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https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Nicola Soranzo
a353b2e88f
using: ``` autopep8 -i -r --exclude $(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -sd,) --select E127 . ```
170 lines
9.0 KiB
Python
170 lines
9.0 KiB
Python
#!/usr/bin/env python
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"""Test driver for tool shed functional tests.
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Launch this script by running ``run_tests.sh -t`` from GALAXY_ROOT.
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"""
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from __future__ import absolute_import, print_function
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import os
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import string
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import sys
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import tempfile
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galaxy_root = os.path.abspath(os.path.join(os.path.dirname(__file__), os.path.pardir, os.path.pardir))
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# Need to remove this directory from sys.path
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sys.path[0:1] = [os.path.join(galaxy_root, "lib"), os.path.join(galaxy_root, "test")]
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from base import driver_util
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# This is for the tool shed application.
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from galaxy.web import buildapp as galaxybuildapp
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from galaxy.webapps.tool_shed import buildapp as toolshedbuildapp
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log = driver_util.build_logger()
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tool_sheds_conf_xml_template = '''<?xml version="1.0"?>
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<tool_sheds>
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<tool_shed name="Galaxy main tool shed" url="http://toolshed.g2.bx.psu.edu/"/>
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<tool_shed name="Galaxy test tool shed" url="http://testtoolshed.g2.bx.psu.edu/"/>
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<tool_shed name="Embedded tool shed for functional tests" url="http://${shed_url}:${shed_port}/"/>
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</tool_sheds>
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'''
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shed_tool_conf_xml_template = '''<?xml version="1.0"?>
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<toolbox tool_path="${shed_tool_path}">
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</toolbox>
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'''
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tool_data_table_conf_xml_template = '''<?xml version="1.0"?>
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<tables>
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</tables>
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'''
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shed_data_manager_conf_xml_template = '''<?xml version="1.0"?>
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<data_managers>
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</data_managers>
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'''
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class ToolShedTestDriver(driver_util.TestDriver):
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"""Instantial a Galaxy-style nose TestDriver for testing the tool shed."""
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def setup(self):
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"""Entry point for test driver script."""
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# ---- Configuration ------------------------------------------------------
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tool_shed_test_tmp_dir = driver_util.setup_tool_shed_tmp_dir()
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if not os.path.isdir(tool_shed_test_tmp_dir):
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os.mkdir(tool_shed_test_tmp_dir)
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self.temp_directories.append(tool_shed_test_tmp_dir)
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shed_db_path = driver_util.database_files_path(tool_shed_test_tmp_dir, prefix="TOOL_SHED")
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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'))
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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'))
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default_tool_data_table_config_path = os.path.join(tool_shed_test_tmp_dir, 'tool_data_table_conf.xml')
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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'))
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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'))
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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'))
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if 'GALAXY_TEST_TOOL_DATA_PATH' in os.environ:
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tool_data_path = os.environ.get('GALAXY_TEST_TOOL_DATA_PATH')
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else:
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tool_data_path = tempfile.mkdtemp(dir=tool_shed_test_tmp_dir)
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os.environ['GALAXY_TEST_TOOL_DATA_PATH'] = tool_data_path
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galaxy_db_path = driver_util.database_files_path(tool_shed_test_tmp_dir)
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shed_file_path = os.path.join(shed_db_path, 'files')
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hgweb_config_file_path = tempfile.mkdtemp(dir=tool_shed_test_tmp_dir)
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new_repos_path = tempfile.mkdtemp(dir=tool_shed_test_tmp_dir)
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galaxy_shed_tool_path = tempfile.mkdtemp(dir=tool_shed_test_tmp_dir)
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galaxy_migrated_tool_path = tempfile.mkdtemp(dir=tool_shed_test_tmp_dir)
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hgweb_config_dir = hgweb_config_file_path
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os.environ['TEST_HG_WEB_CONFIG_DIR'] = hgweb_config_dir
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print("Directory location for hgweb.config:", hgweb_config_dir)
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toolshed_database_conf = driver_util.database_conf(shed_db_path, prefix="TOOL_SHED")
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kwargs = dict(admin_users='test@bx.psu.edu',
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allow_user_creation=True,
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allow_user_deletion=True,
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datatype_converters_config_file='datatype_converters_conf.xml.sample',
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file_path=shed_file_path,
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hgweb_config_dir=hgweb_config_dir,
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job_queue_workers=5,
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id_secret='changethisinproductiontoo',
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log_destination="stdout",
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new_file_path=new_repos_path,
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running_functional_tests=True,
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shed_tool_data_table_config=shed_tool_data_table_conf_file,
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smtp_server='smtp.dummy.string.tld',
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email_from='functional@localhost',
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template_path='templates',
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tool_parse_help=False,
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use_heartbeat=False)
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kwargs.update(toolshed_database_conf)
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# Generate the tool_data_table_conf.xml file.
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open(default_tool_data_table_config_path, 'w').write(tool_data_table_conf_xml_template)
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# Generate the shed_tool_data_table_conf.xml file.
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open(shed_tool_data_table_conf_file, 'w').write(tool_data_table_conf_xml_template)
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os.environ['TOOL_SHED_TEST_TOOL_DATA_TABLE_CONF'] = shed_tool_data_table_conf_file
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# ---- Build Tool Shed Application --------------------------------------------------
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toolshedapp = driver_util.build_shed_app(kwargs)
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# ---- Run tool shed webserver ------------------------------------------------------
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# TODO: Needed for hg middleware ('lib/galaxy/webapps/tool_shed/framework/middleware/hg.py')
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kwargs['global_conf']['database_connection'] = kwargs["database_connection"]
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tool_shed_server_wrapper = driver_util.launch_server(
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toolshedapp,
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toolshedbuildapp.app_factory,
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kwargs,
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prefix="TOOL_SHED",
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)
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self.server_wrappers.append(tool_shed_server_wrapper)
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tool_shed_test_host = tool_shed_server_wrapper.host
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tool_shed_test_port = tool_shed_server_wrapper.port
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log.info("Functional tests will be run against %s:%s" % (tool_shed_test_host, tool_shed_test_port))
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# ---- Optionally start up a Galaxy instance ------------------------------------------------------
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if 'TOOL_SHED_TEST_OMIT_GALAXY' not in os.environ:
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# Generate the shed_tool_conf.xml file.
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tool_sheds_conf_template_parser = string.Template(tool_sheds_conf_xml_template)
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tool_sheds_conf_xml = tool_sheds_conf_template_parser.safe_substitute(shed_url=tool_shed_test_host, shed_port=tool_shed_test_port)
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open(galaxy_tool_sheds_conf_file, 'w').write(tool_sheds_conf_xml)
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# Generate the tool_sheds_conf.xml file.
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shed_tool_conf_template_parser = string.Template(shed_tool_conf_xml_template)
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shed_tool_conf_xml = shed_tool_conf_template_parser.safe_substitute(shed_tool_path=galaxy_shed_tool_path)
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open(galaxy_shed_tool_conf_file, 'w').write(shed_tool_conf_xml)
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# Generate the migrated_tool_conf.xml file.
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migrated_tool_conf_xml = shed_tool_conf_template_parser.safe_substitute(shed_tool_path=galaxy_migrated_tool_path)
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open(galaxy_migrated_tool_conf_file, 'w').write(migrated_tool_conf_xml)
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os.environ['GALAXY_TEST_SHED_TOOL_CONF'] = galaxy_shed_tool_conf_file
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# Generate shed_data_manager_conf.xml
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if not os.environ.get('GALAXY_SHED_DATA_MANAGER_CONF'):
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open(galaxy_shed_data_manager_conf_file, 'wb').write(shed_data_manager_conf_xml_template)
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kwargs = dict(migrated_tools_config=galaxy_migrated_tool_conf_file,
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shed_data_manager_config_file=galaxy_shed_data_manager_conf_file,
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shed_tool_path=galaxy_shed_tool_path,
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tool_data_path=tool_data_path,
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tool_sheds_config_file=galaxy_tool_sheds_conf_file)
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kwargs.update(
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driver_util.setup_galaxy_config(
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galaxy_db_path,
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use_test_file_dir=False,
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default_install_db_merged=False,
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default_tool_data_table_config_path=default_tool_data_table_config_path,
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default_shed_tool_data_table_config=shed_tool_data_table_conf_file,
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enable_tool_shed_check=True,
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shed_tool_conf=galaxy_shed_tool_conf_file,
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update_integrated_tool_panel=True,
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)
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)
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print("Galaxy database connection:", kwargs["database_connection"])
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# ---- Run galaxy webserver ------------------------------------------------------
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galaxyapp = driver_util.build_galaxy_app(kwargs)
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galaxy_server_wrapper = driver_util.launch_server(
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galaxyapp,
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galaxybuildapp.app_factory,
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kwargs,
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)
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log.info("Galaxy tests will be run against %s:%s" % (galaxy_server_wrapper.host, galaxy_server_wrapper.port))
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self.server_wrappers.append(galaxy_server_wrapper)
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if __name__ == "__main__":
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driver_util.drive_test(ToolShedTestDriver)
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