mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Separate different style Galaxy testing behaviors into classes.
This commit is contained in:
John Chilton
+80
-78
@@ -8,7 +8,6 @@ that script for a list of options.
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import os
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import os.path
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import sys
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import tempfile
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galaxy_root = os.path.abspath(os.path.join(os.path.dirname(__file__), os.path.pardir))
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sys.path[1:1] = [ os.path.join( galaxy_root, "lib" ), os.path.join( galaxy_root, "test" ) ]
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@@ -17,93 +16,96 @@ from base import driver_util
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log = driver_util.build_logger()
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from base.api_util import get_master_api_key, get_user_api_key
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from galaxy.web import buildapp
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class GalaxyTestDriver(driver_util.TestDriver):
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"""Instantial a Galaxy-style nose TestDriver for testing Galaxy."""
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class MigratedToolsGalaxyTestDriver(driver_util.GalaxyTestDriver):
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"""Instantiate a Galaxy-style nose TestDriver for testing migrated Galaxy tools."""
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def setup(self):
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"""Setup a Galaxy server for functional test (if needed)."""
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# ---- Configuration ------------------------------------------------------
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testing_migrated_tools = _check_arg('-migrated')
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testing_installed_tools = _check_arg('-installed')
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testing_framework_tools = _check_arg('-framework')
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testing_data_manager = _check_arg('-data_managers')
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testing_workflow = _check_arg('-workflow')
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testing_shed_tools = testing_migrated_tools or testing_installed_tools
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testing_shed_tools = True
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datatypes_conf_override = None
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default_tool_conf = None
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def build_tests(self):
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"""Build migrated tool test methods."""
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self.setup_shed_tools(
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testing_migrated_tools=True,
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)
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self.build_tool_tests()
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if testing_framework_tools:
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default_tool_conf = driver_util.FRAMEWORK_SAMPLE_TOOLS_CONF
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datatypes_conf_override = driver_util.FRAMEWORK_DATATYPES_CONF
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external_galaxy = os.environ.get('GALAXY_TEST_EXTERNAL', None)
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class InstalledToolsGalaxyTestDriver(driver_util.GalaxyTestDriver):
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"""Galaxy-style nose TestDriver for testing installed Galaxy tools."""
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galaxy_test_tmp_dir = driver_util.get_galaxy_test_tmp_dir()
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self.temp_directories.append(galaxy_test_tmp_dir)
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testing_shed_tools = True
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if external_galaxy is None:
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tempdir = tempfile.mkdtemp( dir=galaxy_test_tmp_dir )
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# Configure the database path.
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galaxy_db_path = driver_util.database_files_path(tempdir)
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galaxy_config = driver_util.setup_galaxy_config(
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galaxy_db_path,
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use_test_file_dir=not testing_shed_tools,
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default_install_db_merged=True,
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default_tool_conf=default_tool_conf,
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datatypes_conf=datatypes_conf_override,
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)
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def build_tests(self):
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"""Build installed tool test methods."""
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self.setup_shed_tools(
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testing_installed_tools=True,
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)
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self.build_tool_tests()
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# ---- Build Application --------------------------------------------------
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app = driver_util.build_galaxy_app(galaxy_config)
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server_wrapper = driver_util.launch_server(
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app,
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buildapp.app_factory,
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galaxy_config,
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)
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self.server_wrappers.append(server_wrapper)
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log.info("Functional tests will be run against %s:%s" % (server_wrapper.host, server_wrapper.port))
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else:
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log.info("Functional tests will be run against %s" % external_galaxy)
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if testing_shed_tools:
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driver_util.setup_shed_tools_for_test(
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app,
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galaxy_test_tmp_dir,
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testing_migrated_tools,
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testing_installed_tools,
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)
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if testing_workflow:
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import functional.workflow
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functional.workflow.WorkflowTestCase.master_api_key = get_master_api_key()
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functional.workflow.WorkflowTestCase.user_api_key = get_user_api_key()
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if testing_data_manager:
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import functional.test_data_managers
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functional.test_data_managers.data_managers = app.data_managers # seems like a hack...
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functional.test_data_managers.build_tests(
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tmp_dir=galaxy_test_tmp_dir,
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testing_shed_tools=testing_shed_tools,
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master_api_key=get_master_api_key(),
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user_api_key=get_user_api_key(),
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)
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class DefaultGalaxyTestDriver(driver_util.GalaxyTestDriver):
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"""Default Galaxy-style nose test driver.
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if app is not None:
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# We must make sure that functional.test_toolbox is always imported after
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# database_contexts.galaxy_content is set (which occurs in this method above).
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# If functional.test_toolbox is imported before database_contexts.galaxy_content
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# is set, sa_session will be None in all methods that use it.
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import functional.test_toolbox
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functional.test_toolbox.toolbox = app.toolbox
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# When testing data managers, do not test toolbox.
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functional.test_toolbox.build_tests(
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app=app,
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testing_shed_tools=testing_shed_tools,
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master_api_key=get_master_api_key(),
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user_api_key=get_user_api_key(),
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)
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Just populate non-shed tool tests and run tests. Works
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for tool tests, regular twill tests, and API testing.
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"""
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def build_tests(self):
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"""Build framework tool test methods."""
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self.build_tool_tests()
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class FrameworkToolsGalaxyTestDriver(DefaultGalaxyTestDriver):
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"""Galaxy-style nose TestDriver for testing framework Galaxy tools."""
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default_tool_conf = driver_util.FRAMEWORK_SAMPLE_TOOLS_CONF
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datatypes_conf_override = driver_util.FRAMEWORK_DATATYPES_CONF
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class DataManagersGalaxyTestDriver(driver_util.GalaxyTestDriver):
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"""Galaxy-style nose TestDriver for testing framework Galaxy tools."""
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def build_tests(self):
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"""Build data manager test methods."""
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import functional.test_data_managers
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functional.test_data_managers.data_managers = self.app.data_managers
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functional.test_data_managers.build_tests(
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tmp_dir=self.galaxy_test_tmp_dir,
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testing_shed_tools=self.testing_shed_tools,
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master_api_key=get_master_api_key(),
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user_api_key=get_user_api_key(),
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)
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class WorkflowGalaxyTestDriver(driver_util.GalaxyTestDriver):
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"""Galaxy-style nose TestDriver for testing a Galaxy workflow."""
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def build_tests(self):
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"""Setup WorkflowTestCase for test execution."""
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import functional.workflow
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functional.workflow.WorkflowTestCase.master_api_key = get_master_api_key()
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functional.workflow.WorkflowTestCase.user_api_key = get_user_api_key()
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TEST_DRIVERS = {
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'-migrated': MigratedToolsGalaxyTestDriver,
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'-installed': InstalledToolsGalaxyTestDriver,
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'-framework': FrameworkToolsGalaxyTestDriver,
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'-data_managers': DataManagersGalaxyTestDriver,
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'-workflow': WorkflowGalaxyTestDriver,
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}
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def find_test_driver():
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"""Look at command-line args and find the correct Galaxy test driver."""
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test_driver = DefaultGalaxyTestDriver
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for key in TEST_DRIVERS.keys():
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if _check_arg(key):
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test_driver = TEST_DRIVERS[key]
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return test_driver
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def _check_arg( name ):
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@@ -116,4 +118,4 @@ def _check_arg( name ):
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return ret_val
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if __name__ == "__main__":
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driver_util.drive_test(GalaxyTestDriver)
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driver_util.drive_test(find_test_driver())
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@@ -22,7 +22,7 @@ import nose.plugins.manager
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from paste import httpserver
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from .api_util import get_master_api_key
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from .api_util import get_master_api_key, get_user_api_key
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from .tool_shed_util import parse_tool_panel_config
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from .nose_util import run
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from .instrument import StructuredTestDataPlugin
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@@ -30,6 +30,7 @@ from .instrument import StructuredTestDataPlugin
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from functional import database_contexts
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from galaxy.app import UniverseApplication as GalaxyUniverseApplication
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from galaxy.web import buildapp
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from galaxy.webapps.tool_shed.app import UniverseApplication as ToolshedUniverseApplication
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from galaxy.util import asbool
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from galaxy.util.properties import load_app_properties
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@@ -575,6 +576,72 @@ class TestDriver(object):
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self.tear_down()
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class GalaxyTestDriver(TestDriver):
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"""Instantial a Galaxy-style nose TestDriver for testing Galaxy."""
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testing_shed_tools = False
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def setup(self):
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"""Setup a Galaxy server for functional test (if needed)."""
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self.external_galaxy = os.environ.get('GALAXY_TEST_EXTERNAL', None)
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self.galaxy_test_tmp_dir = get_galaxy_test_tmp_dir()
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self.temp_directories.append(self.galaxy_test_tmp_dir)
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testing_shed_tools = getattr(self, "testing_shed_tools", False)
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default_tool_conf = getattr(self, "default_tool_conf", None)
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datatypes_conf_override = getattr(self, "datatypes_conf_override", None)
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if self.external_galaxy is None:
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tempdir = tempfile.mkdtemp(dir=self.galaxy_test_tmp_dir)
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# Configure the database path.
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galaxy_db_path = database_files_path(tempdir)
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galaxy_config = setup_galaxy_config(
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galaxy_db_path,
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use_test_file_dir=not testing_shed_tools,
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default_install_db_merged=True,
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default_tool_conf=default_tool_conf,
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datatypes_conf=datatypes_conf_override,
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)
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# ---- Build Application --------------------------------------------------
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self.app = build_galaxy_app(galaxy_config)
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server_wrapper = launch_server(
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self.app,
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buildapp.app_factory,
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galaxy_config,
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)
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self.server_wrappers.append(server_wrapper)
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log.info("Functional tests will be run against %s:%s" % (server_wrapper.host, server_wrapper.port))
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else:
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log.info("Functional tests will be run against %s" % self.external_galaxy)
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def setup_shed_tools(self, testing_migrated_tools=False, testing_installed_tools=True):
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setup_shed_tools_for_test(
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self.app,
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self.galaxy_test_tmp_dir,
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testing_migrated_tools,
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testing_installed_tools
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)
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def build_tool_tests(self):
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if self.app is None:
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return
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# We must make sure that functional.test_toolbox is always imported after
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# database_contexts.galaxy_content is set (which occurs in this method above).
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# If functional.test_toolbox is imported before database_contexts.galaxy_content
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# is set, sa_session will be None in all methods that use it.
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import functional.test_toolbox
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functional.test_toolbox.toolbox = self.app.toolbox
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# When testing data managers, do not test toolbox.
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functional.test_toolbox.build_tests(
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app=self.app,
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testing_shed_tools=self.testing_shed_tools,
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master_api_key=get_master_api_key(),
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user_api_key=get_user_api_key(),
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)
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def drive_test(test_driver_class):
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"""Instantiate driver class, run, and exit appropriately."""
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sys.exit(test_driver_class().run())
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@@ -591,7 +658,6 @@ __all__ = [
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"get_webapp_global_conf",
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"nose_config_and_run",
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"setup_galaxy_config",
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"setup_shed_tools_for_test",
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"TestDriver",
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"wait_for_http_server",
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]
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