nose_0_11_report)
+
+
+def _get_test_id(path):
+    xml_tree = galaxy_test.parse_xunit_report(path)
+    root = xml_tree.getroot()
+    first_testcase = galaxy_test.find_testcases(root)[0]
+    test_id = galaxy_test.test_id(first_testcase)
+    assert test_id.label == "cat[0]"
+    expected_id = "functional.test_toolbox.TestForTool_cat.test_tool_000000"
+    assert test_id.id == expected_id
+    assert test_id.num == 0