Merge pull request #6638 from mvdbeek/move_tests_to_pytest_setup

Move tests to pytest setup

.coveragerc

@@ -1,3 +1,4 @@
 [run]
 branch = True
 include = lib/galaxy/*
+disable_warnings = include-ignored

lib/galaxy/jobs/runners/util/kill.py

@@ -23,7 +23,7 @@ def _psutil_kill_pid(pid):
     """
     try:
         parent = Process(pid)
-        for child in parent.get_children(recursive=True):
+        for child in parent.children(recursive=True):
             child.kill()
         parent.kill()
     except NoSuchProcess:

pytest.ini

@@ -1,4 +1,7 @@
 [pytest]
-log_cli=true
-log_level=DEBUG
-python_paths=lib
+addopts = --doctest-continue-on-failure
+log_level = DEBUG
+python_paths = lib
+markers =
+  data_manager: marks test as a data_manager test
+  tool: marks test as a tool test

run_tests.sh

@@ -16,6 +16,7 @@ cat <<EOF
                                     can be pytest selector
 '${0##*/} -toolshed (test_path)'    for running all the test scripts in the ./test/shed_functional/functional directory
 '${0##*/} -installed'               for running tests of Tool Shed installed tools
+'${0##*/} -main'                    for running tests of tools shipped with Galaxy
 '${0##*/} -framework'               for running through example tool tests testing framework features in test/functional/tools"
 '${0##*/} -framework -id toolid'    for testing one framework tool (in test/functional/tools/) with id 'toolid'
 '${0##*/} -data_managers -id data_manager_id'    for testing one Data Manager with id 'data_manager_id'
@@ -273,9 +274,9 @@ DOCKER_DEFAULT_IMAGE='galaxy/testing-base:18.09.0'
 
 test_script="./scripts/functional_tests.py"
 report_file="run_functional_tests.html"
+coverage_arg=""
 xunit_report_file=""
 structured_data_report_file=""
-with_framework_test_tools_arg=""
 skip_client_build="--skip-client-build"
 
 if [ "$1" = "--dockerize" ];
@@ -358,7 +359,7 @@ do
           fi
           ;;
       -a|-api|--api)
-          with_framework_test_tools_arg="-with_framework_test_tools"
+          GALAXY_TEST_TOOL_CONF="config/tool_conf.xml.sample,test/functional/tools/samples_tool_conf.xml"
           test_script="pytest"
           report_file="./run_api_tests.html"
           if [ $# -gt 1 ]; then
@@ -368,9 +369,10 @@ do
               api_script="./test/api"
               shift 1
           fi
+          coverage_file="api_coverage.xml"
           ;;
       -selenium|--selenium)
-          with_framework_test_tools_arg="-with_framework_test_tools"
+          GALAXY_TEST_TOOL_CONF="config/tool_conf.xml.sample,test/functional/tools/samples_tool_conf.xml"
           test_script="./scripts/functional_tests.py"
           report_file="./run_selenium_tests.html"
           skip_client_build=""
@@ -404,10 +406,6 @@ do
           export GALAXY_TEST_SKIP_FLAKEY_TESTS_ON_ERROR
           shift
           ;;
-      -with_framework_test_tools|--with_framework_test_tools)
-          with_framework_test_tools_arg="-with_framework_test_tools"
-          shift
-          ;;
       --external_url)
           GALAXY_TEST_EXTERNAL=$2
           shift 2
@@ -421,19 +419,46 @@ do
           shift 2
           ;;
       -f|-framework|--framework)
+          GALAXY_TEST_TOOL_CONF="test/functional/tools/samples_tool_conf.xml"
+          marker="-m tool"
+          test_script="pytest"
           report_file="run_framework_tests.html"
+          coverage_file="framework_coverage.xml"
+          framework_test=1;
+          shift 1
+          ;;
+      -main|-main_tools|--main_tools)
+          GALAXY_TEST_TOOL_CONF="config/tool_conf.xml.sample,config/tool_conf.xml.main"
+          marker="-m tool"
+          test_script="pytest"
+          report_file="run_framework_tests.html"
+          coverage_file="main_tools_coverage.xml"
           framework_test=1;
           shift 1
           ;;
       -d|-data_managers|--data_managers)
+          marker="-m data_manager"
+          test_script="pytest"
+          report_file="run_data_managers_tests.html"
+          coverage_file="data_managers_coverage.xml"
           data_managers_test=1;
           shift 1
           ;;
       -m|-migrated|--migrated)
+          GALAXY_TEST_TOOL_CONF="config/migrated_tools_conf.xml"
+          marker="-m tool"
+          test_script="pytest"
+          report_file="run_migrated_tests.html"
+          coverage_file="migrated_coverage.xml"
           migrated_test=1;
           shift
           ;;
       -i|-installed|--installed)
+          GALAXY_TEST_TOOL_CONF="config/shed_tool_conf.xml"
+          marker="-m tool"
+          test_script="pytest"
+          report_file="run_installed_tests.html"
+          coverage_file="installed_coverage.xml"
           installed_test=1;
           shift
           ;;
@@ -484,16 +509,19 @@ do
           ;;
       -u|-unit|--unit)
           report_file="run_unit_tests.html"
-          test_script="./scripts/nosetests.py"
+          test_script="pytest"
+          unit_extra='--doctest-modules --ignore lib/galaxy/webapps/tool_shed/controllers --ignore lib/galaxy/jobs/runners/chronos.py --ignore lib/galaxy/webapps/tool_shed/model/migrate --ignore lib/galaxy/util/jstree.py'
           if [ $# -gt 1 ]; then
-              unit_extra=$2
+              unit_extra="$unit_extra $2"
               shift 2
           else
-              unit_extra='--exclude=functional --exclude="^get" --exclude=controllers --exclude=runners --exclude dictobj --exclude=jstree lib test/unit'
+              unit_extra="$unit_extra lib test/unit"
               shift 1
           fi
+          coverage_file="unit_coverage.xml"
           ;;
       -i|-integration|--integration)
+          GALAXY_TEST_TOOL_CONF="config/tool_conf.xml.sample,test/functional/tools/samples_tool_conf.xml"
           test_script="pytest"
           report_file="./run_integration_tests.html"
           if [ $# -gt 1 ]; then
@@ -502,6 +530,7 @@ do
           else
               integration_extra="./test/integration"
               shift 1
+          coverage_file="integration_coverage.xml"
           fi
           ;;
       --no_cleanup)
@@ -578,31 +607,19 @@ fi
 
 setup_python
 
-if [ -n "$migrated_test" ] ; then
-    [ -n "$test_id" ] && class=":TestForTool_$test_id" || class=""
-    extra_args="functional.test_toolbox$class -migrated"
-elif [ -n "$installed_test" ] ; then
-    [ -n "$test_id" ] && class=":TestForTool_$test_id" || class=""
-    extra_args="functional.test_toolbox$class -installed"
-elif [ -n "$framework_test" ] ; then
-    [ -n "$test_id" ] && class=":TestForTool_$test_id" || class=""
-    extra_args="functional.test_toolbox$class -framework"
+if [ -n "$framework_test" -o -n "$installed_test" -o -n "$migrated_test" -o -n "$data_managers_test" ] ; then
+    [ -n "$test_id" ] && selector="-k $test_id" || selector=""
+    extra_args="test/functional/test_toolbox_pytest.py $selector $marker"
 elif [ -n "$selenium_test" ] ; then
     extra_args="$selenium_script -selenium"
-elif [ -n "$data_managers_test" ] ; then
-    [ -n "$test_id" ] && class=":TestForDataManagerTool_$test_id" || class=""
-    extra_args="functional.test_data_managers$class -data_managers"
 elif [ -n "$toolshed_script" ]; then
     extra_args="$toolshed_script"
 elif [ -n "$api_script" ]; then
     extra_args="$api_script"
 elif [ -n "$section_id" ]; then
     extra_args=`python tool_list.py $section_id`
-elif [ -n "$test_id" ]; then
-    class=":TestForTool_$test_id"
-    extra_args="functional.test_toolbox$class"
 elif [ -n "$unit_extra" ]; then
-    extra_args="--with-doctest $unit_extra"
+    extra_args="$unit_extra"
 elif [ -n "$integration_extra" ]; then
     extra_args="$integration_extra"
 elif [ -n "$test_target" ] ; then
@@ -627,12 +644,12 @@ if [ -n "$structured_data_report_file" ]; then
 else
     structured_data_args=""
 fi
-if [ -n "$with_framework_test_tools_arg" ]; then
-    GALAXY_TEST_TOOL_CONF="config/tool_conf.xml.sample,test/functional/tools/samples_tool_conf.xml"
-    export GALAXY_TEST_TOOL_CONF
-fi
+export GALAXY_TEST_TOOL_CONF
 if [ "$test_script" = 'pytest' ]; then
-    python -m "$test_script" -v --html "$report_file" $xunit_args $extra_args "$@"
+    if [ "$coverage_arg" = "--with_coverage" ]; then
+        coverage_arg="--cov-report term --cov-report xml:cov-unit.xml --cov=lib"
+    fi
+    "$test_script" -v --html "$report_file" $coverage_arg  $xunit_args $extra_args "$@"
 else
     python $test_script $coverage_arg -v --with-nosehtml --html-report-file $report_file $xunit_args $structured_data_args $extra_args "$@"
 fi

test/functional/known_broken_tools.txt

@@ -0,0 +1,11 @@
+# Deprecated, IUC provides same tool, kept for backwards compat?
+Extract genomic DNA 1
+# Relies on data table, but data table not available
+Interval2Maf1
+Interval2Maf_pairwise1
+maf_stats1
+Interval_Maf_Merged_Fasta2
+# No dependency available
+hgv_lps
+# Some weird parameter issue
+maf_by_block_number1

test/functional/test_toolbox_pytest.py

@@ -7,6 +7,7 @@ sys.path[1:1] = [os.path.join(galaxy_root, "lib"), os.path.join(galaxy_root, "te
 import pytest
 from base import driver_util
 
+SKIPTEST = os.path.join(os.path.dirname(__file__), 'known_broken_tools.txt')
 TEST_PREFIX = 'TestForTool_'
 
 
@@ -16,12 +17,20 @@ class DefaultGalaxyTestDriver(driver_util.GalaxyTestDriver):
     Just populate non-shed tool tests and run tests. Works
     for tool tests, regular twill tests, and API testing.
     """
+    conda_auto_init = True
+    conda_auto_install = True
 
     def build_tests(self):
         """Build framework tool test methods."""
         return self.build_tool_tests(return_test_classes=True)
 
 
+def get_skiplist():
+    with open(SKIPTEST) as skiptest:
+        skiplist = [l.strip() for l in skiptest if l.strip() and not l.startswith('#')]
+        return skiplist
+
+
 def galaxy_driver():
     driver = DefaultGalaxyTestDriver()
     driver.setup()
@@ -34,19 +43,34 @@ def driver(request):
     return DRIVER
 
 
-def cases():
+def get_cases():
     # We setup a global driver, so that the driver fixture can tear down the driver
     # Ideally `galaxy_driver` or `cases` would be fixtures and clean up after the yield,
     # but that's not compatible with the use use of pytest.mark.parametrize
     global DRIVER
     DRIVER = galaxy_driver()
     tests = DRIVER.build_tests()
+    cases = []
     for test_name, test_class in tests.items():
         if test_name.startswith(TEST_PREFIX):
             test_class.runTest = lambda : None
             test_instance = test_class()
-            for index in range(test_instance.test_count):
-                yield (test_name[len(TEST_PREFIX):] + "_test_%d" % (index + 1), test_instance, index)
+            cases.append(test_instance)
+    return cases
+
+
+def cases():
+    skiplist = get_skiplist()
+    for test_instance in get_cases():
+        for index in range(test_instance.test_count):
+            test = (test_instance.tool_id + "_test_%d" % (index + 1), test_instance, index)
+            marks = []
+            marks.append(pytest.mark.skipif(test_instance.tool_id in skiplist, reason="tool in skiplist"))
+            if 'data_manager_' in test_instance.tool_id:
+                marks.append(pytest.mark.data_manager(test))
+            else:
+                marks.append(pytest.mark.tool(test))
+            yield pytest.param(test, marks=marks)
 
 
 def idfn(val):

test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py

@@ -97,7 +97,7 @@ class TestDynamicToolDestination(unittest.TestCase):
     def test_brokenDestYML(self, l):
         self.assertRaises(JobMappingException, map_tool_to_destination, runJob, theApp, vanillaTool, "user@email.com", True, broken_default_dest_path, job_conf_path)
 
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'No global default destination specified in config!'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
@@ -110,7 +110,7 @@ class TestDynamicToolDestination(unittest.TestCase):
         self.assertRaises(JobMappingException, map_tool_to_destination, emptyJob, theApp, vanillaTool, "user@email.com", True, path, job_conf_path)
         self.assertRaises(JobMappingException, map_tool_to_destination, emptyJob, theApp, vanillaTool, "user@email.com", True, priority_path, job_conf_path)
 
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Loading file: input1' + script_dir + '/data/test.empty'),
@@ -129,7 +129,7 @@ class TestDynamicToolDestination(unittest.TestCase):
         self.assertRaises(JobMappingException, map_tool_to_destination, zeroJob, theApp, vanillaTool, "user@email.com", True, path, job_conf_path)
         self.assertRaises(JobMappingException, map_tool_to_destination, zeroJob, theApp, vanillaTool, "user@email.com", True, priority_path, job_conf_path)
 
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Total size: 0.00 B'),
@@ -146,7 +146,7 @@ class TestDynamicToolDestination(unittest.TestCase):
         self.assertRaises(JobMappingException, map_tool_to_destination, failJob, theApp, vanillaTool, "user@email.com", True, path, job_conf_path)
         self.assertRaises(JobMappingException, map_tool_to_destination, failJob, theApp, vanillaTool, "user@email.com", True, priority_path, job_conf_path)
 
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Loading file: input1' + script_dir + '/data/test1.full'),
@@ -167,7 +167,7 @@ class TestDynamicToolDestination(unittest.TestCase):
         priority_job = map_tool_to_destination(runJob, theApp, vanillaTool, "user@email.com", True, priority_path, job_conf_path)
         self.assertEquals(priority_job, 'Destination1_high')
 
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Loading file: input1' + script_dir + '/data/test3.full'),
@@ -190,7 +190,7 @@ class TestDynamicToolDestination(unittest.TestCase):
         priority_job = map_tool_to_destination(runJob, theApp, defaultTool, "user@email.com", True, priority_path, job_conf_path)
         self.assertEquals(priority_job, 'cluster_default_high')
 
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Tool 'test_tooldefault' not specified in config. Using default destination."),
@@ -209,7 +209,7 @@ class TestDynamicToolDestination(unittest.TestCase):
         priority_job = map_tool_to_destination(argJob, theApp, argTool, "user@email.com", True, priority_path, job_conf_path)
         self.assertEquals(priority_job, 'Destination6_med')
 
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Running 'test_arguments' with 'Destination6'."),
@@ -226,7 +226,7 @@ class TestDynamicToolDestination(unittest.TestCase):
         priority_job = map_tool_to_destination(argNotFoundJob, theApp, argTool, "user@email.com", True, priority_path, job_conf_path)
         self.assertEquals(priority_job, 'cluster_default_high')
 
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Running 'test_arguments' with 'cluster_default'."),
@@ -243,7 +243,7 @@ class TestDynamicToolDestination(unittest.TestCase):
         priority_job = map_tool_to_destination(runJob, theApp, unTool, "user@email.com", True, priority_path, job_conf_path)
         self.assertEquals(priority_job, 'cluster_default_high')
 
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Tool 'unregistered' not specified in config. Using default destination."),
@@ -262,7 +262,7 @@ class TestDynamicToolDestination(unittest.TestCase):
         priority_job = map_tool_to_destination(dbJob, theApp, dbTool, "user@email.com", True, priority_path, job_conf_path)
         self.assertEquals(priority_job, 'Destination4_high')
 
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Loading file: input1' + script_dir + '/data/test.fasta'),
@@ -283,7 +283,7 @@ class TestDynamicToolDestination(unittest.TestCase):
         priority_job = map_tool_to_destination(dbcountJob, theApp, dbTool, "user@email.com", True, priority_path, job_conf_path)
         self.assertEquals(priority_job, 'Destination4_high')
 
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Loading file: input1' + script_dir + '/data/test.fasta'),
@@ -302,7 +302,7 @@ class TestDynamicToolDestination(unittest.TestCase):
         job = map_tool_to_destination(runJob, theApp, noVBTool, "user@email.com", True, no_verbose_path, job_conf_path)
         self.assertEquals(job, 'Destination1')
 
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Running 'test_no_verbose' with 'Destination1'.")
         )
 
@@ -311,7 +311,7 @@ class TestDynamicToolDestination(unittest.TestCase):
         job = map_tool_to_destination(runJob, theApp, usersTool, "user@email.com", True, users_test_path, job_conf_path)
         self.assertEquals(job, 'special_cluster')
 
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Running 'test_users' with 'special_cluster'."),
         )
 
@@ -320,7 +320,7 @@ class TestDynamicToolDestination(unittest.TestCase):
         job = map_tool_to_destination(runJob, theApp, usersTool, "userblah@email.com", True, users_test_path, job_conf_path)
         self.assertEquals(job, 'lame_cluster')
 
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Running 'test_users' with 'lame_cluster'.")
         )
 
@@ -329,12 +329,12 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_no_file(self, l):
         self.assertRaises(IOError, dt.parse_yaml, path="")
-        l.check()
+        l.check_present()
 
     @log_capture()
     def test_bad_nice(self, l):
         dt.parse_yaml(path=yt.ivYMLTest11, job_conf_path=job_conf_path, test=True)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG',
              "Running config validation..."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG',
@@ -349,7 +349,7 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_no_tool_name(self, l):
         self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest3, job_conf_path=job_conf_path, test=True), yt.iv3dict)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Malformed YML; expected job name, but found a list instead!'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
@@ -358,7 +358,7 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_no_rule_type(self, l):
         self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest4, job_conf_path=job_conf_path, test=True), yt.ivDict)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No rule_type found for rule 1 in 'spades'."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
@@ -367,7 +367,7 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_no_rule_lower_bound(self, l):
         self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest51, job_conf_path=job_conf_path, test=True), yt.ivDict)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Missing bounds for rule 1 in 'spades'. Ignoring rule."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
@@ -376,7 +376,7 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_no_rule_upper_bound(self, l):
         self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest52, job_conf_path=job_conf_path, test=True), yt.ivDict)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Missing bounds for rule 1 in 'spades'. Ignoring rule."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
@@ -385,7 +385,7 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_no_rule_arg(self, l):
         self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest53, job_conf_path=job_conf_path, test=True), yt.ivDict53)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Found a fail_message for rule 1 in 'spades', but destination is not 'fail'! Setting destination to 'fail'."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
@@ -394,7 +394,7 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_bad_rule_type(self, l):
         self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest6, job_conf_path=job_conf_path, test=True), yt.ivDict)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Unrecognized rule_type 'iencs' found in 'spades'. Ignoring..."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
@@ -403,7 +403,7 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_no_err_msg(self, l):
         self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest91, job_conf_path=job_conf_path, test=True), yt.iv91dict)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No nice_value found for rule 1 in 'spades'. Setting nice_value to 0."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Missing a fail_message for rule 1 in 'spades'. Adding generic fail_message."),
@@ -413,7 +413,7 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_no_default_dest(self, l):
         dt.parse_yaml(path=yt.ivYMLTest7, job_conf_path=job_conf_path, test=True)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'No global default destination specified in config!'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
@@ -422,7 +422,7 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_invalid_category(self, l):
         dt.parse_yaml(path=yt.ivYMLTest8, job_conf_path=job_conf_path, test=True)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'No global default destination specified in config!'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Unrecognized category 'ice_cream' found in config file!"),
@@ -432,7 +432,7 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_arguments_no_err_msg(self, l):
         self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest12, job_conf_path=job_conf_path, test=True), yt.iv12dict)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG',
              "Missing a fail_message for rule 1 in 'spades'. Adding generic fail_message."),
@@ -442,7 +442,7 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_arguments_no_args(self, l):
         self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest131, job_conf_path=job_conf_path, test=True), yt.iv131dict)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG',
              "No arguments found for rule 1 in 'spades' despite being of type arguments. Ignoring rule."),
@@ -452,7 +452,7 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_arguments_no_arg(self, l):
         self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest132, job_conf_path=job_conf_path, test=True), yt.iv132dict)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Found a fail_message for rule 1 in 'spades', but destination is not 'fail'! Setting destination to 'fail'."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
@@ -461,14 +461,14 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_return_bool_for_multiple_jobs(self, l):
         self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest133, job_conf_path=job_conf_path, test=True, return_bool=True))
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Missing a fail_message for rule 1 in 'smalt'.")
         )
 
     @log_capture()
     def test_return_rule_for_multiple_jobs(self, l):
         self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest133, job_conf_path=job_conf_path, test=True), yt.iv133dict)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Missing a fail_message for rule 1 in 'smalt'. Adding generic fail_message."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
@@ -477,14 +477,14 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_return_bool_for_no_destination(self, l):
         self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest134, job_conf_path=job_conf_path, test=True, return_bool=True))
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No destination specified for rule 1 in 'spades'.")
         )
 
     @log_capture()
     def test_return_rule_for_no_destination(self, l):
         self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest134, job_conf_path=job_conf_path, test=True), yt.iv134dict)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No destination specified for rule 1 in 'spades'. Ignoring..."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
@@ -493,7 +493,7 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_return_rule_for_reversed_bounds(self, l):
         self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest135, job_conf_path=job_conf_path, test=True), yt.iv135dict)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "lower_bound exceeds upper_bound for rule 1 in 'spades'. Reversing bounds."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
@@ -502,14 +502,14 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_return_bool_for_missing_tool_fields(self, l):
         self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest136, job_conf_path=job_conf_path, test=True, return_bool=True))
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Tool 'spades' does not have rules nor a default_destination!")
         )
 
     @log_capture()
     def test_return_rule_for_missing_tool_fields(self, l):
         self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest136, job_conf_path=job_conf_path, test=True), yt.iv136dict)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Tool 'spades' does not have rules nor a default_destination!"),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
@@ -518,14 +518,14 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_return_bool_for_blank_tool(self, l):
         self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest137, job_conf_path=job_conf_path, test=True, return_bool=True))
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Config section for tool 'spades' is blank!")
         )
 
     @log_capture()
     def test_return_rule_for_blank_tool(self, l):
         self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest137, job_conf_path=job_conf_path, test=True), yt.iv137dict)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Config section for tool 'spades' is blank!"),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
@@ -534,7 +534,7 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_return_bool_for_malformed_users(self, l):
         self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest138, job_conf_path=job_conf_path, test=True, return_bool=True))
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Entry '123' in users for rule 1 in tool 'spades' is in an invalid format!"),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Supplied email 'invaliduser.email@com' for rule 1 in tool 'spades' is in an invalid format!")
         )
@@ -542,7 +542,7 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_return_rule_for_malformed_users(self, l):
         self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest138, job_conf_path=job_conf_path, test=True), yt.iv138dict)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Entry '123' in users for rule 1 in tool 'spades' is in an invalid format! Ignoring entry."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Supplied email 'invaliduser.email@com' for rule 1 in tool 'spades' is in an invalid format! Ignoring email."),
@@ -552,14 +552,14 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_return_bool_for_no_users(self, l):
         self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest139, job_conf_path=job_conf_path, test=True, return_bool=True))
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Couldn't find a list under 'users:'!")
         )
 
     @log_capture()
     def test_return_rule_for_no_users(self, l):
         self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest139, job_conf_path=job_conf_path, test=True), yt.iv139dict)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Couldn't find a list under 'users:'! Ignoring rule."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
@@ -568,7 +568,7 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_return_bool_for_malformed_user_email(self, l):
         self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest140, job_conf_path=job_conf_path, test=True, return_bool=True))
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Supplied email 'invalid.user2@com' for rule 2 in tool 'spades' is in an invalid format!"),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Supplied email 'invalid.user1@com' for rule 2 in tool 'spades' is in an invalid format!"),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No valid user emails were specified for rule 2 in tool 'spades'!")
@@ -577,7 +577,7 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_return_rule_for_malformed_user_email(self, l):
         self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest140, job_conf_path=job_conf_path, test=True), yt.iv140dict)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Supplied email 'invalid.user2@com' for rule 2 in tool 'spades' is in an invalid format! Ignoring email."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Supplied email 'invalid.user1@com' for rule 2 in tool 'spades' is in an invalid format! Ignoring email."),
@@ -588,7 +588,7 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_return_bool_for_empty_users(self, l):
         self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest141, job_conf_path=job_conf_path, test=True, return_bool=True))
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Entry 'None' in users for rule 2 in tool 'spades' is in an invalid format!"),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Entry 'None' in users for rule 2 in tool 'spades' is in an invalid format!"),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No valid user emails were specified for rule 2 in tool 'spades'!")
@@ -597,7 +597,7 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_return_rule_for_empty_users(self, l):
         self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest141, job_conf_path=job_conf_path, test=True), yt.iv141dict)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Entry 'None' in users for rule 2 in tool 'spades' is in an invalid format! Ignoring entry."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Entry 'None' in users for rule 2 in tool 'spades' is in an invalid format! Ignoring entry."),
@@ -608,7 +608,7 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_return_bool_for_bad_num_input_datasets_bounds(self, l):
         self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest142, job_conf_path=job_conf_path, test=True, return_bool=True))
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Error: lower_bound is set to Infinity, but must be lower than upper_bound!"),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "lower_bound exceeds upper_bound for rule 1 in 'smalt'.")
         )
@@ -616,7 +616,7 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_return_rule_for_bad_num_input_datasets_bound(self, l):
         self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest142, job_conf_path=job_conf_path, test=True), yt.iv142dict)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Error: lower_bound is set to Infinity, but must be lower than upper_bound! Setting lower_bound to 0!"),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
@@ -625,14 +625,14 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_return_bool_for_worse_num_input_datasets_bounds(self, l):
         self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest143, job_conf_path=job_conf_path, test=True, return_bool=True))
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Error: lower_bound is set to Infinity, but must be lower than upper_bound!")
         )
 
     @log_capture()
     def test_return_rule_for_worse_num_input_datasets_bound(self, l):
         self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest143, job_conf_path=job_conf_path, test=True), yt.iv143dict)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Error: lower_bound is set to Infinity, but must be lower than upper_bound! Setting lower_bound to 0!"),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
@@ -641,7 +641,7 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_tool_without_low_default_destination(self, l):
         dt.parse_yaml(path=yt.ivYMLTest146, job_conf_path=job_conf_path, test=True)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default_priority section found in config. Setting 'med' as default priority."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Invalid priority 'low' for rule 1 in 'smalt'. Ignoring..."),
@@ -651,7 +651,7 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_tool_with_invalid_priority_destination(self, l):
         dt.parse_yaml(path=yt.ivYMLTest147, job_conf_path=job_conf_path, test=True)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default_priority section found in config. Setting 'med' as default priority."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Invalid priority 'mine' for rule 1 in 'smalt'. Ignoring..."),
@@ -661,7 +661,7 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_not_all_priorities_in_tool(self, l):
         dt.parse_yaml(path=yt.ivYMLTest149, job_conf_path=job_conf_path, test=True)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default_priority section found in config. Setting 'med' as default priority."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
@@ -670,7 +670,7 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_rule_destination_not_in_job_conf(self, l):
         dt.parse_yaml(path=yt.ivYMLTest150, job_conf_path=job_conf_path, test=True)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default_priority section found in config. Setting 'med' as default priority."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Destination for 'blegh', rule 1: 'fake_destination' does not exist in job configuration. Ignoring..."),
@@ -680,7 +680,7 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_tool_default_destination_not_in_job_conf_with_no_rules(self, l):
         dt.parse_yaml(path=yt.ivYMLTest151, job_conf_path=job_conf_path, test=True)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default_priority section found in config. Setting 'med' as default priority."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Default destination for 'blah': 'not_true_destination' does not appear in the job configuration."),
@@ -691,7 +691,7 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_default_destination_not_in_job_conf(self, l):
         dt.parse_yaml(path=yt.ivYMLTest152, job_conf_path=job_conf_path, test=True)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Default destination 'no_such_dest' does not appear in the job configuration."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default_priority section found in config. Setting 'med' as default priority."),
@@ -701,7 +701,7 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_rule_destination_without_priority_not_in_job_conf(self, l):
         dt.parse_yaml(path=yt.ivYMLTest153, job_conf_path=job_conf_path, test=True)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default_priority section found in config. Setting 'med' as default priority."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Destination for 'blegh', rule 1: 'fake_destination' does not exist in job configuration. Ignoring..."),
@@ -711,7 +711,7 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_tool_default_destination_without_priority_not_in_job_conf_with_no_rules(self, l):
         dt.parse_yaml(path=yt.ivYMLTest154, job_conf_path=job_conf_path, test=True)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default_priority section found in config. Setting 'med' as default priority."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Default destination for 'blah': 'not_true_destination' does not appear in the job configuration."),
@@ -722,7 +722,7 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_default_destination_without_priority_not_in_job_conf(self, l):
         dt.parse_yaml(path=yt.ivYMLTest155, job_conf_path=job_conf_path, test=True)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Default destination 'no_such_dest' does not appear in the job configuration."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
@@ -731,7 +731,7 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_tool_rule_priority_does_not_exist(self, l):
         dt.parse_yaml(path=yt.ivYMLTest156, job_conf_path=job_conf_path, test=True)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default_priority section found in config. Setting 'med' as default priority."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Invalid priority 'notAPriority' for rule 1 in 'aTool'. Ignoring..."),
@@ -741,7 +741,7 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_tool_default_destination_priority_does_not_exist(self, l):
         dt.parse_yaml(path=yt.ivYMLTest157, job_conf_path=job_conf_path, test=True)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default_priority section found in config. Setting 'med' as default priority."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Invalid default destination priority 'notAPriority' for 'aTool'."),
@@ -751,7 +751,7 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_tool_default_destination_not_in_job_conf(self, l):
         dt.parse_yaml(path=yt.ivYMLTest158, job_conf_path=job_conf_path, test=True)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default_priority section found in config. Setting 'med' as default priority."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Default destination for 'blah': 'not_true_destination' does not appear in the job configuration."),
@@ -761,7 +761,7 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_tool_default_destination_without_priority_not_in_job_conf(self, l):
         dt.parse_yaml(path=yt.ivYMLTest159, job_conf_path=job_conf_path, test=True)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Default destination for 'blah': 'not_true_destination' does not appear in the job configuration."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
@@ -770,7 +770,7 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_empty_priority_dict(self, l):
         dt.parse_yaml(path=yt.ivYMLTest163, job_conf_path=job_conf_path, test=True)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No global default destinations specified in config!"),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
@@ -779,7 +779,7 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_default_dest_is_string_but_priorities_used_in_rule(self, l):
         dt.parse_yaml(path=yt.ivYMLTest161, job_conf_path=job_conf_path, test=True)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Invalid priority 'med' for rule 1 in 'blah'. Ignoring..."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
@@ -788,7 +788,7 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_default_dest_is_string_but_priorities_used_in_tool_default_dest(self, l):
         dt.parse_yaml(path=yt.ivYMLTest162, job_conf_path=job_conf_path, test=True)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Invalid default destination priority 'med' for 'blah'."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
@@ -797,7 +797,7 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_typo_in_str_default_dest(self, l):
         dt.parse_yaml(path=yt.ivYMLTest164, job_conf_path=job_conf_path, test=True)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Default destination 'cluster-kow' does not appear in the job configuration. Did you mean 'cluster_low'?"),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
@@ -806,7 +806,7 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_typo_in_dict_default_dest(self, l):
         dt.parse_yaml(path=yt.ivYMLTest165, job_conf_path=job_conf_path, test=True)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Default destination 'cluster_kow' does not appear in the job configuration. Did you mean 'cluster_low'?"),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
@@ -815,7 +815,7 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_typo_in_dict_tool_default_dest(self, l):
         dt.parse_yaml(path=yt.ivYMLTest166, job_conf_path=job_conf_path, test=True)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Default destination for 'blah': 'cluster_defaut' does not appear in the job configuration. Did you mean 'cluster_default'?"),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
@@ -824,7 +824,7 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_typo_in_str_tool_default_dest(self, l):
         dt.parse_yaml(path=yt.ivYMLTest167, job_conf_path=job_conf_path, test=True)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Default destination for 'blah': 'Destination_3_med' does not appear in the job configuration. Did you mean 'Destination3_med'?"),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
@@ -833,7 +833,7 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_typo_in_str_tool_rule_dest(self, l):
         dt.parse_yaml(path=yt.ivYMLTest168, job_conf_path=job_conf_path, test=True)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Destination for 'blah', rule 1: 'thig' does not exist in job configuration. Did you mean 'things'? Ignoring..."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
@@ -842,7 +842,7 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_typo_in_dict_tool_rule_dest(self, l):
         dt.parse_yaml(path=yt.ivYMLTest169, job_conf_path=job_conf_path, test=True)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Destination for 'blah', rule 1: 'even_lamerr_cluster' does not exist in job configuration. Did you mean 'even_lamer_cluster'? Ignoring..."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
@@ -851,7 +851,7 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_typo_in_case(self, l):
         dt.parse_yaml(path=yt.ivYMLTest170, job_conf_path=job_conf_path, test=True)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Default destination 'destinationf' does not appear in the job configuration. Did you mean 'DestinationF'?"),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
@@ -860,7 +860,7 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_invalid_verbose_value(self, l):
         dt.parse_yaml(path=yt.ivYMLTest171, job_conf_path=job_conf_path, test=True)
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Verbose value 'notavalue' is not True or False! Falling back to verbose..."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
@@ -869,14 +869,14 @@ class TestDynamicToolDestination(unittest.TestCase):
     @log_capture()
     def test_invalid_default_dest_valid_tool_default_dest_bool(self, l):
         self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest172, job_conf_path=job_conf_path, test=True, return_bool=True))
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Default destination 'fake_destination' does not appear in the job configuration."),
         )
 
     @log_capture()
     def test_valid_default_dest_invalid_tool_default_dest_bool(self, l):
         self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest173, job_conf_path=job_conf_path, test=True, return_bool=True))
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Default destination for 'blah': 'fake_destination' does not appear in the job configuration."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Tool 'blah' does not have rules nor a default_destination!"),
         )
@@ -900,7 +900,7 @@ class TestDynamicToolDestination(unittest.TestCase):
         self.assertTrue(dt.parse_yaml(yt.vYMLTest164, job_conf_path=job_conf_path, test=True, return_bool=True))
         self.assertEqual(dt.parse_yaml(yt.vYMLTest164, job_conf_path=job_conf_path, test=True), yt.vdictTest164_yml)
 
-        l.check(
+        l.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),

tox.ini

@@ -42,8 +42,6 @@ setenv =
     GALAXY_VIRTUAL_ENV={envdir}
     GALAXY_ENABLE_BETA_COMPRESSED_GENBANK_SNIFFING=1
 deps =
-    nose
-    NoseHTML
     mock
     mock-ssh-server
 
@@ -65,8 +63,6 @@ whitelist_externals = bash
 setenv =
     GALAXY_VIRTUAL_ENV={envdir}
 deps =
-    nose
-    NoseHTML
     mock
     mock-ssh-server