def setup(self):
"""Entry point for test driver script."""
# ---- Configuration ------------------------------------------------------
tool_shed_test_tmp_dir = driver_util.setup_tool_shed_tmp_dir()
if not os.path.isdir(tool_shed_test_tmp_dir):
os.mkdir(tool_shed_test_tmp_dir)
self.temp_directories.append(tool_shed_test_tmp_dir)
shed_db_path = driver_util.database_files_path(tool_shed_test_tmp_dir,
prefix="TOOL_SHED")
shed_tool_data_table_conf_file = os.environ.get(
'TOOL_SHED_TEST_TOOL_DATA_TABLE_CONF',
os.path.join(tool_shed_test_tmp_dir,
'shed_tool_data_table_conf.xml'))
galaxy_shed_data_manager_conf_file = os.environ.get(
'GALAXY_SHED_DATA_MANAGER_CONF',
os.path.join(tool_shed_test_tmp_dir,
'test_shed_data_manager_conf.xml'))
default_tool_data_table_config_path = os.path.join(
tool_shed_test_tmp_dir, 'tool_data_table_conf.xml')
galaxy_shed_tool_conf_file = os.environ.get(
'GALAXY_TEST_SHED_TOOL_CONF',
os.path.join(tool_shed_test_tmp_dir, 'test_shed_tool_conf.xml'))
galaxy_migrated_tool_conf_file = os.environ.get(
'GALAXY_TEST_MIGRATED_TOOL_CONF',
os.path.join(tool_shed_test_tmp_dir,
'test_migrated_tool_conf.xml'))
galaxy_tool_sheds_conf_file = os.environ.get(
'GALAXY_TEST_TOOL_SHEDS_CONF',
os.path.join(tool_shed_test_tmp_dir, 'test_sheds_conf.xml'))
if 'GALAXY_TEST_TOOL_DATA_PATH' in os.environ:
tool_data_path = os.environ.get('GALAXY_TEST_TOOL_DATA_PATH')
else:
tool_data_path = tempfile.mkdtemp(dir=tool_shed_test_tmp_dir)
os.environ['GALAXY_TEST_TOOL_DATA_PATH'] = tool_data_path
galaxy_db_path = driver_util.database_files_path(
tool_shed_test_tmp_dir)
shed_file_path = os.path.join(shed_db_path, 'files')
hgweb_config_file_path = tempfile.mkdtemp(dir=tool_shed_test_tmp_dir)
new_repos_path = tempfile.mkdtemp(dir=tool_shed_test_tmp_dir)
galaxy_shed_tool_path = tempfile.mkdtemp(dir=tool_shed_test_tmp_dir)
galaxy_migrated_tool_path = tempfile.mkdtemp(
dir=tool_shed_test_tmp_dir)
hgweb_config_dir = hgweb_config_file_path
os.environ['TEST_HG_WEB_CONFIG_DIR'] = hgweb_config_dir
print("Directory location for hgweb.config:", hgweb_config_dir)
toolshed_database_conf = driver_util.database_conf(shed_db_path,
prefix="TOOL_SHED")
kwargs = dict(
admin_users='*****@*****.**',
allow_user_creation=True,
allow_user_deletion=True,
datatype_converters_config_file=
'datatype_converters_conf.xml.sample',
file_path=shed_file_path,
hgweb_config_dir=hgweb_config_dir,
job_queue_workers=5,
id_secret='changethisinproductiontoo',
log_destination="stdout",
new_file_path=new_repos_path,
running_functional_tests=True,
shed_tool_data_table_config=shed_tool_data_table_conf_file,
smtp_server='smtp.dummy.string.tld',
email_from='functional@localhost',
template_path='templates',
tool_parse_help=False,
use_heartbeat=False)
kwargs.update(toolshed_database_conf)
# Generate the tool_data_table_conf.xml file.
open(default_tool_data_table_config_path,
'w').write(tool_data_table_conf_xml_template)
# Generate the shed_tool_data_table_conf.xml file.
open(shed_tool_data_table_conf_file,
'w').write(tool_data_table_conf_xml_template)
os.environ[
'TOOL_SHED_TEST_TOOL_DATA_TABLE_CONF'] = shed_tool_data_table_conf_file
# ---- Build Tool Shed Application --------------------------------------------------
toolshedapp = driver_util.build_shed_app(kwargs)
# ---- Run tool shed webserver ------------------------------------------------------
# TODO: Needed for hg middleware ('lib/galaxy/webapps/tool_shed/framework/middleware/hg.py')
kwargs['global_conf']['database_connection'] = kwargs[
"database_connection"]
tool_shed_server_wrapper = driver_util.launch_server(
toolshedapp,
toolshedbuildapp.app_factory,
kwargs,
prefix="TOOL_SHED",
)
self.server_wrappers.append(tool_shed_server_wrapper)
tool_shed_test_host = tool_shed_server_wrapper.host
tool_shed_test_port = tool_shed_server_wrapper.port
log.info("Functional tests will be run against %s:%s" %
(tool_shed_test_host, tool_shed_test_port))
# ---- Optionally start up a Galaxy instance ------------------------------------------------------
if 'TOOL_SHED_TEST_OMIT_GALAXY' not in os.environ:
# Generate the shed_tool_conf.xml file.
tool_sheds_conf_template_parser = string.Template(
tool_sheds_conf_xml_template)
tool_sheds_conf_xml = tool_sheds_conf_template_parser.safe_substitute(
shed_url=tool_shed_test_host, shed_port=tool_shed_test_port)
open(galaxy_tool_sheds_conf_file, 'w').write(tool_sheds_conf_xml)
# Generate the tool_sheds_conf.xml file.
shed_tool_conf_template_parser = string.Template(
shed_tool_conf_xml_template)
shed_tool_conf_xml = shed_tool_conf_template_parser.safe_substitute(
shed_tool_path=galaxy_shed_tool_path)
open(galaxy_shed_tool_conf_file, 'w').write(shed_tool_conf_xml)
# Generate the migrated_tool_conf.xml file.
migrated_tool_conf_xml = shed_tool_conf_template_parser.safe_substitute(
shed_tool_path=galaxy_migrated_tool_path)
open(galaxy_migrated_tool_conf_file,
'w').write(migrated_tool_conf_xml)
os.environ[
'GALAXY_TEST_SHED_TOOL_CONF'] = galaxy_shed_tool_conf_file
# Generate shed_data_manager_conf.xml
if not os.environ.get('GALAXY_SHED_DATA_MANAGER_CONF'):
open(galaxy_shed_data_manager_conf_file,
'wb').write(shed_data_manager_conf_xml_template)
kwargs = dict(migrated_tools_config=galaxy_migrated_tool_conf_file,
shed_data_manager_config_file=
galaxy_shed_data_manager_conf_file,
shed_tool_path=galaxy_shed_tool_path,
tool_data_path=tool_data_path,
tool_sheds_config_file=galaxy_tool_sheds_conf_file)
kwargs.update(
driver_util.setup_galaxy_config(
galaxy_db_path,
use_test_file_dir=False,
default_install_db_merged=False,
default_tool_data_table_config_path=
default_tool_data_table_config_path,
default_shed_tool_data_table_config=
shed_tool_data_table_conf_file,
enable_tool_shed_check=True,
shed_tool_conf=galaxy_shed_tool_conf_file,
update_integrated_tool_panel=True,
))
print("Galaxy database connection:", kwargs["database_connection"])
# ---- Run galaxy webserver ------------------------------------------------------
galaxyapp = driver_util.build_galaxy_app(kwargs)
galaxy_server_wrapper = driver_util.launch_server(
galaxyapp,
galaxybuildapp.app_factory,
kwargs,
)
log.info("Galaxy tests will be run against %s:%s" %
(galaxy_server_wrapper.host, galaxy_server_wrapper.port))
self.server_wrappers.append(galaxy_server_wrapper)
def setup(self):
"""Entry point for test driver script."""
# ---- Configuration ------------------------------------------------------
tool_shed_test_tmp_dir = driver_util.setup_tool_shed_tmp_dir()
if not os.path.isdir(tool_shed_test_tmp_dir):
os.mkdir(tool_shed_test_tmp_dir)
self.temp_directories.append(tool_shed_test_tmp_dir)
shed_db_path = driver_util.database_files_path(tool_shed_test_tmp_dir, prefix="TOOL_SHED")
shed_tool_data_table_conf_file = os.environ.get('TOOL_SHED_TEST_TOOL_DATA_TABLE_CONF', os.path.join(tool_shed_test_tmp_dir, 'shed_tool_data_table_conf.xml'))
galaxy_shed_data_manager_conf_file = os.environ.get('GALAXY_SHED_DATA_MANAGER_CONF', os.path.join(tool_shed_test_tmp_dir, 'test_shed_data_manager_conf.xml'))
default_tool_data_table_config_path = os.path.join(tool_shed_test_tmp_dir, 'tool_data_table_conf.xml')
galaxy_shed_tool_conf_file = os.environ.get('GALAXY_TEST_SHED_TOOL_CONF', os.path.join(tool_shed_test_tmp_dir, 'test_shed_tool_conf.xml'))
galaxy_migrated_tool_conf_file = os.environ.get('GALAXY_TEST_MIGRATED_TOOL_CONF', os.path.join(tool_shed_test_tmp_dir, 'test_migrated_tool_conf.xml'))
galaxy_tool_sheds_conf_file = os.environ.get('GALAXY_TEST_TOOL_SHEDS_CONF', os.path.join(tool_shed_test_tmp_dir, 'test_sheds_conf.xml'))
if 'GALAXY_TEST_TOOL_DATA_PATH' in os.environ:
tool_data_path = os.environ.get('GALAXY_TEST_TOOL_DATA_PATH')
else:
tool_data_path = tempfile.mkdtemp(dir=tool_shed_test_tmp_dir)
os.environ['GALAXY_TEST_TOOL_DATA_PATH'] = tool_data_path
galaxy_db_path = driver_util.database_files_path(tool_shed_test_tmp_dir)
shed_file_path = os.path.join(shed_db_path, 'files')
hgweb_config_file_path = tempfile.mkdtemp(dir=tool_shed_test_tmp_dir)
new_repos_path = tempfile.mkdtemp(dir=tool_shed_test_tmp_dir)
galaxy_shed_tool_path = tempfile.mkdtemp(dir=tool_shed_test_tmp_dir)
galaxy_migrated_tool_path = tempfile.mkdtemp(dir=tool_shed_test_tmp_dir)
hgweb_config_dir = hgweb_config_file_path
os.environ['TEST_HG_WEB_CONFIG_DIR'] = hgweb_config_dir
print("Directory location for hgweb.config:", hgweb_config_dir)
toolshed_database_conf = driver_util.database_conf(shed_db_path, prefix="TOOL_SHED")
kwargs = dict(admin_users='*****@*****.**',
allow_user_creation=True,
allow_user_deletion=True,
datatype_converters_config_file='datatype_converters_conf.xml.sample',
file_path=shed_file_path,
hgweb_config_dir=hgweb_config_dir,
job_queue_workers=5,
id_secret='changethisinproductiontoo',
log_destination="stdout",
new_file_path=new_repos_path,
running_functional_tests=True,
shed_tool_data_table_config=shed_tool_data_table_conf_file,
smtp_server='smtp.dummy.string.tld',
email_from='functional@localhost',
template_path='templates',
tool_parse_help=False,
use_heartbeat=False)
kwargs.update(toolshed_database_conf)
# Generate the tool_data_table_conf.xml file.
open(default_tool_data_table_config_path, 'w').write(tool_data_table_conf_xml_template)
# Generate the shed_tool_data_table_conf.xml file.
open(shed_tool_data_table_conf_file, 'w').write(tool_data_table_conf_xml_template)
os.environ['TOOL_SHED_TEST_TOOL_DATA_TABLE_CONF'] = shed_tool_data_table_conf_file
# ---- Build Tool Shed Application --------------------------------------------------
toolshedapp = driver_util.build_shed_app(kwargs)
# ---- Run tool shed webserver ------------------------------------------------------
# TODO: Needed for hg middleware ('lib/galaxy/webapps/tool_shed/framework/middleware/hg.py')
kwargs['global_conf']['database_connection'] = kwargs["database_connection"]
tool_shed_server_wrapper = driver_util.launch_server(
toolshedapp,
toolshedbuildapp.app_factory,
kwargs,
prefix="TOOL_SHED",
)
self.server_wrappers.append(tool_shed_server_wrapper)
tool_shed_test_host = tool_shed_server_wrapper.host
tool_shed_test_port = tool_shed_server_wrapper.port
log.info("Functional tests will be run against %s:%s" % (tool_shed_test_host, tool_shed_test_port))
# ---- Optionally start up a Galaxy instance ------------------------------------------------------
if 'TOOL_SHED_TEST_OMIT_GALAXY' not in os.environ:
# Generate the shed_tool_conf.xml file.
tool_sheds_conf_template_parser = string.Template(tool_sheds_conf_xml_template)
tool_sheds_conf_xml = tool_sheds_conf_template_parser.safe_substitute(shed_url=tool_shed_test_host, shed_port=tool_shed_test_port)
open(galaxy_tool_sheds_conf_file, 'w').write(tool_sheds_conf_xml)
# Generate the tool_sheds_conf.xml file.
shed_tool_conf_template_parser = string.Template(shed_tool_conf_xml_template)
shed_tool_conf_xml = shed_tool_conf_template_parser.safe_substitute(shed_tool_path=galaxy_shed_tool_path)
open(galaxy_shed_tool_conf_file, 'w').write(shed_tool_conf_xml)
# Generate the migrated_tool_conf.xml file.
migrated_tool_conf_xml = shed_tool_conf_template_parser.safe_substitute(shed_tool_path=galaxy_migrated_tool_path)
open(galaxy_migrated_tool_conf_file, 'w').write(migrated_tool_conf_xml)
os.environ['GALAXY_TEST_SHED_TOOL_CONF'] = galaxy_shed_tool_conf_file
# Generate shed_data_manager_conf.xml
if not os.environ.get('GALAXY_SHED_DATA_MANAGER_CONF'):
open(galaxy_shed_data_manager_conf_file, 'wb').write(shed_data_manager_conf_xml_template)
kwargs = dict(migrated_tools_config=galaxy_migrated_tool_conf_file,
shed_data_manager_config_file=galaxy_shed_data_manager_conf_file,
shed_tool_path=galaxy_shed_tool_path,
tool_data_path=tool_data_path,
tool_sheds_config_file=galaxy_tool_sheds_conf_file)
kwargs.update(
driver_util.setup_galaxy_config(
galaxy_db_path,
use_test_file_dir=False,
default_install_db_merged=False,
default_tool_data_table_config_path=default_tool_data_table_config_path,
default_shed_tool_data_table_config=shed_tool_data_table_conf_file,
enable_tool_shed_check=True,
shed_tool_conf=galaxy_shed_tool_conf_file,
update_integrated_tool_panel=True,
)
)
print("Galaxy database connection:", kwargs["database_connection"])
# ---- Run galaxy webserver ------------------------------------------------------
galaxyapp = driver_util.build_galaxy_app(kwargs)
galaxy_server_wrapper = driver_util.launch_server(
galaxyapp,
galaxybuildapp.app_factory,
kwargs,
)
log.info("Galaxy tests will be run against %s:%s" % (galaxy_server_wrapper.host, galaxy_server_wrapper.port))
self.server_wrappers.append(galaxy_server_wrapper)