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.web import buildapp as galaxybuildapp
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
        # ---- 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(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 ------------------------------------------------------
            galaxyapp = driver_util.build_galaxy_app(kwargs)
            galaxy_server_wrapper = driver_util.launch_server(
                galaxyapp,
                galaxybuildapp.app_factory,
                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)