mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-21 22:06:53 +08:00
John Chilton
3c47105732
Instead of writing it below GALAXY_ROOT (which it shouldn't do at all) - add to the temp directory managed for the test so that special clean up logic isn't required for it. The global switch GALAXY_TEST_NO_CLEANUP can be used to recover the state of this file if needed now also.
184 lines
7.7 KiB
Python
184 lines
7.7 KiB
Python
#!/usr/bin/env python
|
|
"""Test driver for many Galaxy Python functional tests.
|
|
|
|
Launch this script by running ``run_tests.sh`` from GALAXY_ROOT, see
|
|
that script for a list of options.
|
|
"""
|
|
|
|
import os
|
|
import os.path
|
|
import sys
|
|
import tempfile
|
|
|
|
galaxy_root = os.path.abspath(os.path.join(os.path.dirname(__file__), os.path.pardir))
|
|
sys.path[1:1] = [ os.path.join( galaxy_root, "lib" ), os.path.join( galaxy_root, "test" ) ]
|
|
|
|
from base import driver_util
|
|
driver_util.configure_environment()
|
|
log = driver_util.build_logger()
|
|
|
|
from base.api_util import get_master_api_key, get_user_api_key
|
|
from base.test_logging import logging_config_file
|
|
from galaxy.web import buildapp
|
|
|
|
|
|
def main():
|
|
"""Entry point for test driver script."""
|
|
# ---- Configuration ------------------------------------------------------
|
|
testing_migrated_tools = _check_arg( '-migrated' )
|
|
testing_installed_tools = _check_arg( '-installed' )
|
|
datatypes_conf_override = None
|
|
|
|
testing_shed_tools = testing_migrated_tools or testing_installed_tools
|
|
if testing_shed_tools:
|
|
# We need the upload tool for functional tests, so we'll create a temporary tool panel config that defines it.
|
|
tool_config_file = driver_util.FRAMEWORK_UPLOAD_TOOL_CONF
|
|
else:
|
|
framework_test = _check_arg( '-framework' ) # Run through suite of tests testing framework.
|
|
if framework_test:
|
|
tool_conf = driver_util.FRAMEWORK_SAMPLE_TOOLS_CONF
|
|
datatypes_conf_override = driver_util.FRAMEWORK_DATATYPES_CONF
|
|
else:
|
|
# Use tool_conf.xml toolbox.
|
|
tool_conf = None
|
|
if _check_arg( '-with_framework_test_tools' ):
|
|
tool_conf = "%s,%s" % ( 'config/tool_conf.xml.sample', driver_util.FRAMEWORK_SAMPLE_TOOLS_CONF )
|
|
tool_config_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', tool_conf )
|
|
|
|
start_server = 'GALAXY_TEST_EXTERNAL' not in os.environ
|
|
tool_data_table_config_path = None
|
|
# ... otherise find whatever Galaxy would use as the default and
|
|
# the sample data for fucntional tests to that.
|
|
default_tool_data_config = 'config/tool_data_table_conf.xml.sample'
|
|
for tool_data_config in ['config/tool_data_table_conf.xml', 'tool_data_table_conf.xml' ]:
|
|
if os.path.exists( tool_data_config ):
|
|
default_tool_data_config = tool_data_config
|
|
tool_data_table_config_path = '%s,test/functional/tool-data/sample_tool_data_tables.xml' % default_tool_data_config
|
|
|
|
default_data_manager_config = 'config/data_manager_conf.xml.sample'
|
|
for data_manager_config in ['config/data_manager_conf.xml', 'data_manager_conf.xml' ]:
|
|
if os.path.exists( data_manager_config ):
|
|
default_data_manager_config = data_manager_config
|
|
data_manager_config_file = "%s,test/functional/tools/sample_data_manager_conf.xml" % default_data_manager_config
|
|
shed_tool_data_table_config = 'config/shed_tool_data_table_conf.xml'
|
|
galaxy_test_tmp_dir = os.environ.get( 'GALAXY_TEST_TMP_DIR', None )
|
|
if galaxy_test_tmp_dir is None:
|
|
galaxy_test_tmp_dir = tempfile.mkdtemp()
|
|
|
|
if start_server:
|
|
tempdir = tempfile.mkdtemp( dir=galaxy_test_tmp_dir )
|
|
# Configure the database path.
|
|
galaxy_db_path = driver_util.database_files_path(tempdir)
|
|
galaxy_config = driver_util.setup_galaxy_config(
|
|
galaxy_db_path,
|
|
use_test_file_dir=not testing_shed_tools,
|
|
default_install_db_merged=True,
|
|
)
|
|
|
|
# Data Manager testing temp path
|
|
# For storing Data Manager outputs and .loc files so that real ones don't get clobbered
|
|
data_manager_test_tmp_path = tempfile.mkdtemp( prefix='data_manager_test_tmp', dir=galaxy_test_tmp_dir )
|
|
galaxy_data_manager_data_path = tempfile.mkdtemp( prefix='data_manager_tool-data', dir=data_manager_test_tmp_path )
|
|
master_api_key = get_master_api_key()
|
|
|
|
app = None
|
|
server_wrapper = None
|
|
|
|
if start_server:
|
|
# ---- Build Application --------------------------------------------------
|
|
kwargs = dict( shed_tool_data_table_config=shed_tool_data_table_config,
|
|
test_conf="test.conf",
|
|
tool_config_file=tool_config_file,
|
|
tool_data_table_config_path=tool_data_table_config_path,
|
|
galaxy_data_manager_data_path=galaxy_data_manager_data_path,
|
|
update_integrated_tool_panel=False,
|
|
master_api_key=master_api_key,
|
|
cleanup_job='onsuccess',
|
|
enable_beta_tool_formats=True,
|
|
auto_configure_logging=logging_config_file is None,
|
|
data_manager_config_file=data_manager_config_file )
|
|
kwargs.update(galaxy_config)
|
|
if datatypes_conf_override:
|
|
kwargs[ 'datatypes_config_file' ] = datatypes_conf_override
|
|
|
|
app = driver_util.build_galaxy_app(kwargs)
|
|
server_wrapper = driver_util.launch_server(
|
|
app,
|
|
buildapp.app_factory,
|
|
kwargs,
|
|
)
|
|
log.info("Functional tests will be run against %s:%s" % (server_wrapper.host, server_wrapper.port))
|
|
|
|
# ---- Find tests ---------------------------------------------------------
|
|
success = False
|
|
try:
|
|
if testing_shed_tools:
|
|
driver_util.setup_shed_tools_for_test(
|
|
app,
|
|
galaxy_test_tmp_dir,
|
|
testing_migrated_tools,
|
|
testing_installed_tools,
|
|
)
|
|
workflow_test = _check_arg( '-workflow', param=True )
|
|
if workflow_test:
|
|
import functional.workflow
|
|
functional.workflow.WorkflowTestCase.workflow_test_file = workflow_test
|
|
functional.workflow.WorkflowTestCase.master_api_key = master_api_key
|
|
functional.workflow.WorkflowTestCase.user_api_key = get_user_api_key()
|
|
data_manager_test = _check_arg( '-data_managers', param=False )
|
|
if data_manager_test:
|
|
import functional.test_data_managers
|
|
functional.test_data_managers.data_managers = app.data_managers # seems like a hack...
|
|
functional.test_data_managers.build_tests(
|
|
tmp_dir=data_manager_test_tmp_path,
|
|
testing_shed_tools=testing_shed_tools,
|
|
master_api_key=master_api_key,
|
|
user_api_key=get_user_api_key(),
|
|
)
|
|
|
|
# We must make sure that functional.test_toolbox is always imported after
|
|
# database_contexts.galaxy_content is set (which occurs in this method above).
|
|
# If functional.test_toolbox is imported before database_contexts.galaxy_content
|
|
# is set, sa_session will be None in all methods that use it.
|
|
import functional.test_toolbox
|
|
functional.test_toolbox.toolbox = app.toolbox
|
|
# When testing data managers, do not test toolbox.
|
|
functional.test_toolbox.build_tests(
|
|
app=app,
|
|
testing_shed_tools=testing_shed_tools,
|
|
master_api_key=master_api_key,
|
|
user_api_key=get_user_api_key(),
|
|
)
|
|
|
|
success = driver_util.nose_config_and_run()
|
|
except:
|
|
log.exception( "Failure running tests" )
|
|
|
|
log.info( "Shutting down" )
|
|
# ---- Tear down -----------------------------------------------------------
|
|
if server_wrapper is not None:
|
|
server_wrapper.stop()
|
|
server_wrapper = None
|
|
driver_util.cleanup_directory(tempdir)
|
|
if success:
|
|
return 0
|
|
else:
|
|
return 1
|
|
|
|
|
|
def _check_arg( name, param=False ):
|
|
try:
|
|
index = sys.argv.index( name )
|
|
del sys.argv[ index ]
|
|
if param:
|
|
ret_val = sys.argv[ index ]
|
|
del sys.argv[ index ]
|
|
else:
|
|
ret_val = True
|
|
except ValueError:
|
|
ret_val = False
|
|
return ret_val
|
|
|
|
if __name__ == "__main__":
|
|
sys.exit( main() )
|