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Source code for galaxy_test.driver.driver_util
"""Scripts for drivers of Galaxy functional tests."""
import http.client
import logging
import os
import random
import re
import shlex
import shutil
import signal
import socket
import string
import subprocess
import sys
import tempfile
import threading
import time
from typing import Optional
from urllib.parse import urlparse
import nose.config
import nose.core
import nose.loader
import nose.plugins.manager
import yaml
from paste import httpserver
from galaxy.app import UniverseApplication as GalaxyUniverseApplication
from galaxy.app_unittest_utils.celery_helper import rebind_container_to_task
from galaxy.config import LOGGING_CONFIG_DEFAULT
from galaxy.model import mapping
from galaxy.model.database_utils import create_database, database_exists
from galaxy.model.tool_shed_install import mapping as toolshed_mapping
from galaxy.tool_util.verify.interactor import GalaxyInteractorApi, verify_tool
from galaxy.util import asbool, download_to_file, galaxy_directory
from galaxy.util.properties import load_app_properties
from galaxy.webapps.galaxy import buildapp
from galaxy_test.base.api_util import get_admin_api_key, get_user_api_key
from galaxy_test.base.env import (
DEFAULT_WEB_HOST,
target_url_parts,
)
from galaxy_test.base.instrument import StructuredTestDataPlugin
from galaxy_test.base.nose_util import run
from tool_shed.webapp.app import UniverseApplication as ToolshedUniverseApplication
from .test_logging import logging_config_file
galaxy_root = galaxy_directory()
DEFAULT_CONFIG_PREFIX = "GALAXY"
GALAXY_TEST_DIRECTORY = os.path.join(galaxy_root, "test")
GALAXY_TEST_FILE_DIR = "test-data,https://github.com/galaxyproject/galaxy-test-data.git"
TOOL_SHED_TEST_DATA = os.path.join(galaxy_root, "lib", "tool_shed", "test", "test_data")
TEST_WEBHOOKS_DIR = os.path.join(galaxy_root, "test", "functional", "webhooks")
FRAMEWORK_TOOLS_DIR = os.path.join(GALAXY_TEST_DIRECTORY, "functional", "tools")
FRAMEWORK_UPLOAD_TOOL_CONF = os.path.join(FRAMEWORK_TOOLS_DIR, "upload_tool_conf.xml")
FRAMEWORK_SAMPLE_TOOLS_CONF = os.path.join(FRAMEWORK_TOOLS_DIR, "samples_tool_conf.xml")
FRAMEWORK_DATATYPES_CONF = os.path.join(FRAMEWORK_TOOLS_DIR, "sample_datatypes_conf.xml")
MIGRATED_TOOL_PANEL_CONFIG = 'config/migrated_tools_conf.xml'
INSTALLED_TOOL_PANEL_CONFIGS = [
os.environ.get('GALAXY_TEST_SHED_TOOL_CONF', 'config/shed_tool_conf.xml')
]
REALTIME_PROXY_TEMPLATE = string.Template(r"""
uwsgi:
http-raw-body: true
interactivetools_map: $tempdir/interactivetools_map.sqlite
python-raw: scripts/interactivetools/key_type_token_mapping.py
# if interactive tool path, jump to interactive tool, else skip to
# endendend (default uwsgi params).
route-host: ^([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)-([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)\.([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)\.(interactivetool\.$test_host:$test_port)$ goto:interactivetool
route-run: goto:endendend
route-label: interactivetool
route-host: ^([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)-([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)\.([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)\.(interactivetool\.$test_host:$test_port)$ rpcvar:TARGET_HOST rtt_key_type_token_mapper_cached $1 $3 $2 $4 $0 5
route-if-not: empty:${TARGET_HOST} httpdumb:${TARGET_HOST}
route: .* break:404 Not Found
route-label: endendend
""")
DEFAULT_LOCALES = "en"
USE_UVICORN = asbool(os.environ.get('GALAXY_TEST_USE_UVICORN', True))
log = logging.getLogger("test_driver")
# Global variables to pass database contexts around - only needed for older
# Tool Shed twill tests that didn't utilize the API for such interactions.
galaxy_context = None
tool_shed_context = None
install_context = None
def setup_tool_shed_tmp_dir():
tool_shed_test_tmp_dir = os.environ.get('TOOL_SHED_TEST_TMP_DIR', None)
if tool_shed_test_tmp_dir is None:
tool_shed_test_tmp_dir = os.path.realpath(tempfile.mkdtemp())
# Here's the directory where everything happens. Temporary directories are created within this directory to contain
# the hgweb.config file, the database, new repositories, etc. Since the tool shed browses repository contents via HTTP,
# the full path to the temporary directroy wher eht repositories are located cannot contain invalid url characters.
os.environ['TOOL_SHED_TEST_TMP_DIR'] = tool_shed_test_tmp_dir
return tool_shed_test_tmp_dir
def get_galaxy_test_tmp_dir():
"""Create test directory for use by Galaxy server being setup for testing."""
galaxy_test_tmp_dir = os.environ.get('GALAXY_TEST_TMP_DIR', None)
if galaxy_test_tmp_dir is None:
galaxy_test_tmp_dir = tempfile.mkdtemp()
return galaxy_test_tmp_dir
def configure_environment():
"""Hack up environment for test cases."""
# no op remove if unused
if 'HTTP_ACCEPT_LANGUAGE' not in os.environ:
os.environ['HTTP_ACCEPT_LANGUAGE'] = DEFAULT_LOCALES
# Used by get_filename in tool shed's twilltestcase.
if "TOOL_SHED_TEST_FILE_DIR" not in os.environ:
os.environ["TOOL_SHED_TEST_FILE_DIR"] = TOOL_SHED_TEST_DATA
os.environ["GALAXY_TEST_ENVIRONMENT_CONFIGURED"] = "1"
def ensure_test_file_dir_set():
"""Ensure GALAXY_TEST_FILE_DIR setup in environment for test data resolver.
Return first directory for backward compat.
"""
galaxy_test_file_dir = os.environ.get('GALAXY_TEST_FILE_DIR', GALAXY_TEST_FILE_DIR)
os.environ['GALAXY_TEST_FILE_DIR'] = galaxy_test_file_dir
first_test_file_dir = galaxy_test_file_dir.split(",")[0]
return first_test_file_dir
[docs]def setup_galaxy_config(
tmpdir,
use_test_file_dir=False,
default_install_db_merged=True,
default_tool_data_table_config_path=None,
default_shed_tool_data_table_config=None,
default_job_config_file=None,
enable_tool_shed_check=False,
default_tool_conf=None,
shed_tool_conf=None,
datatypes_conf=None,
update_integrated_tool_panel=False,
prefer_template_database=False,
log_format=None,
conda_auto_init=False,
conda_auto_install=False,
use_shared_connection_for_amqp=False,
allow_tool_conf_override: bool = True,
allow_path_paste=False,
):
"""Setup environment and build config for test Galaxy instance."""
# For certain docker operations this needs to be evaluated out - e.g. for cwltool.
tmpdir = os.path.realpath(tmpdir)
if not os.path.exists(tmpdir):
os.makedirs(tmpdir)
template_cache_path = tempfile.mkdtemp(prefix='compiled_templates_', dir=tmpdir)
new_file_path = tempfile.mkdtemp(prefix='new_files_path_', dir=tmpdir)
job_working_directory = tempfile.mkdtemp(prefix='job_working_directory_', dir=tmpdir)
user_library_import_dir: Optional[str]
if use_test_file_dir:
first_test_file_dir = ensure_test_file_dir_set()
if not os.path.isabs(first_test_file_dir):
first_test_file_dir = os.path.join(galaxy_root, first_test_file_dir)
library_import_dir = first_test_file_dir
import_dir = os.path.join(first_test_file_dir, 'users')
if os.path.exists(import_dir):
user_library_import_dir = import_dir
else:
user_library_import_dir = None
else:
user_library_import_dir = None
library_import_dir = None
job_config_file = os.environ.get('GALAXY_TEST_JOB_CONFIG_FILE', default_job_config_file)
tool_path = os.environ.get('GALAXY_TEST_TOOL_PATH', 'tools')
tool_data_table_config_path = _tool_data_table_config_path(default_tool_data_table_config_path)
default_data_manager_config = None
for data_manager_config in ['config/data_manager_conf.xml', 'data_manager_conf.xml']:
if os.path.exists(data_manager_config):
default_data_manager_config = data_manager_config
data_manager_config_file = 'test/functional/tools/sample_data_manager_conf.xml'
if default_data_manager_config is not None:
data_manager_config_file = f"{default_data_manager_config},{data_manager_config_file}"
master_api_key = get_admin_api_key()
cleanup_job = 'never' if ("GALAXY_TEST_NO_CLEANUP" in os.environ
or "TOOL_SHED_TEST_NO_CLEANUP" in os.environ) else 'onsuccess'
# Data Manager testing temp path
# For storing Data Manager outputs and .loc files so that real ones don't get clobbered
galaxy_data_manager_data_path = tempfile.mkdtemp(prefix='data_manager_tool-data', dir=tmpdir)
if allow_tool_conf_override:
tool_conf = os.environ.get('GALAXY_TEST_TOOL_CONF', default_tool_conf)
else:
tool_conf = default_tool_conf
conda_auto_install = os.environ.get('GALAXY_TEST_CONDA_AUTO_INSTALL', conda_auto_install)
conda_auto_init = os.environ.get('GALAXY_TEST_CONDA_AUTO_INIT', conda_auto_init)
conda_prefix = os.environ.get('GALAXY_TEST_CONDA_PREFIX')
if tool_conf is None:
# As a fallback always at least allow upload.
tool_conf = FRAMEWORK_UPLOAD_TOOL_CONF
if shed_tool_conf is not None:
tool_conf = f"{tool_conf},{shed_tool_conf}"
# Resolve these paths w.r.t. galaxy root; otherwise galaxy's config system will resolve them w.r.t.
# their parent directories, as per schema.
data_manager_config_file = _resolve_relative_config_paths(data_manager_config_file)
tool_config_file = _resolve_relative_config_paths(tool_conf)
tool_data_table_config_path = _resolve_relative_config_paths(tool_data_table_config_path)
config = dict(
admin_users='test@bx.psu.edu',
allow_library_path_paste=True,
allow_path_paste=allow_path_paste,
allow_user_creation=True,
allow_user_deletion=True,
api_allow_run_as='test@bx.psu.edu',
auto_configure_logging=logging_config_file is None,
chunk_upload_size=100,
conda_prefix=conda_prefix,
conda_auto_init=conda_auto_init,
conda_auto_install=conda_auto_install,
cleanup_job=cleanup_job,
retry_metadata_internally=False,
data_dir=tmpdir,
data_manager_config_file=data_manager_config_file,
enable_beta_tool_formats=True,
expose_dataset_path=True,
ftp_upload_purge=False,
galaxy_data_manager_data_path=galaxy_data_manager_data_path,
id_secret='changethisinproductiontoo',
job_config_file=job_config_file,
job_working_directory=job_working_directory,
library_import_dir=library_import_dir,
log_destination="stdout",
new_file_path=new_file_path,
override_tempdir=False,
master_api_key=master_api_key,
running_functional_tests=True,
template_cache_path=template_cache_path,
tool_config_file=tool_config_file,
tool_data_table_config_path=tool_data_table_config_path,
tool_parse_help=False,
tool_path=tool_path,
update_integrated_tool_panel=update_integrated_tool_panel,
use_tasked_jobs=True,
use_heartbeat=False,
user_library_import_dir=user_library_import_dir,
webhooks_dir=TEST_WEBHOOKS_DIR,
logging=LOGGING_CONFIG_DEFAULT,
monitor_thread_join_timeout=5,
object_store_store_by="uuid",
simplified_workflow_run_ui="off",
)
if default_shed_tool_data_table_config:
config["shed_tool_data_table_config"] = default_shed_tool_data_table_config
if not use_shared_connection_for_amqp:
config["amqp_internal_connection"] = f"sqlalchemy+sqlite:///{os.path.join(tmpdir, 'control.sqlite')}?isolation_level=IMMEDIATE"
config.update(database_conf(tmpdir, prefer_template_database=prefer_template_database))
config.update(install_database_conf(tmpdir, default_merged=default_install_db_merged))
if asbool(os.environ.get("GALAXY_TEST_USE_HIERARCHICAL_OBJECT_STORE")):
object_store_config = os.path.join(tmpdir, "object_store_conf.yml")
with open(object_store_config, "w") as f:
contents = """
type: hierarchical
backends:
- id: files1
type: disk
weight: 1
files_dir: "${temp_directory}/files1"
extra_dirs:
- type: temp
path: "${temp_directory}/tmp1"
- type: job_work
path: "${temp_directory}/job_working_directory1"
- id: files2
type: disk
weight: 1
files_dir: "${temp_directory}/files2"
extra_dirs:
- type: temp
path: "${temp_directory}/tmp2"
- type: job_work
path: "${temp_directory}/job_working_directory2"
"""
contents_template = string.Template(contents)
expanded_contents = contents_template.safe_substitute(temp_directory=tmpdir)
f.write(expanded_contents)
config["object_store_config_file"] = object_store_config
if datatypes_conf is not None:
config['datatypes_config_file'] = datatypes_conf
if enable_tool_shed_check:
config["enable_tool_shed_check"] = enable_tool_shed_check
config["hours_between_check"] = 0.001
tool_dependency_dir = os.environ.get('GALAXY_TOOL_DEPENDENCY_DIR')
if tool_dependency_dir:
config["tool_dependency_dir"] = tool_dependency_dir
# Used by shed's twill dependency stuff
# TODO: read from Galaxy's config API.
os.environ["GALAXY_TEST_TOOL_DEPENDENCY_DIR"] = tool_dependency_dir or os.path.join(tmpdir, 'dependencies')
return config
def _resolve_relative_config_paths(config_option):
# If option is not None, split into paths, resolve each w.r.t. root, then rebuild as csv string.
if config_option is not None:
resolved = []
for path in config_option.split(','):
resolved.append(os.path.join(galaxy_root, path.strip()))
return ','.join(resolved)
def _tool_data_table_config_path(default_tool_data_table_config_path=None):
tool_data_table_config_path = os.environ.get('GALAXY_TEST_TOOL_DATA_TABLE_CONF', default_tool_data_table_config_path)
if tool_data_table_config_path is None:
# ... otherwise find whatever Galaxy would use as the default and
# the sample data for functional tests to that.
default_tool_data_config = 'lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
for tool_data_config in ['config/tool_data_table_conf.xml', 'tool_data_table_conf.xml']:
if os.path.exists(tool_data_config):
default_tool_data_config = tool_data_config
test_tool_data_config = 'test/functional/tool-data/sample_tool_data_tables.xml'
tool_data_table_config_path = f'{default_tool_data_config},{test_tool_data_config}'
return tool_data_table_config_path
[docs]def nose_config_and_run(argv=None, env=None, ignore_files=None, plugins=None):
"""Setup a nose context and run tests.
Tests are specified by argv (defaulting to sys.argv).
"""
if env is None:
env = os.environ
if ignore_files is None:
ignore_files = []
if plugins is None:
plugins = nose.plugins.manager.DefaultPluginManager()
if argv is None:
argv = sys.argv
test_config = nose.config.Config(
env=os.environ,
ignoreFiles=ignore_files,
plugins=plugins,
)
# Add custom plugin to produce JSON data used by planemo.
test_config.plugins.addPlugin(StructuredTestDataPlugin())
test_config.configure(argv)
result = run(test_config)
success = result.wasSuccessful()
return success
[docs]def copy_database_template(source, db_path):
"""Copy a 'clean' sqlite template database.
From file or URL to specified path for sqlite database.
"""
db_path_dir = os.path.dirname(db_path)
if not os.path.exists(db_path_dir):
os.makedirs(db_path_dir)
if os.path.exists(source):
shutil.copy(source, db_path)
assert os.path.exists(db_path)
elif source.lower().startswith(("http://", "https://", "ftp://")):
try:
download_to_file(source, db_path)
except Exception as e:
# We log the exception but don't fail startup, since we can
# do all migration steps instead of downloading a template.
log.exception(e)
else:
raise Exception(f"Failed to copy database template from source {source}")
[docs]def database_conf(db_path, prefix="GALAXY", prefer_template_database=False):
"""Find (and populate if needed) Galaxy database connection."""
database_auto_migrate = False
check_migrate_databases = True
dburi_var = f"{prefix}_TEST_DBURI"
template_name = None
if dburi_var in os.environ:
database_connection = os.environ[dburi_var]
# only template if postgres - not mysql or sqlite
do_template = prefer_template_database and database_connection.startswith("p")
if do_template:
database_template_parsed = urlparse(database_connection)
template_name = database_template_parsed.path[1:] # drop / from /galaxy
actual_db = f"gxtest{''.join(random.choice(string.ascii_uppercase) for _ in range(10))}"
actual_database_parsed = database_template_parsed._replace(path=f"/{actual_db}")
database_connection = actual_database_parsed.geturl()
if not database_exists(database_connection):
# We pass by migrations and instantiate the current table
create_database(database_connection)
mapping.init('/tmp', database_connection, create_tables=True, map_install_models=True)
toolshed_mapping.init(database_connection, create_tables=True)
check_migrate_databases = False
else:
default_db_filename = f"{prefix.lower()}.sqlite"
template_var = f"{prefix}_TEST_DB_TEMPLATE"
db_path = os.path.join(db_path, default_db_filename)
if template_var in os.environ:
# Middle ground between recreating a completely new
# database and pointing at existing database with
# GALAXY_TEST_DBURI. The former requires a lot of setup
# time, the latter results in test failures in certain
# cases (namely tool shed tests expecting clean database).
copy_database_template(os.environ[template_var], db_path)
database_auto_migrate = True
database_connection = f'sqlite:///{db_path}'
config = {
"check_migrate_databases": check_migrate_databases,
"database_connection": database_connection,
"database_auto_migrate": database_auto_migrate
}
if not database_connection.startswith("sqlite://"):
config["database_engine_option_max_overflow"] = "20"
config["database_engine_option_pool_size"] = "10"
if template_name:
config["database_template"] = template_name
return config
def install_database_conf(db_path, default_merged=False):
install_galaxy_database_connection: Optional[str]
if 'GALAXY_TEST_INSTALL_DBURI' in os.environ:
install_galaxy_database_connection = os.environ['GALAXY_TEST_INSTALL_DBURI']
elif asbool(os.environ.get('GALAXY_TEST_INSTALL_DB_MERGED', default_merged)):
install_galaxy_database_connection = None
else:
install_galaxy_db_path = os.path.join(db_path, 'install.sqlite')
install_galaxy_database_connection = f'sqlite:///{install_galaxy_db_path}'
conf = {}
if install_galaxy_database_connection is not None:
conf["install_database_connection"] = install_galaxy_database_connection
return conf
def database_files_path(test_tmpdir, prefix="GALAXY"):
"""Create a mock database/ directory like in GALAXY_ROOT.
Use prefix to default this if TOOL_SHED_TEST_DBPATH or
GALAXY_TEST_DBPATH is set in the environment.
"""
environ_var = f"{prefix}_TEST_DBPATH"
if environ_var in os.environ:
db_path = os.environ[environ_var]
else:
tempdir = tempfile.mkdtemp(dir=test_tmpdir)
db_path = os.path.join(tempdir, 'database')
return db_path
def _get_static_settings():
"""Configuration required for Galaxy static middleware.
Returns dictionary of the settings necessary for a galaxy App
to be wrapped in the static middleware.
This mainly consists of the filesystem locations of url-mapped
static resources.
"""
static_dir = os.path.join(galaxy_root, "static")
# TODO: these should be copied from config/galaxy.ini
return dict(
static_enabled=True,
static_cache_time=360,
static_dir=static_dir,
static_images_dir=os.path.join(static_dir, 'images', ''),
static_favicon_dir=os.path.join(static_dir, 'favicon.ico'),
static_scripts_dir=os.path.join(static_dir, 'scripts', ''),
static_style_dir=os.path.join(static_dir, 'style'),
static_robots_txt=os.path.join(static_dir, 'robots.txt'),
)
[docs]def get_webapp_global_conf():
"""Get the global_conf dictionary sent to ``app_factory``."""
# (was originally sent 'dict()') - nothing here for now except static settings
global_conf = dict()
global_conf.update(_get_static_settings())
return global_conf
[docs]def wait_for_http_server(host, port, prefix=None, sleep_amount=0.1, sleep_tries=150):
"""Wait for an HTTP server to boot up."""
# Test if the server is up
prefix = prefix or '/'
if not prefix.endswith('/'):
prefix = f"{prefix}/"
for _ in range(sleep_tries):
# directly test the app, not the proxy
conn = http.client.HTTPConnection(host, port)
try:
conn.request("GET", prefix)
response = conn.getresponse()
if response.status == 200:
break
except OSError as e:
if e.errno not in [61, 111]:
raise
time.sleep(sleep_amount)
else:
template = "Test HTTP server on host %s and port %s did not return '200 OK' after 10 tries"
message = template % (host, port)
raise Exception(message)
def attempt_port(port):
sock = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
try:
sock.bind(('', port))
sock.close()
return port
except OSError:
return None
def attempt_ports(port):
if port is not None:
return port
raise Exception(f"An existing process seems bound to specified test server port [{port}]")
else:
random.seed()
for _ in range(0, 9):
port = attempt_port(random.randint(8000, 10000))
if port:
port = str(port)
os.environ['GALAXY_WEB_PORT'] = port
return port
raise Exception(f"Unable to open a port between {8000} and {10000} to start Galaxy server")
def serve_webapp(webapp, port=None, host=None):
"""Serve the webapp on a recommend port or a free one.
Return the port the webapp is running on.
"""
server = None
port = attempt_ports(port)
server = httpserver.serve(webapp, host=host, port=port, start_loop=False)
t = threading.Thread(target=server.serve_forever)
t.start()
return server, port
def uvicorn_serve(app, port, host=None):
"""Serve the webapp on a recommend port or a free one.
Return the port the webapp is running on.
"""
import asyncio
from uvicorn.server import Server
from uvicorn.config import Config
access_log = False if 'GALAXY_TEST_DISABLE_ACCESS_LOG' in os.environ else True
config = Config(app, host=host, port=int(port), access_log=access_log)
server = Server(config=config)
def run_in_loop(loop):
try:
asyncio.set_event_loop(loop)
loop.run_until_complete(server.serve())
finally:
loop.close()
asyncio.set_event_loop(None)
log.info("Event loop for uvicorn closed")
loop = asyncio.new_event_loop()
t = threading.Thread(target=run_in_loop, args=(loop,))
t.start()
return server, port, t
def cleanup_directory(tempdir):
"""Clean up temporary files used by test unless GALAXY_TEST_NO_CLEANUP is set.
Also respect TOOL_SHED_TEST_NO_CLEANUP for legacy reasons.
"""
skip_cleanup = "GALAXY_TEST_NO_CLEANUP" in os.environ or "TOOL_SHED_TEST_NO_CLEANUP" in os.environ
if skip_cleanup:
log.info(f"GALAXY_TEST_NO_CLEANUP is on. Temporary files in {tempdir}")
return
try:
if os.path.exists(tempdir) and not skip_cleanup:
shutil.rmtree(tempdir)
except Exception:
pass
def setup_shed_tools_for_test(app, tmpdir, testing_migrated_tools, testing_installed_tools):
"""Modify Galaxy app's toolbox for migrated or installed tool tests."""
if testing_installed_tools:
# TODO: Do this without modifying app - that is a pretty violation
# of Galaxy's abstraction - we shouldn't require app at all let alone
# be modifying it.
tool_configs = app.config.tool_configs
# Eliminate the migrated_tool_panel_config from the app's tool_configs, append the list of installed_tool_panel_configs,
# and reload the app's toolbox.
relative_migrated_tool_panel_config = os.path.join(app.config.root, MIGRATED_TOOL_PANEL_CONFIG)
if relative_migrated_tool_panel_config in tool_configs:
tool_configs.remove(relative_migrated_tool_panel_config)
for installed_tool_panel_config in INSTALLED_TOOL_PANEL_CONFIGS:
tool_configs.append(installed_tool_panel_config)
from galaxy import tools # delay import because this brings in so many modules for small tests # noqa: E402
app.toolbox = tools.ToolBox(tool_configs, app.config.tool_path, app)
def build_galaxy_app(simple_kwargs) -> GalaxyUniverseApplication:
"""Build a Galaxy app object from a simple keyword arguments.
Construct paste style complex dictionary and use load_app_properties so
Galaxy override variables are respected. Also setup "global" references
to sqlalchemy database context for Galaxy and install databases.
"""
log.info("Galaxy database connection: %s", simple_kwargs["database_connection"])
simple_kwargs['global_conf'] = get_webapp_global_conf()
simple_kwargs['global_conf']['__file__'] = "lib/galaxy/config/sample/galaxy.yml.sample"
simple_kwargs = load_app_properties(
kwds=simple_kwargs
)
# Build the Universe Application
app = GalaxyUniverseApplication(**simple_kwargs)
if not simple_kwargs.get("enable_celery_tasks"):
rebind_container_to_task(app)
log.info("Embedded Galaxy application started")
global galaxy_context
global install_context
galaxy_context = app.model.context
install_context = app.install_model.context
# Toolbox indexing happens via the work queue out of band recently, and,
# beyond potentially running async after tests execute doesn't execute
# without building a uwsgi app (app.is_webapp = False for this test kit).
# We need to ensure to build an index for the test galaxy app -- this is
# pretty fast with the limited toolset
app.reindex_tool_search()
return app
def build_shed_app(simple_kwargs):
"""Build a Galaxy app object from a simple keyword arguments.
Construct paste style complex dictionary. Also setup "global" reference
to sqlalchemy database context for tool shed database.
"""
log.info("Tool shed database connection: %s", simple_kwargs["database_connection"])
# TODO: Simplify global_conf to match Galaxy above...
simple_kwargs['__file__'] = 'tool_shed_wsgi.yml.sample'
simple_kwargs['global_conf'] = get_webapp_global_conf()
app = ToolshedUniverseApplication(**simple_kwargs)
log.info("Embedded Toolshed application started")
global tool_shed_context
tool_shed_context = app.model.context
return app
def explicitly_configured_host_and_port(prefix, config_object):
host_env_key = f"{prefix}_TEST_HOST"
port_env_key = f"{prefix}_TEST_PORT"
port_random_env_key = f"{prefix}_TEST_PORT_RANDOM"
default_web_host = getattr(config_object, "default_web_host", DEFAULT_WEB_HOST)
host = os.environ.get(host_env_key, default_web_host)
if os.environ.get(port_random_env_key, None) is not None:
# Ignore the port environment variable, it wasn't explictly configured.
port = None
else:
port = os.environ.get(port_env_key, None)
# If an explicit port wasn't assigned for this test or test case, set this
# environment variable so we know it is random. We can then randomly re-assign
# for new tests.
if port is None:
os.environ["GALAXY_TEST_PORT_RANDOM"] = "1"
else:
os.environ['GALAXY_WEB_PORT'] = port
return host, port
def set_and_wait_for_http_target(prefix, host, port, url_prefix, sleep_amount=0.1, sleep_tries=150):
host_env_key = f"{prefix}_TEST_HOST"
port_env_key = f"{prefix}_TEST_PORT"
os.environ[host_env_key] = host
os.environ[port_env_key] = port
wait_for_http_server(host, port, url_prefix, sleep_amount=sleep_amount, sleep_tries=sleep_tries)
class ServerWrapper:
def __init__(self, name, host, port, prefix=""):
self.name = name
self.host = host
self.port = port
self.prefix = prefix
@property
def app(self):
raise NotImplementedError("Test can be run against target - requires a Galaxy app object.")
def stop(self):
raise NotImplementedError()
class EmbeddedServerWrapper(ServerWrapper):
def __init__(self, app, server, name, host, port, prefix="", thread=None):
super().__init__(name, host, port, prefix)
self._app = app
self._server = server
self._thread = thread
@property
def app(self):
return self._app
def stop(self):
log.info(f"{threading.active_count()} threads were active before stopping embedded server")
if self._server is not None and hasattr(self._server, "server_close"):
log.info(f"Shutting down embedded {self.name} Paste server")
self._server.server_close()
log.info(f"Embedded web server {self.name} stopped")
if self._server is not None and hasattr(self._server, "shutdown"):
log.info(f"Shutting down embedded {self.name} uvicorn server")
self._server.should_exit = True
log.info(f"Embedded web server {self.name} stopped")
if self._thread is not None:
log.info("Stopping embedded server thread")
self._thread.join()
log.info("Embedded server thread stopped")
if self._app is not None:
log.info(f"Stopping application {self.name}")
self._app.shutdown()
log.info(f"Application {self.name} stopped.")
log.info(f"{threading.active_count()} active after stopping embedded server")
class UwsgiServerWrapper(ServerWrapper):
def __init__(self, p, name, host, port):
super().__init__(name, host, port)
self._p = p
self._r = None
self._t = threading.Thread(target=self.wait)
self._t.start()
def __del__(self):
self._t.join()
def wait(self):
self._r = self._p.wait()
def stop(self):
try:
os.killpg(os.getpgid(self._p.pid), signal.SIGTERM)
except Exception:
pass
time.sleep(.1)
try:
os.killpg(os.getpgid(self._p.pid), signal.SIGKILL)
except Exception:
pass
self._t.join()
def launch_uwsgi(kwargs, tempdir, prefix=DEFAULT_CONFIG_PREFIX, config_object=None):
name = prefix.lower()
host, port = explicitly_configured_host_and_port(prefix, config_object)
config = {}
config["galaxy"] = kwargs.copy()
enable_realtime_mapping = getattr(config_object, "enable_realtime_mapping", False)
if enable_realtime_mapping:
interactive_tool_defaults = {
"interactivetools_prefix": "interactivetool",
"interactivetools_map": os.path.join(tempdir, "interactivetools_map.sqlite"),
"interactivetools_enable": True
}
for key, value in interactive_tool_defaults.items():
if key not in config["galaxy"]:
config["galaxy"][key] = value
yaml_config_path = os.path.join(tempdir, "galaxy.yml")
with open(yaml_config_path, "w") as f:
yaml.dump(config, f)
if enable_realtime_mapping:
# Avoid YAML.dump configuration since uwsgi doesn't like real YAML :( -
# though maybe it would work?
with open(yaml_config_path) as f:
old_contents = f.read()
with open(yaml_config_path, "w") as f:
test_port = str(port) if port else r"[0-9]+"
test_host = re.escape(host) if host else "localhost"
uwsgi_section = REALTIME_PROXY_TEMPLATE.safe_substitute(test_host=test_host, test_port=test_port, tempdir=tempdir)
f.write(uwsgi_section)
f.write(old_contents)
def attempt_port_bind(port):
uwsgi_command = [
"uwsgi",
"--http",
f"{host}:{port}",
"--yaml",
yaml_config_path,
"--module",
"galaxy.webapps.galaxy.buildapp:uwsgi_app_factory()",
"--enable-threads",
"--die-on-term",
]
for path in sys.path:
uwsgi_command.append('--pythonpath')
uwsgi_command.append(path)
handle_uwsgi_cli_command = getattr(
config_object, "handle_uwsgi_cli_command", None
)
if handle_uwsgi_cli_command is not None:
handle_uwsgi_cli_command(uwsgi_command)
# we don't want to quote every argument but we don't want to print unquoted ones either, so do this
log.info("Starting uwsgi with command line: %s", ' '.join(shlex.quote(x) for x in uwsgi_command))
p = subprocess.Popen(
uwsgi_command,
cwd=galaxy_root,
preexec_fn=os.setsid,
)
return UwsgiServerWrapper(
p, name, host, port
)
port = attempt_ports(port)
server_wrapper = attempt_port_bind(port)
try:
set_and_wait_for_http_target(prefix, host, port, url_prefix="/", sleep_tries=50)
log.info(f"Test-managed uwsgi web server for {name} started at {host}:{port}")
return server_wrapper
except Exception:
server_wrapper.stop()
def launch_uvicorn(webapp_factory, prefix=DEFAULT_CONFIG_PREFIX, galaxy_config=None, config_object=None):
name = prefix.lower()
host, port = explicitly_configured_host_and_port(prefix, config_object)
port = attempt_ports(port)
gx_app = build_galaxy_app(galaxy_config)
gx_wsgi_webapp = webapp_factory(
galaxy_config['global_conf'],
app=gx_app,
use_translogger=False,
static_enabled=True,
register_shutdown_at_exit=False
)
from galaxy.webapps.galaxy.fast_app import initialize_fast_app
app = initialize_fast_app(gx_wsgi_webapp, gx_app)
server, port, thread = uvicorn_serve(app, host=host, port=port)
set_and_wait_for_http_target(prefix, host, port, url_prefix=gx_app.config.galaxy_url_prefix)
log.info(f"Embedded uvicorn web server for {name} started at {host}:{port}{gx_app.config.galaxy_url_prefix}")
return EmbeddedServerWrapper(
gx_app, server, name, host, port, thread=thread, prefix=gx_app.config.galaxy_url_prefix
)
def launch_server(app, webapp_factory, kwargs, prefix=DEFAULT_CONFIG_PREFIX, config_object=None):
"""Launch a web server for a given app using supplied factory.
Consistently read either GALAXY_TEST_HOST and GALAXY_TEST_PORT or
TOOL_SHED_TEST_HOST and TOOL_SHED_TEST_PORT and ensure these are
all set after this method has been called.
"""
name = prefix.lower()
host, port = explicitly_configured_host_and_port(prefix, config_object)
webapp = webapp_factory(
kwargs['global_conf'],
app=app,
use_translogger=False,
static_enabled=True,
register_shutdown_at_exit=False
)
server, port = serve_webapp(
webapp,
host=host, port=port
)
set_and_wait_for_http_target(prefix, host, port, url_prefix="/")
log.info(f"Embedded paste web server for {name} started at {host}:{port}")
return EmbeddedServerWrapper(
app, server, name, host, port
)
[docs]class TestDriver:
"""Responsible for the life-cycle of a Galaxy-style functional test.
Sets up servers, configures tests, runs nose, and tears things
down. This is somewhat like a Python TestCase - but different
because it is meant to provide a main() endpoint.
"""
__test__ = False # Prevent pytest from discovering this class (issue #12071)
[docs] def __init__(self):
"""Setup tracked resources."""
self.server_wrappers = []
self.temp_directories = []
[docs] def tear_down(self):
"""Cleanup resources tracked by this object."""
self.stop_servers()
for temp_directory in self.temp_directories:
cleanup_directory(temp_directory)
[docs] def stop_servers(self):
for server_wrapper in self.server_wrappers:
server_wrapper.stop()
self.server_wrappers = []
[docs] def mkdtemp(self):
"""Return a temp directory that is properly cleaned up or not based on the config."""
temp_directory = tempfile.mkdtemp()
self.temp_directories.append(temp_directory)
return temp_directory
[docs] def run(self):
"""Driver whole test.
Setup environment, build tests (if needed), run test,
and finally cleanup resources.
"""
configure_environment()
self.setup()
self.build_tests()
try:
success = nose_config_and_run()
return 0 if success else 1
except Exception as e:
log.info("Failure running tests")
raise e
finally:
log.info("Shutting down")
self.tear_down()
class GalaxyTestDriver(TestDriver):
"""Instantial a Galaxy-style nose TestDriver for testing Galaxy."""
testing_shed_tools = False
def _configure(self, config_object=None):
"""Setup various variables used to launch a Galaxy server."""
config_object = self._ensure_config_object(config_object)
self.external_galaxy = os.environ.get('GALAXY_TEST_EXTERNAL', None)
# Allow a particular test to force uwsgi or any test to use uwsgi with
# the GALAXY_TEST_UWSGI environment variable.
use_uwsgi = bool(os.environ.get('GALAXY_TEST_UWSGI', None))
if not use_uwsgi:
if getattr(config_object, "require_uwsgi", None):
use_uwsgi = True
self.use_uwsgi = use_uwsgi
if getattr(config_object, "use_uvicorn", USE_UVICORN):
self.else_use_uvicorn = True
else:
self.else_use_uvicorn = False
# Allow controlling the log format
log_format = os.environ.get('GALAXY_TEST_LOG_FORMAT', None)
if not log_format and use_uwsgi:
log_format = "%(name)s %(levelname)-5.5s %(asctime)s " \
"[p:%(process)s,w:%(worker_id)s,m:%(mule_id)s] " \
"[%(threadName)s] %(message)s"
self.log_format = log_format
self.galaxy_test_tmp_dir = get_galaxy_test_tmp_dir()
self.temp_directories.append(self.galaxy_test_tmp_dir)
self.testing_shed_tools = getattr(config_object, "testing_shed_tools", False)
default_tool_conf: Optional[str]
datatypes_conf_override: Optional[str]
if getattr(config_object, "framework_tool_and_types", False):
default_tool_conf = FRAMEWORK_SAMPLE_TOOLS_CONF
datatypes_conf_override = FRAMEWORK_DATATYPES_CONF
else:
default_tool_conf = getattr(config_object, "default_tool_conf", None)
datatypes_conf_override = getattr(config_object, "datatypes_conf_override", None)
allow_tool_conf_override = getattr(config_object, "allow_tool_conf_override", True)
self.allow_tool_conf_override = allow_tool_conf_override
self.default_tool_conf = default_tool_conf
self.datatypes_conf_override = datatypes_conf_override
def setup(self, config_object=None):
"""Setup a Galaxy server for functional test (if needed).
Configuration options can be specified as attributes on the supplied
```config_object``` (defaults to self).
"""
self._saved_galaxy_config = None
self._configure(config_object)
self._register_and_run_servers(config_object)
def restart(self, config_object=None, handle_config=None):
self.stop_servers()
self._register_and_run_servers(config_object, handle_config=handle_config)
def _register_and_run_servers(self, config_object=None, handle_config=None):
config_object = self._ensure_config_object(config_object)
self.app = None
if self.external_galaxy is None:
if self._saved_galaxy_config is not None:
galaxy_config = self._saved_galaxy_config
else:
tempdir = tempfile.mkdtemp(dir=self.galaxy_test_tmp_dir)
# Configure the database path.
galaxy_db_path = database_files_path(tempdir)
# Allow config object to specify a config dict or a method to produce
# one - other just read the properties above and use the default
# implementation from this file.
galaxy_config = getattr(config_object, "galaxy_config", None)
if callable(galaxy_config):
galaxy_config = galaxy_config()
if galaxy_config is None:
galaxy_config = setup_galaxy_config(
galaxy_db_path,
use_test_file_dir=not self.testing_shed_tools,
default_install_db_merged=True,
default_tool_conf=self.default_tool_conf,
datatypes_conf=self.datatypes_conf_override,
prefer_template_database=getattr(config_object, "prefer_template_database", False),
log_format=self.log_format,
conda_auto_init=getattr(config_object, "conda_auto_init", False),
conda_auto_install=getattr(config_object, "conda_auto_install", False),
use_shared_connection_for_amqp=getattr(config_object, "use_shared_connection_for_amqp", False),
allow_tool_conf_override=self.allow_tool_conf_override,
allow_path_paste=getattr(config_object, "allow_path_paste", False),
)
isolate_galaxy_config = getattr(config_object, "isolate_galaxy_config", False)
if isolate_galaxy_config:
galaxy_config["config_dir"] = tempdir
self._saved_galaxy_config = galaxy_config
if galaxy_config is not None:
handle_galaxy_config_kwds = handle_config or getattr(
config_object, "handle_galaxy_config_kwds", None
)
if handle_galaxy_config_kwds is not None:
handle_galaxy_config_kwds(galaxy_config)
if self.use_uwsgi:
server_wrapper = launch_uwsgi(
galaxy_config,
tempdir=tempdir,
config_object=config_object,
)
elif self.else_use_uvicorn:
server_wrapper = launch_uvicorn(
lambda *args, **kwd: buildapp.app_factory(*args, wsgi_preflight=False, **kwd),
galaxy_config=galaxy_config,
config_object=config_object,
)
self.app = server_wrapper.app
else:
# ---- Build Application --------------------------------------------------
self.app = build_galaxy_app(galaxy_config)
server_wrapper = launch_server(
self.app,
buildapp.app_factory,
galaxy_config,
config_object=config_object,
)
log.info(f"Functional tests will be run against external Galaxy server {server_wrapper.host}:{server_wrapper.port}")
self.server_wrappers.append(server_wrapper)
else:
log.info(f"Functional tests will be run against test managed Galaxy server {self.external_galaxy}")
# Ensure test file directory setup even though galaxy config isn't built.
ensure_test_file_dir_set()
def _ensure_config_object(self, config_object):
if config_object is None:
config_object = self
return config_object
def setup_shed_tools(self, testing_migrated_tools=False, testing_installed_tools=True):
setup_shed_tools_for_test(
self.app,
self.galaxy_test_tmp_dir,
testing_migrated_tools,
testing_installed_tools
)
def build_tool_tests(self, testing_shed_tools=None, return_test_classes=False):
if self.app is None:
return
if testing_shed_tools is None:
testing_shed_tools = getattr(self, "testing_shed_tools", False)
# We must make sure that functional.test_toolbox is always imported after
# database_contexts.galaxy_content is set (which occurs in this method above).
# If functional.test_toolbox is imported before database_contexts.galaxy_content
# is set, sa_session will be None in all methods that use it.
import functional.test_toolbox
functional.test_toolbox.toolbox = self.app.toolbox
# When testing data managers, do not test toolbox.
test_classes = functional.test_toolbox.build_tests(
app=self.app,
testing_shed_tools=testing_shed_tools,
master_api_key=get_admin_api_key(),
user_api_key=get_user_api_key(),
)
if return_test_classes:
return test_classes
return functional.test_toolbox
def run_tool_test(self, tool_id, index=0, resource_parameters=None, **kwd):
if resource_parameters is None:
resource_parameters = {}
host, port, url = target_url_parts()
galaxy_interactor_kwds = {
"galaxy_url": url,
"master_api_key": get_admin_api_key(),
"api_key": get_user_api_key(),
"keep_outputs_dir": None,
}
galaxy_interactor = GalaxyInteractorApi(**galaxy_interactor_kwds)
verify_tool(
tool_id=tool_id,
test_index=index,
galaxy_interactor=galaxy_interactor,
resource_parameters=resource_parameters,
**kwd
)
[docs]def drive_test(test_driver_class):
"""Instantiate driver class, run, and exit appropriately."""
test_driver = test_driver_class()
sys.exit(test_driver.run())
__all__ = (
"copy_database_template",
"build_logger",
"drive_test",
"FRAMEWORK_UPLOAD_TOOL_CONF",
"FRAMEWORK_SAMPLE_TOOLS_CONF",
"FRAMEWORK_DATATYPES_CONF",
"database_conf",
"get_webapp_global_conf",
"nose_config_and_run",
"setup_galaxy_config",
"TestDriver",
"wait_for_http_server",
)