Warning

This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

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)