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Source code for galaxy_test.driver.driver_util

"""Scripts for drivers of Galaxy functional tests."""

import http.client
import json
import logging
import os
import random
import shutil
import socket
import string
import subprocess
import sys
import tempfile
import threading
import time
from pathlib import Path
from typing import (
    Any,
    Dict,
    List,
    Optional,
)
from urllib.parse import urlparse

from galaxy.app import UniverseApplication as GalaxyUniverseApplication
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.webapps.galaxy.fast_app import initialize_fast_app as init_galaxy_fast_app
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 tool_shed.webapp.app import UniverseApplication as ToolshedUniverseApplication
from tool_shed.webapp.fast_app import initialize_fast_app as init_tool_shed_fast_app
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, "sample_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")]
DEFAULT_LOCALES = "en"

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.
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


[docs]def build_logger(): """Build a logger for test driver script.""" return log
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_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", fetch_url_allowlist=["127.0.0.0/24"], job_handler_monitor_sleep=0.2, job_runner_monitor_sleep=0.2, workflow_monitor_sleep=0.2, ) 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 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}")
def init_database(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)
[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): init_database(database_connection) 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 if port and isinstance(port, str): port = int(port) 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: message = f"Test HTTP server on host {host} and port {port} did not return '200 OK' after {sleep_tries} tries" raise Exception(message)
def attempt_port(port: int) -> Optional[int]: 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=None, set_galaxy_web_port=True) -> str: if port is not None: if not attempt_port(int(port)): raise Exception(f"An existing process seems bound to specified test server port [{port}]") return port else: random.seed() for _ in range(0, 9): port = attempt_port(random.randint(8000, 10000)) if port: port = str(port) if set_galaxy_web_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 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.config import Config from uvicorn.server import Server 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: str) -> None: """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 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, is_webapp=True) log.info("Embedded Galaxy application started") global install_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 webapp (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 def get_logs(self) -> Optional[str]: # Subclasses can implement a way to return relevant logs pass @property def app(self): raise NotImplementedError("Test can be run against target - requires a Galaxy app object.") def stop(self) -> None: 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.") thread_count = threading.active_count() log.info(f"{thread_count} active after stopping embedded server") class GravityServerWrapper(ServerWrapper): def __init__(self, name, host, port, state_dir, stop_command): super().__init__(name, host, port) self.url_prefix = os.environ.get("GALAXY_CONFIG_GALAXY_URL_PREFIX", "/") self.state_dir = Path(state_dir) self.stop_command = stop_command def wait_for_server(self): try: set_and_wait_for_http_target( "GALAXY", self.host, self.port, url_prefix=self.url_prefix, sleep_amount=0.4, ) except Exception: log.error("Gravity logs:\n%s", self.get_logs()) def get_logs(self): gunicorn_logs = (self.state_dir / "log" / "gunicorn.log").read_text() gxit_logs = (self.state_dir / "log" / "gx-it-proxy.log").read_text() celery_logs = (self.state_dir / "log" / "celery.log").read_text() return f"Gunicorn logs:{os.linesep}{gunicorn_logs}{os.linesep}gx-it-proxy logs:{os.linesep}{gxit_logs}celery logs:{os.linesep}{celery_logs}" def stop(self): self.stop_command() def launch_gravity(port, gxit_port=None, galaxy_config=None): galaxy_config = galaxy_config or {} if not gxit_port: gxit_port = attempt_ports(set_galaxy_web_port=False) if "interactivetools_proxy_host" not in galaxy_config: galaxy_config["interactivetools_proxy_host"] = f"localhost:{gxit_port}" # Can't use in-memory celery broker, just fall back to sqlalchemy celery_conf = galaxy_config.get("celery_conf", {}) celery_conf.update({"broker_url": None}) galaxy_config["celery_conf"] = celery_conf state_dir = tempfile.mkdtemp(suffix="state") config = { "gravity": { "log_dir": os.path.join(state_dir, "log"), "gunicorn": {"bind": f"localhost:{port}", "preload": "false"}, "gx_it_proxy": { "enable": galaxy_config.get("interactivetools_enable", False), "port": gxit_port, "verbose": True, "sessions": galaxy_config.get("interactivetools_map"), }, }, "galaxy": galaxy_config, } with tempfile.NamedTemporaryFile("w", dir=state_dir, delete=False, suffix=".galaxy.yml") as config_fh: json.dump(config, config_fh) with tempfile.NamedTemporaryFile(delete=True) as socket: supervisord_socket = socket.name gravity_env = os.environ.copy() gravity_env["SUPERVISORD_SOCKET"] = supervisord_socket subprocess.check_output(["galaxyctl", "--config-file", config_fh.name, "update"], env=gravity_env) subprocess.check_output(["galaxyctl", "--config-file", config_fh.name, "start"], env=gravity_env) return state_dir, lambda: subprocess.check_output( ["galaxyctl", "--config-file", config_fh.name, "shutdown"], env=gravity_env ) def launch_server(app_factory, 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) enable_realtime_mapping = getattr(config_object, "enable_realtime_mapping", False) if enable_realtime_mapping: interactive_tool_defaults = { "interactivetools_map": tempfile.NamedTemporaryFile( delete=False, suffix="interactivetools_map.sqlite" ).name, "interactivetools_enable": True, "interactivetools_upstream_proxy": False, "galaxy_infrastructure_url": f"http://localhost:{port}", } interactive_tool_defaults.update(galaxy_config or {}) galaxy_config = interactive_tool_defaults if enable_realtime_mapping or os.environ.get("GALAXY_TEST_GRAVITY"): galaxy_config["root"] = galaxy_root state_dir, stop_command = launch_gravity(port=port, galaxy_config=galaxy_config) gravity_wrapper = GravityServerWrapper(name, host, port, state_dir, stop_command) gravity_wrapper.wait_for_server() return gravity_wrapper app = app_factory() url_prefix = getattr(app.config, f"{name}_url_prefix", "/") wsgi_webapp = webapp_factory( galaxy_config["global_conf"], app=app, use_translogger=False, static_enabled=True, register_shutdown_at_exit=False, ) if name == "galaxy": asgi_app = init_galaxy_fast_app(wsgi_webapp, app) elif name == "tool_shed": asgi_app = init_tool_shed_fast_app(wsgi_webapp, app) else: raise NotImplementedError(f"Launching {name} not implemented") server, port, thread = uvicorn_serve(asgi_app, host=host, port=port) set_and_wait_for_http_target(prefix, host, port, url_prefix=url_prefix) log.debug(f"Embedded uvicorn web server for {name} started at {host}:{port}{url_prefix}") return EmbeddedServerWrapper(app, server, name, host, port, thread=thread, prefix=url_prefix)
[docs]class TestDriver: """Responsible for the life-cycle of a Galaxy-style functional test. Sets up servers, configures tests, 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: List[ServerWrapper] = [] self.temp_directories: List[str] = []
[docs] def setup(self, config_object=None) -> None: """Called before tests are built."""
[docs] def tear_down(self) -> None: """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) -> None: for server_wrapper in self.server_wrappers: server_wrapper.stop() for th in threading.enumerate(): log.debug(f"After stopping all servers thread {th} is alive.") if (active_count := threading.active_count()) > 100: # For an unknown reason running iRODS tests results in application threads not shutting down immediately, # but if we've accumulated over 100 active threads something else is wrong that needs to be fixed. raise Exception( f"{active_count} active threads after stopping embedded server. Have all threads been shut down?" ) self.server_wrappers = []
[docs] def mkdtemp(self) -> str: """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
class GalaxyTestDriver(TestDriver): """Instantial a Galaxy-style TestDriver for testing Galaxy.""" testing_shed_tools = False def _configure(self, config_object=None) -> 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) if not self.external_galaxy: os.environ["GALAXY_TEST_STRICT_CHECKS"] = "1" # Allow controlling the log format self.log_format = os.environ.get("GALAXY_TEST_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 get_logs(self) -> Optional[str]: if not self.server_wrappers: return None server_wrapper = self.server_wrappers[0] return server_wrapper.get_logs() def restart(self, config_object=None, handle_config=None) -> 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) -> None: config_object = self._ensure_config_object(config_object) self.app: Optional[GalaxyUniverseApplication] = 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) server_wrapper = launch_server( app_factory=lambda: self.build_galaxy_app(galaxy_config), webapp_factory=lambda *args, **kwd: buildapp.app_factory(*args, wsgi_preflight=False, **kwd), galaxy_config=galaxy_config, config_object=config_object, ) self.server_wrappers.append(server_wrapper) else: log.info(f"Functional tests will be run against test external Galaxy server {self.external_galaxy}") # Ensure test file directory setup even though galaxy config isn't built. ensure_test_file_dir_set() def build_galaxy_app(self, galaxy_config) -> GalaxyUniverseApplication: self.app = build_galaxy_app(galaxy_config) return self.app def _ensure_config_object(self, config_object): if config_object is None: config_object = self return config_object def run_tool_test( self, tool_id: str, index: int = 0, resource_parameters: Optional[Dict[str, Any]] = None, **kwd ) -> None: if resource_parameters is None: resource_parameters = {} _, _, 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", "setup_galaxy_config", "TestDriver", "wait_for_http_server", )