Merge pull request #6430 from NicHerndon/dev

Unit testing with Python 3

lib/galaxy/datatypes/binary.py

@@ -683,7 +683,7 @@ class BcfUncompressed(Bcf):
 
     def sniff(self, filename):
         try:
-            header = open(filename).read(3)
+            header = open(filename, mode='rb').read(3)
             # The first 3 bytes of any BCF file are 'BCF', and the file is binary.
             if header == b'BCF':
                 return True

lib/galaxy/tools/parser/xml.py

@@ -252,7 +252,8 @@ class XmlToolSource(ToolSource):
             data_dict[output_def.name] = output_def
             return output_def
 
-        map(_parse, out_elem.findall("data"))
+        for _ in out_elem.findall("data"):
+            _parse(_)
 
         for collection_elem in out_elem.findall("collection"):
             name = collection_elem.get("name")

lib/galaxy/util/checkers.py

@@ -79,7 +79,7 @@ def check_gzip(file_path, check_content=True):
     # If the file is Bam, it should already have been detected as such, so we'll just check
     # for sff format.
     try:
-        header = gzip.open(file_path).read(4)
+        header = gzip.open(file_path, 'rb').read(4)
         if header == b'.sff':
             return (True, True)
     except Exception:

test/unit/jobs/test_runner_params.py

@@ -21,7 +21,7 @@ def test_missing_parameter():
         runners.RunnerParams(specs={}, params=dict(foo="bar"))
     except Exception as e:
         exception = e
-    assert exception.message == runners.JOB_RUNNER_PARAMETER_UNKNOWN_MESSAGE % "foo"
+    assert str(exception) == runners.JOB_RUNNER_PARAMETER_UNKNOWN_MESSAGE % "foo"
 
 
 def test_invalid_parameter():
@@ -30,7 +30,7 @@ def test_invalid_parameter():
         runners.RunnerParams(specs=dict(foo=dict(valid=lambda x: x != "bar", defualt="baz")), params=dict(foo="bar"))
     except Exception as e:
         exception = e
-    assert exception.message == runners.JOB_RUNNER_PARAMETER_VALIDATION_FAILED_MESSAGE % "foo"
+    assert str(exception) == runners.JOB_RUNNER_PARAMETER_VALIDATION_FAILED_MESSAGE % "foo"
 
 
 def test_map_problem():
@@ -39,7 +39,7 @@ def test_map_problem():
         runners.RunnerParams(specs=dict(foo=dict(map=lambda x: 1 / 0, default="baz")), params=dict(foo="bar"))
     except Exception as e:
         exception = e
-    assert exception.message == runners.JOB_RUNNER_PARAMETER_MAP_PROBLEM_MESSAGE % ("foo", "bar")
+    assert str(exception) == runners.JOB_RUNNER_PARAMETER_MAP_PROBLEM_MESSAGE % ("foo", "bar")
 
 
 def test_param_default():

test/unit/tools/test_evaluation.py

@@ -148,7 +148,7 @@ class ToolEvaluatorTestCase(TestCase, UsesApp):
         parameter = SelectToolParameter(self.tool, xml)
 
         def get_field_by_name_for_value(name, value, trans, other_values):
-            assert value == "/old/path/human"
+            assert value == b"/old/path/human"
             assert name == "path"
             return ["/old/path/human"]
 

test/unit/tools/test_parsing.py

@@ -177,11 +177,11 @@ class XmlLoaderTestCase(BaseLoaderTestCase):
     def test_requirements(self):
         requirements, containers = self._tool_source.parse_requirements_and_containers()
         assert requirements[0].type == "package"
-        assert containers[0].identifier == "mycool/bwa"
+        assert list(containers)[0].identifier == "mycool/bwa"
 
     def test_outputs(self):
         outputs, output_collections = self._tool_source.parse_outputs(object())
-        assert len(outputs) == 1
+        assert len(outputs) == 1, outputs
         assert len(output_collections) == 0
 
     def test_stdio(self):
@@ -339,7 +339,7 @@ class YamlLoaderTestCase(BaseLoaderTestCase):
         page_sources = input_pages.page_sources
         assert len(page_sources) == 1
         page_source = page_sources[0]
-        input_sources = page_source.parse_input_sources()
+        input_sources = list(page_source.parse_input_sources())
         assert len(input_sources) == 2
 
     def test_tests(self):

test/unit/tools/test_tool_dependency_description.py

@@ -35,7 +35,7 @@ def test_serialization():
     assert result_requirement.version == "2.0"
     assert result_requirement.type == "package"
 
-    result_tool_shed_dependency = result_descript.installed_tool_dependencies[0]
+    result_tool_shed_dependency = list(result_descript.installed_tool_dependencies)[0]
     result_tool_shed_dependency.name = "tophat"
     result_tool_shed_dependency.version = "2.0"
     result_tool_shed_dependency.type = "package"

test/unit/tools/test_tool_deps.py

@@ -453,7 +453,7 @@ def __assert_foo_exported(commands):
     command = ["bash", "-c", "%s; echo \"$FOO\"" % "".join(commands)]
     process = Popen(command, stdout=PIPE)
     output = process.communicate()[0].strip()
-    assert output == 'bar', "Command %s exports FOO as %s, not bar" % (command, output)
+    assert output == b'bar', "Command %s exports FOO as %s, not bar" % (command, output)
 
 
 def __setup_galaxy_package_dep(base_path, name, version, contents=""):

test/unit/workflows/test_extract_summary.py

@@ -55,7 +55,7 @@ class TestWorkflowExtractSummary(unittest.TestCase):
         assert len(job_dict) == 1
         fake_job = job_dict.keys()[0]
         assert fake_job.id.startswith("fake_")
-        datasets = job_dict.values()[0]
+        datasets = list(job_dict.values())[0]
         assert datasets == [(None, hda)]
 
     def test_fake_job_hdca(self):