Merge pull request #12549 from jmchilton/test_app_1

Establish galaxy-app unit tests.

.circleci/config.yml

@@ -17,8 +17,8 @@ variables:
         - ~/.cache/yarn
   install_tox: &install_tox
     run: sudo pip install tox
-  install_ffprobe: &install_ffprobe
-    run: sudo apt-get update && sudo apt-get install ffmpeg -y
+  install_deb_reqs: &install_deb_reqs
+    run: sudo apt-get update && sudo apt-get install ffmpeg nodejs -y
   set_workdir: &set_workdir
     working_directory: ~/repo
   requires_get_code: &requires_get_code
@@ -100,7 +100,7 @@ jobs:
     steps:
       - *restore_repo_cache
       - *install_tox
-      - *install_ffprobe
+      - *install_deb_reqs
       - run: tox -e test_galaxy_release
   test_galaxy_packages:
     docker:
@@ -109,7 +109,7 @@ jobs:
     steps:
       - *restore_repo_cache
       - *install_tox
-      - *install_ffprobe
+      - *install_deb_reqs
       - run: tox -e test_galaxy_packages
   js_lint:
     docker:

lib/galaxy/app_unittest_utils/galaxy_mock.py

@@ -25,7 +25,7 @@ from galaxy.util import StructuredExecutionTimer
 from galaxy.util.bunch import Bunch
 from galaxy.util.dbkeys import GenomeBuilds
 from galaxy.web_stack import ApplicationStack
-from galaxy_test.base.celery_helper import rebind_container_to_task
+from .celery_helper import rebind_container_to_task
 
 
 # =============================================================================

lib/galaxy/app_unittest_utils/tools_support.py

@@ -11,10 +11,10 @@ from collections import defaultdict
 
 import galaxy.datatypes.registry
 import galaxy.model
+from galaxy.app_unittest_utils.galaxy_mock import MockApp
 from galaxy.tool_util.parser import get_tool_source
 from galaxy.tools import create_tool_from_source
 from galaxy.util.bunch import Bunch
-from .unittest_utils import galaxy_mock
 
 
 datatypes_registry = galaxy.datatypes.registry.Registry()
@@ -26,7 +26,7 @@ class UsesApp:
 
     def setup_app(self):
         self.test_directory = tempfile.mkdtemp()
-        self.app = galaxy_mock.MockApp()
+        self.app = MockApp()
         self.app.config.new_file_path = os.path.join(self.test_directory, "new_files")
         self.app.config.admin_users = "mary@example.com"
         self.app.job_search = None

lib/galaxy/util/__init__.py

@@ -1527,6 +1527,7 @@ def safe_str_cmp(a, b):
     return rv == 0
 
 
+#  Don't use these two directly, prefer method version that "works" with packaged Galaxy.
 galaxy_root_path = os.path.join(__path__[0], os.pardir, os.pardir, os.pardir)  # type: ignore
 galaxy_samples_path = os.path.join(__path__[0], os.pardir, 'config', 'sample')  # type: ignore
 
@@ -1539,7 +1540,7 @@ def galaxy_directory():
 
 
 def galaxy_samples_directory():
-    return os.path.abspath(galaxy_samples_path)
+    return os.path.join(galaxy_directory(), 'lib', 'galaxy', 'config', 'sample')
 
 
 def config_directories_from_setting(directories_setting, galaxy_root=galaxy_root_path):

lib/galaxy_test/driver/driver_util.py

@@ -26,6 +26,7 @@ import yaml
 from paste import httpserver
 
 from galaxy.app import UniverseApplication as GalaxyUniverseApplication
+from galaxy.app_unittest_utils.celery_helper import rebind_container_to_task
 from galaxy.config import LOGGING_CONFIG_DEFAULT
 from galaxy.model import mapping
 from galaxy.model.database_utils import create_database, database_exists
@@ -35,7 +36,6 @@ from galaxy.util import asbool, download_to_file, galaxy_directory
 from galaxy.util.properties import load_app_properties
 from galaxy.webapps.galaxy import buildapp
 from galaxy_test.base.api_util import get_admin_api_key, get_user_api_key
-from galaxy_test.base.celery_helper import rebind_container_to_task
 from galaxy_test.base.env import (
     DEFAULT_WEB_HOST,
     target_url_parts,

packages/app/MANIFEST.in

@@ -1,5 +1,5 @@
 include *.rst *.txt LICENSE
 include galaxy/*.yml
-include galaxy/config/sample/*.sample
+include galaxy/config/sample/*.sample*
 include galaxy/jobs/runners/util/job_script/*.sh
 include galaxy/tools/*tsv

packages/app/galaxy/app_unittest_utils

@@ -0,0 +1 @@
+../../../lib/galaxy/app_unittest_utils/

packages/app/galaxy/authnz

@@ -0,0 +1 @@
+../../../lib/galaxy/authnz/

packages/app/galaxy/dependencies

@@ -0,0 +1 @@
+../../../lib/galaxy/dependencies/

packages/app/galaxy_ext

@@ -0,0 +1 @@
+../../lib/galaxy_ext/

packages/app/requirements.txt

@@ -6,6 +6,8 @@ galaxy-web-framework
 galaxy-web-stack
 
 celery
+cloudauthz==0.6.0
+cwltool==3.0.20201109103151
 kombu
 Beaker
 pykwalify

packages/app/setup.py

@@ -32,7 +32,10 @@ TEST_DIR = 'tests'
 PACKAGES = [
     'galaxy',
     'galaxy.actions',
+    'galaxy.app_unittest_utils',
+    'galaxy.authnz',
     'galaxy.config',
+    'galaxy.dependencies',
     'galaxy.files',
     'galaxy.files.sources',
     'galaxy.forms',
@@ -90,6 +93,10 @@ PACKAGES = [
     'galaxy.workflow.reports',
     'galaxy.workflow.resources',
     'galaxy.workflow.schedulers',
+    'galaxy_ext',
+    'galaxy_ext.container_monitor',
+    'galaxy_ext.expressions',
+    'galaxy_ext.metadata',
 ]
 ENTRY_POINTS = '''
         [console_scripts]
@@ -99,6 +106,10 @@ ENTRY_POINTS = '''
 PACKAGE_DATA = {
     # Be sure to update MANIFEST.in for source dist.
     'galaxy': [
+        'config_schema.yml',
+        'job_config_schema.yml',
+        'uwsgi_schema.yml',
+        'config/sample/*',
     ],
     'tool_shed': [
         'scripts/bootstrap_tool_shed/user_info.xml',

packages/app/test-requirements.txt

@@ -1 +1,2 @@
 pytest
+testfixtures

packages/app/tests/app

@@ -0,0 +1 @@
+../../../test/unit/app/

packages/test.sh

@@ -14,7 +14,7 @@ TEST_ENV_DIR=${TEST_ENV_DIR:-$(mktemp -d -t gxpkgtestenvXXXXXX)}
 
 virtualenv -p "$TEST_PYTHON" "$TEST_ENV_DIR"
 . "${TEST_ENV_DIR}/bin/activate"
-pip install --upgrade pip setuptools wheel
+pip install --upgrade pip 'setuptools<58' wheel
 pip install -r../lib/galaxy/dependencies/pinned-lint-requirements.txt
 
 # ensure ordered by dependency dag

test/unit/app/authnz/test_custos_authnz.py

@@ -13,10 +13,10 @@ from urllib.parse import (
 import jwt
 import requests
 
+from galaxy.app_unittest_utils.galaxy_mock import MockTrans
 from galaxy.authnz import custos_authnz
 from galaxy.model import CustosAuthnzToken, User
 from galaxy.util import unicodify
-from ..unittest_utils.galaxy_mock import MockTrans
 
 
 class CustosAuthnzTestCase(unittest.TestCase):

test/unit/app/files/file_sources_conf.yml

@@ -0,0 +1 @@
+../../../integration/file_sources_conf.yml

test/unit/app/jobs/test_job_configuration.py

@@ -97,7 +97,19 @@ class BaseJobConfXmlParserTestCase(unittest.TestCase):
 
     def _write_config_from(self, path, template=None):
         template = template or {}
-        contents = open(path).read()
+        try:
+            contents = open(path).read()
+        except FileNotFoundError:
+            dir_path = os.path.dirname(path)
+            if os.path.exists(dir_path):
+                contents = os.listdir(dir_path)
+                raise Exception(f"Failed to find file {path}, directory {dir_path} exists and contains {contents}")
+            else:
+                dir_that_exists = dir_path
+                while not os.path.exists(dir_that_exists):
+                    dir_that_exists = os.path.dirname(dir_that_exists)
+                contents = os.listdir(dir_that_exists)
+                raise Exception(f"Failed to find file {path}, directory {dir_path} does not exist - {dir_that_exists} is the first root that exists and contains {contents}.")
         if template:
             contents = contents.format(**template)
         self._write_config(contents)

test/unit/app/jobs/test_job_wrapper.py

@@ -2,6 +2,7 @@ import os
 from contextlib import contextmanager
 from unittest import TestCase
 
+from galaxy.app_unittest_utils.tools_support import UsesApp
 from galaxy.jobs import (
     JobWrapper,
     TaskWrapper
@@ -13,7 +14,6 @@ from galaxy.model import (
 )
 from galaxy.tools import evaluation
 from galaxy.util.bunch import Bunch
-from ..tools_support import UsesApp
 
 TEST_TOOL_ID = "cufftest"
 TEST_VERSION_COMMAND = "bwa --version"

test/unit/app/jobs/test_runner_local.py

@@ -7,12 +7,12 @@ import psutil
 
 from galaxy import job_metrics
 from galaxy import model
+from galaxy.app_unittest_utils.tools_support import (
+    UsesApp,
+    UsesTools,
+)
 from galaxy.jobs.runners import local
 from galaxy.util import bunch
-from ..tools_support import (
-    UsesApp,
-    UsesTools
-)
 
 
 class TestLocalJobRunner(TestCase, UsesApp, UsesTools):

test/unit/app/managers/base.py

@@ -6,8 +6,8 @@ import unittest
 
 import sqlalchemy
 
+from galaxy.app_unittest_utils import galaxy_mock
 from galaxy.managers.users import UserManager
-from ..unittest_utils import galaxy_mock
 
 # =============================================================================
 admin_email = 'admin@admin.admin'
@@ -26,9 +26,6 @@ class BaseTestCase(unittest.TestCase):
     def tearDownClass(cls):
         print('\n', '-' * 20, 'end class', cls)
 
-    def __init__(self, *args):
-        unittest.TestCase.__init__(self, *args)
-
     def setUp(self):
         self.log('.' * 20, 'begin test', self)
         self.set_up_mocks()

test/unit/app/managers/test_HistoryManager.py

@@ -10,6 +10,7 @@ from galaxy import (
     exceptions,
     model
 )
+from galaxy.app_unittest_utils import galaxy_mock
 from galaxy.managers import (
     base,
     hdas
@@ -21,7 +22,6 @@ from galaxy.managers.histories import (
     HistorySerializer
 )
 from .base import BaseTestCase
-from ..unittest_utils import galaxy_mock
 
 default_password = '123456'
 user2_data = dict(email='user2@user2.user2', username='user2', password=default_password)

test/unit/app/managers/test_UserManager.py

@@ -3,9 +3,8 @@ User Manager testing.
 
 Executable directly using: python -m test.unit.managers.test_UserManager
 """
-import json
 import unittest
-from datetime import datetime, timedelta
+from datetime import datetime
 
 from sqlalchemy import desc
 
@@ -13,7 +12,6 @@ from galaxy import exceptions, model
 from galaxy.managers import base as base_manager
 from galaxy.managers import histories, users
 from galaxy.security.passwords import check_password
-from galaxy.webapps.galaxy.controllers.user import User
 from .base import BaseTestCase
 
 
@@ -139,32 +137,6 @@ class UserManagerTestCase(BaseTestCase):
         self.assertIsNotNone(user2.id)
         self.assertEqual(user2.email, user2_data["email"])
         self.assertTrue(check_password(default_password, user2.password))
-        controller = User(self.app)
-        response = json.loads(controller.login(self.trans))
-        self.assertEqual(response["err_msg"], "Please specify a username and password.")
-        response = json.loads(controller.login(self.trans, payload={"login": user2.email, "password": changed_password}))
-        self.assertEqual(response["err_msg"], "Invalid password.")
-        response = json.loads(controller.login(self.trans, payload={"login": user2.username, "password": changed_password}))
-        self.assertEqual(response["err_msg"], "Invalid password.")
-        user2.deleted = True
-        response = json.loads(controller.login(self.trans, payload={"login": user2.username, "password": default_password}))
-        self.assertEqual(response["err_msg"], "This account has been marked deleted, contact your local Galaxy administrator to restore the account. Contact: admin@email.to.")
-        user2.deleted = False
-        user2.external = True
-        response = json.loads(controller.login(self.trans, payload={"login": user2.username, "password": default_password}))
-        self.assertEqual(response["err_msg"], "This account was created for use with an external authentication method, contact your local Galaxy administrator to activate it. Contact: admin@email.to.")
-        user2.external = False
-        self.trans.app.config.password_expiration_period = timedelta(days=1)
-        user2.last_password_change = datetime.today() - timedelta(days=1)
-        response = json.loads(controller.login(self.trans, payload={"login": user2.username, "password": default_password}))
-        self.assertEqual(response["message"], "Your password has expired. Please reset or change it to access Galaxy.")
-        self.assertEqual(response["expired_user"], self.trans.security.encode_id(user2.id))
-        self.trans.app.config.password_expiration_period = timedelta(days=10)
-        response = json.loads(controller.login(self.trans, payload={"login": user2.username, "password": default_password}))
-        self.assertEqual(response["message"], "Your password will expire in 11 day(s).")
-        self.trans.app.config.password_expiration_period = timedelta(days=100)
-        response = json.loads(controller.login(self.trans, payload={"login": user2.username, "password": default_password}))
-        self.assertEqual(response["message"], "Success.")
 
     def test_empty_password(self):
         self.log("should be able to create a user with no password")

test/unit/app/queue_worker/conftest.py

@@ -8,8 +8,8 @@ try:
 except ImportError:
     psycopg2 = None
 
+from galaxy.app_unittest_utils import galaxy_mock
 from galaxy.util import which
-from ..unittest_utils import galaxy_mock
 
 
 def create_base_test(connection, amqp_type, amqp_connection=None):

test/unit/app/tools/test_actions.py

@@ -2,6 +2,7 @@ import string
 import unittest
 
 from galaxy import model
+from galaxy.app_unittest_utils import tools_support
 from galaxy.exceptions import UserActivationRequiredException
 from galaxy.tool_util.parser.output_objects import ToolOutput
 from galaxy.tools.actions import (
@@ -10,7 +11,6 @@ from galaxy.tools.actions import (
     on_text_for_names
 )
 from galaxy.util import XML
-from .. import tools_support
 
 
 # I cannot think of a saner way to test if data is being wrapped than use a

test/unit/app/tools/test_collect_primary_datasets.py

@@ -6,9 +6,9 @@ from galaxy import (
     model,
     util
 )
+from galaxy.app_unittest_utils import tools_support
 from galaxy.tool_util.parser import output_collection_def
 from galaxy.tool_util.provided_metadata import LegacyToolProvidedMetadata, NullToolProvidedMetadata
-from .. import tools_support
 
 DEFAULT_TOOL_OUTPUT = "out1"
 DEFAULT_EXTRA_NAME = "test1"

test/unit/app/tools/test_column_parameters.py

@@ -2,9 +2,9 @@
 test_select_parameters.py.
 """
 from galaxy import model
+from galaxy.app_unittest_utils.tools_support import datatypes_registry
 from galaxy.util import bunch
 from .util import BaseParameterTestCase
-from ..tools_support import datatypes_registry
 
 
 class DataColumnParameterTestCase(BaseParameterTestCase):

test/unit/app/tools/test_data_parameters.py

@@ -1,6 +1,6 @@
 from galaxy import model
+from galaxy.app_unittest_utils import galaxy_mock
 from .util import BaseParameterTestCase
-from ..unittest_utils import galaxy_mock
 
 
 class DataToolParameterTestCase(BaseParameterTestCase):

test/unit/app/tools/test_dataset_matcher.py

@@ -1,6 +1,7 @@
 from unittest import TestCase
 
 from galaxy import model
+from galaxy.app_unittest_utils.tools_support import UsesApp
 from galaxy.tools.parameters import (
     basic,
     dataset_matcher
@@ -10,7 +11,6 @@ from galaxy.util import (
     XML,
 )
 from .test_data_parameters import MockHistoryDatasetAssociation
-from ..tools_support import UsesApp
 
 
 class DatasetMatcherTestCase(TestCase, UsesApp):

test/unit/app/tools/test_evaluation.py

@@ -1,6 +1,7 @@
 import os
 from unittest import TestCase
 
+from galaxy.app_unittest_utils.tools_support import UsesApp
 from galaxy.job_execution.datasets import DatasetPath
 from galaxy.jobs import SimpleComputeEnvironment
 from galaxy.model import (
@@ -28,8 +29,6 @@ from galaxy.tools.parameters.grouping import (
 )
 from galaxy.util import XML
 from galaxy.util.bunch import Bunch
-# Test fixtures for Galaxy infrastructure.
-from ..tools_support import UsesApp
 
 # To Test:
 # - param_file handling.

test/unit/app/tools/test_execution.py

@@ -6,9 +6,9 @@ from unittest import TestCase
 import webob.exc
 
 import galaxy.model
+from galaxy.app_unittest_utils import tools_support
 from galaxy.tools.parameters import params_to_incoming
 from galaxy.util.bunch import Bunch
-from .. import tools_support
 
 BASE_REPEAT_TOOL_CONTENTS = '''<tool id="test_tool" name="Test Tool">
     <command>echo "$param1" #for $r in $repeat# "$r.param2" #end for# &lt; $out1</command>

test/unit/app/tools/test_history_imp_exp.py

@@ -5,13 +5,14 @@ import tempfile
 from shutil import rmtree
 
 from galaxy import model
+from galaxy.app_unittest_utils.galaxy_mock import MockApp
 from galaxy.exceptions import MalformedContents
 from galaxy.objectstore.unittest_utils import (
     Config as TestConfig,
 )
 from galaxy.tools.imp_exp import JobExportHistoryArchiveWrapper, JobImportHistoryArchiveWrapper, unpack_tar_gz_archive
 from galaxy.tools.imp_exp.export_history import create_archive
-from ..unittest_utils.galaxy_mock import MockApp
+from galaxy.util import galaxy_directory
 
 
 # good enough for the very specific tests we're writing as of now...
@@ -22,6 +23,10 @@ HISTORY_ATTRS = '''{"hid_counter": 2, "update_time": "2016-02-08 18:38:38.705058
 JOBS_ATTRS = '''[{"info": null, "tool_id": "upload1", "update_time": "2016-02-08T18:39:23.356482", "stdout": "", "input_mapping": {}, "tool_version": "1.1.4", "traceback": null, "command_line": "python /galaxy/tools/data_source/upload.py /galaxy /scratch/tmppwU9rD /scratch/tmpP4_45Y 1:/scratch/jobs/000/dataset_1_files:/data/000/dataset_1.dat", "exit_code": 0, "output_datasets": [1], "state": "ok", "create_time": "2016-02-08T18:38:39.153873", "params": {"files": [{"to_posix_lines": "Yes", "NAME": "None", "file_data": null, "space_to_tab": null, "url_paste": "/scratch/strio_url_paste_o6nrv8", "__index__": 0, "ftp_files": "", "uuid": "None"}], "paramfile": "/scratch/tmpP4_45Y", "file_type": "auto", "files_metadata": {"file_type": "auto", "__current_case__": 41}, "async_datasets": "None", "dbkey": "?"}, "stderr": ""}]'''
 
 
+def t_data_path(name):
+    return os.path.join(galaxy_directory(), "test-data", name)
+
+
 def _run_jihaw_cleanup(archive_dir, app=None):
     app = app or _mock_app()
     job = model.Job()
@@ -133,8 +138,8 @@ def test_export_dataset():
     sa_session.add(j)
     sa_session.flush()
 
-    app.object_store.update_from_file(d1, file_name="test-data/1.txt", create=True)
-    app.object_store.update_from_file(d2, file_name="test-data/2.bed", create=True)
+    app.object_store.update_from_file(d1, file_name=t_data_path("1.txt"), create=True)
+    app.object_store.update_from_file(d2, file_name=t_data_path("2.bed"), create=True)
 
     imported_history = _import_export(app, h)
 
@@ -201,8 +206,8 @@ def test_export_dataset_with_deleted_and_purged():
 
     assert d1.deleted
 
-    app.object_store.update_from_file(d1, file_name="test-data/1.txt", create=True)
-    app.object_store.update_from_file(d2, file_name="test-data/2.bed", create=True)
+    app.object_store.update_from_file(d1, file_name=t_data_path("1.txt"), create=True)
+    app.object_store.update_from_file(d2, file_name=t_data_path("2.bed"), create=True)
 
     imported_history = _import_export(app, h)
 
@@ -237,9 +242,9 @@ def test_multi_inputs():
     sa_session.add(j)
     sa_session.flush()
 
-    app.object_store.update_from_file(d1, file_name="test-data/1.txt", create=True)
-    app.object_store.update_from_file(d2, file_name="test-data/2.bed", create=True)
-    app.object_store.update_from_file(d3, file_name="test-data/4.bed", create=True)
+    app.object_store.update_from_file(d1, file_name=t_data_path("1.txt"), create=True)
+    app.object_store.update_from_file(d2, file_name=t_data_path("2.bed"), create=True)
+    app.object_store.update_from_file(d3, file_name=t_data_path("4.bed"), create=True)
 
     imported_history = _import_export(app, h)
 
@@ -444,8 +449,8 @@ def test_export_collection_with_copied_datasets_and_overlapping_hids():
     sa_session.add(dataset_history)
     sa_session.flush()
 
-    app.object_store.update_from_file(d1, file_name="test-data/1.txt", create=True)
-    app.object_store.update_from_file(d2, file_name="test-data/2.bed", create=True)
+    app.object_store.update_from_file(d1, file_name=t_data_path("1.txt"), create=True)
+    app.object_store.update_from_file(d2, file_name=t_data_path("2.bed"), create=True)
 
     d1_copy = d1.copy()
     d2_copy = d2.copy()
@@ -653,7 +658,7 @@ def _import_export(app, h, dest_export=None):
 
 
 def test_import_1901_default():
-    app, new_history = import_archive('test-data/exports/1901_two_datasets.tgz')
+    app, new_history = import_archive(t_data_path('exports/1901_two_datasets.tgz'))
     assert new_history
 
     datasets = new_history.datasets

test/unit/app/tools/test_metadata.py

@@ -3,11 +3,11 @@ import subprocess
 import unittest
 
 from galaxy import model
+from galaxy.app_unittest_utils import tools_support
 from galaxy.job_execution.datasets import DatasetPath
 from galaxy.metadata import get_metadata_compute_strategy
 from galaxy.objectstore import ObjectStorePopulator
-from galaxy.util import safe_makedirs
-from .. import tools_support
+from galaxy.util import galaxy_directory, safe_makedirs
 
 
 class MetadataTestCase(unittest.TestCase, tools_support.UsesApp, tools_support.UsesTools):
@@ -42,7 +42,7 @@ class MetadataTestCase(unittest.TestCase, tools_support.UsesApp, tools_support.U
         self._test_simple_output()
 
     def _test_simple_output(self):
-        source_file_name = os.path.join(os.getcwd(), "test/functional/tools/for_workflows/cat.xml")
+        source_file_name = os.path.join(galaxy_directory(), "test/functional/tools/for_workflows/cat.xml")
         self._init_tool_for_path(source_file_name)
         output_dataset = self._create_output_dataset(
             extension="fasta",
@@ -67,7 +67,7 @@ class MetadataTestCase(unittest.TestCase, tools_support.UsesApp, tools_support.U
         self._test_primary_dataset_output_extension()
 
     def _test_primary_dataset_output_extension(self):
-        source_file_name = os.path.join(os.getcwd(), "test/functional/tools/for_workflows/cat.xml")
+        source_file_name = os.path.join(galaxy_directory(), "test/functional/tools/for_workflows/cat.xml")
         self._init_tool_for_path(source_file_name)
         # setting extension to 'auto' here, results in the extension specified in
         # galaxy.json (below) being respected.
@@ -100,7 +100,7 @@ class MetadataTestCase(unittest.TestCase, tools_support.UsesApp, tools_support.U
         self._test_primary_dataset_output_metadata_override()
 
     def _test_primary_dataset_output_metadata_override(self):
-        source_file_name = os.path.join(os.getcwd(), "test/functional/tools/for_workflows/cat.xml")
+        source_file_name = os.path.join(galaxy_directory(), "test/functional/tools/for_workflows/cat.xml")
         self._init_tool_for_path(source_file_name)
         output_dataset = self._create_output_dataset(
             extension="auto",
@@ -124,7 +124,7 @@ class MetadataTestCase(unittest.TestCase, tools_support.UsesApp, tools_support.U
 
     def test_list_discovery_extended(self):
         self.app.config.metadata_strategy = "extended"
-        source_file_name = os.path.join(os.getcwd(), "test/functional/tools/collection_split_on_column.xml")
+        source_file_name = os.path.join(galaxy_directory(), "test/functional/tools/collection_split_on_column.xml")
         self._init_tool_for_path(source_file_name)
         collection = model.DatasetCollection(populated=False)
         collection.collection_type = "list"