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)