Source code for planemo.galaxy.serve

"""Abstractions for serving out development Galaxy servers."""

import contextlib
import os
import time

from planemo import (
from .config import galaxy_config
from .ephemeris_sleep import sleep
from .run import run_galaxy_command

INSTALLING_MESSAGE = "Installing repositories - this may take some time..."

[docs]def serve(ctx, runnables=None, **kwds): if runnables is None: runnables = [] """Serve a Galaxy instance with artifacts defined by paths.""" try: return _serve(ctx, runnables, **kwds) except Exception as e: ctx.vlog("Problem serving Galaxy", exception=e) raise
def _serve(ctx, runnables, **kwds): engine = kwds.get("engine", "galaxy") if engine == "docker_galaxy": kwds["dockerize"] = True daemon = kwds.get("daemon", False) if daemon: kwds["no_cleanup"] = True port = kwds.get("port", None) if port is None: port = network_util.get_free_port() kwds["port"] = port with galaxy_config(ctx, runnables, **kwds) as config: cmd = config.startup_command(ctx, **kwds) action = "Starting Galaxy" exit_code = run_galaxy_command( ctx, cmd, config.env, action, ) if exit_code: message = "Problem running Galaxy command [%s]." % config.log_contents io.warn(message) raise Exception(message) host = kwds.get("host", "") timeout = 500 galaxy_url = f"http://{host}:{port}" galaxy_alive = sleep(galaxy_url, verbose=ctx.verbose, timeout=timeout) if not galaxy_alive: raise Exception( "Attempted to serve Galaxy at %s, but it failed to start in %d seconds." % (galaxy_url, timeout) ) config.install_workflows() if kwds.get("pid_file"): real_pid_file = config.pid_file if os.path.exists(config.pid_file): os.symlink(real_pid_file, kwds["pid_file"]) else: io.warn("Can't find Galaxy pid file [%s] to link" % real_pid_file) return config
[docs]@contextlib.contextmanager def shed_serve(ctx, install_args_list, **kwds): """Serve a daemon instance of Galaxy with specified repositories installed.""" with serve_daemon(ctx, **kwds) as config: install_deps = not kwds.get("skip_dependencies", False) print(INSTALLING_MESSAGE) for install_args in install_args_list: install_args["install_tool_dependencies"] = install_deps install_args["install_repository_dependencies"] = True install_args["new_tool_panel_section_label"] = "Shed Installs" config.install_repo(**install_args) try: config.wait_for_all_installed() except Exception: if ctx.verbose: print("Failed to install tool repositories, Galaxy log:") print(config.log_contents) print("Galaxy root:")["ls", config.galaxy_root]) raise yield config
[docs]@contextlib.contextmanager def serve_daemon(ctx, runnables=None, **kwds): """Serve a daemonized Galaxy instance with artifacts defined by paths.""" if runnables is None: runnables = [] config = None try: kwds["daemon"] = True config = serve(ctx, runnables, **kwds) yield config finally: if config: if ctx.verbose: print("Galaxy Log:") print(config.log_contents) config.kill() if not kwds.get("no_cleanup", False): config.cleanup()
def sleep_for_serve(): # This is bad, do something better... time.sleep(1000000) __all__ = ( "serve", "serve_daemon", "shed_serve", )