Source code for tool_shed.test.functional_tests
#!/usr/bin/env python
"""Test driver for tool shed functional tests.
Launch this script by running ``run_tests.sh -t`` from GALAXY_ROOT.
"""
import os
import string
import sys
import tempfile
galaxy_root = os.path.abspath(os.path.join(os.path.dirname(__file__), os.path.pardir, os.path.pardir, os.path.pardir))
# Need to remove this directory from sys.path
sys.path[0:1] = [os.path.join(galaxy_root, "lib")]
# This is for the tool shed application.
from galaxy.webapps.galaxy.buildapp import app_factory as galaxy_app_factory
from galaxy_test.driver import driver_util
from tool_shed.webapp import buildapp as toolshedbuildapp
log = driver_util.build_logger()
tool_sheds_conf_xml_template = """<?xml version="1.0"?>
<tool_sheds>
<tool_shed name="Galaxy main tool shed" url="http://toolshed.g2.bx.psu.edu/"/>
<tool_shed name="Galaxy test tool shed" url="http://testtoolshed.g2.bx.psu.edu/"/>
<tool_shed name="Embedded tool shed for functional tests" url="http://${shed_url}:${shed_port}/"/>
</tool_sheds>
"""
shed_tool_conf_xml_template = """<?xml version="1.0"?>
<toolbox tool_path="${shed_tool_path}">
</toolbox>
"""
tool_data_table_conf_xml_template = """<?xml version="1.0"?>
<tables>
</tables>
"""
shed_data_manager_conf_xml_template = """<?xml version="1.0"?>
<data_managers>
</data_managers>
"""
[docs]class ToolShedTestDriver(driver_util.TestDriver):
"""Instantial a Galaxy-style nose TestDriver for testing the tool shed."""
[docs] 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="test@bx.psu.edu",
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,
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",
tool_parse_help=False,
use_heartbeat=False,
)
kwargs.update(toolshed_database_conf)
# Generate the tool_data_table_conf.xml file.
with open(default_tool_data_table_config_path, "w") as fh:
fh.write(tool_data_table_conf_xml_template)
# Generate the shed_tool_data_table_conf.xml file.
with open(shed_tool_data_table_conf_file, "w") as fh:
fh.write(tool_data_table_conf_xml_template)
os.environ["TOOL_SHED_TEST_TOOL_DATA_TABLE_CONF"] = shed_tool_data_table_conf_file
# ---- Run tool shed webserver ------------------------------------------------------
# TODO: Needed for hg middleware ('lib/galaxy/webapps/tool_shed/framework/middleware/hg.py')
tool_shed_server_wrapper = driver_util.launch_server(
app_factory=lambda: driver_util.build_shed_app(kwargs),
webapp_factory=toolshedbuildapp.app_factory,
galaxy_config=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(f"Functional tests will be run against {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
)
with open(galaxy_tool_sheds_conf_file, "w") as fh:
fh.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)
with open(galaxy_shed_tool_conf_file, "w") as fh:
fh.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
)
with open(galaxy_migrated_tool_conf_file, "w") as fh:
fh.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"):
with open(galaxy_shed_data_manager_conf_file, "w") as fh:
fh.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 ------------------------------------------------------
galaxy_server_wrapper = driver_util.launch_server(
app_factory=lambda: driver_util.build_galaxy_app(kwargs),
webapp_factory=galaxy_app_factory,
galaxy_config=kwargs,
)
log.info(f"Galaxy tests will be run against {galaxy_server_wrapper.host}:{galaxy_server_wrapper.port}")
self.server_wrappers.append(galaxy_server_wrapper)
if __name__ == "__main__":
driver_util.drive_test(ToolShedTestDriver)