mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Nicola Soranzo
048d79242f
Otherwise a `<GALAXY_ROOT>/database/toolshed_whoosh_indexes` would be reused, leading to failing tests when running tests locally.
188 lines
9.2 KiB
Python
188 lines
9.2 KiB
Python
#!/usr/bin/env python
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"""Test driver for tool shed functional tests.
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"""
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import os
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import string
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import tempfile
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# This is for the tool shed application.
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from galaxy.webapps.galaxy.buildapp import app_factory as galaxy_app_factory
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from galaxy_test.driver import driver_util
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from tool_shed.test.base.api_util import get_admin_api_key
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from tool_shed.webapp 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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"""Instantiate a Galaxy-style 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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self.external_shed = bool(os.environ.get("TOOL_SHED_TEST_EXTERNAL", None))
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if not self.external_shed:
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self._setup_local()
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else:
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# Going to also need to set TOOL_SHED_TEST_HOST.
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assert os.environ["TOOL_SHED_TEST_HOST"]
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def _setup_local(self):
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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(
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"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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)
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galaxy_shed_data_manager_conf_file = os.environ.get(
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"GALAXY_SHED_DATA_MANAGER_CONF", os.path.join(tool_shed_test_tmp_dir, "test_shed_data_manager_conf.xml")
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)
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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(
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"GALAXY_TEST_SHED_TOOL_CONF", os.path.join(tool_shed_test_tmp_dir, "test_shed_tool_conf.xml")
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)
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galaxy_migrated_tool_conf_file = os.environ.get(
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"GALAXY_TEST_MIGRATED_TOOL_CONF", os.path.join(tool_shed_test_tmp_dir, "test_migrated_tool_conf.xml")
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)
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galaxy_tool_sheds_conf_file = os.environ.get(
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"GALAXY_TEST_TOOL_SHEDS_CONF", os.path.join(tool_shed_test_tmp_dir, "test_sheds_conf.xml")
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)
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if "GALAXY_TEST_TOOL_DATA_PATH" in os.environ:
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tool_data_path = os.environ["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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whoosh_index_dir = os.path.join(shed_db_path, "toolshed_whoosh_indexes")
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hgweb_config_dir = 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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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(
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admin_users="test@bx.psu.edu",
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bootstrap_admin_api_key=get_admin_api_key(),
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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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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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use_heartbeat=False,
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whoosh_index_dir=whoosh_index_dir,
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)
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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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with open(default_tool_data_table_config_path, "w") as fh:
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fh.write(tool_data_table_conf_xml_template)
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# Generate the shed_tool_data_table_conf.xml file.
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with open(shed_tool_data_table_conf_file, "w") as fh:
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fh.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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# ---- 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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tool_shed_server_wrapper = driver_util.launch_server(
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app_factory=lambda: driver_util.build_shed_app(kwargs),
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webapp_factory=toolshedbuildapp.app_factory,
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galaxy_config=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(f"Functional tests will be run against {tool_shed_test_host}:{tool_shed_test_port}")
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# Used by get_filename in tool shed's twilltestcase
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if "TOOL_SHED_TEST_FILE_DIR" not in os.environ:
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os.environ["TOOL_SHED_TEST_FILE_DIR"] = driver_util.TOOL_SHED_TEST_DATA
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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(
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shed_url=tool_shed_test_host, shed_port=tool_shed_test_port
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)
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with open(galaxy_tool_sheds_conf_file, "w") as fh:
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fh.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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with open(galaxy_shed_tool_conf_file, "w") as fh:
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fh.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(
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shed_tool_path=galaxy_migrated_tool_path
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)
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with open(galaxy_migrated_tool_conf_file, "w") as fh:
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fh.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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with open(galaxy_shed_data_manager_conf_file, "w") as fh:
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fh.write(shed_data_manager_conf_xml_template)
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kwargs = dict(
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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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)
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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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galaxy_server_wrapper = driver_util.launch_server(
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app_factory=lambda: driver_util.build_galaxy_app(kwargs),
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webapp_factory=galaxy_app_factory,
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galaxy_config=kwargs,
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)
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log.info(f"Galaxy tests will be run against {galaxy_server_wrapper.host}:{galaxy_server_wrapper.port}")
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self.server_wrappers.append(galaxy_server_wrapper)
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