Source code for planemo.galaxy.config

"""Abstractions for setting up a Galaxy instance."""

import abc
import contextlib
import hashlib
import importlib.util
import json
import os
import random
import shlex
import shutil
import threading
import time
from string import Template
from tempfile import (
    mkdtemp,
    NamedTemporaryFile,
)
from typing import (
    List,
    Optional,
    Set,
    TYPE_CHECKING,
)

from galaxy.containers.docker_model import DockerVolume
from galaxy.tool_util.deps import docker_util
from galaxy.util.commands import argv_to_str
from packaging.version import parse as parse_version

from planemo import git
from planemo.config import OptionSource
from planemo.deps import ensure_dependency_resolvers_conf_configured
from planemo.docker import docker_host_args
from planemo.galaxy.workflows import remote_runnable_to_workflow_id
from planemo.io import (
    communicate,
    kill_pid_file,
    shell,
    shell_join,
    stop_gravity,
    untar_to,
    wait_on,
    warn,
    write_file,
)
from planemo.mulled import build_involucro_context
from planemo.shed import tool_shed_url
from .api import (
    DEFAULT_ADMIN_API_KEY,
    gi,
    user_api_key,
)
from .distro_tools import DISTRO_TOOLS_ID_TO_PATH
from .run import setup_venv
from .workflows import (
    find_tool_ids,
    import_workflow,
    install_shed_repos,
)

if TYPE_CHECKING:
    from planemo.runnable import Runnable

NO_TEST_DATA_MESSAGE = (
    "planemo couldn't find a target test-data directory, you should likely "
    "create a test-data directory or pass an explicit path using --test_data."
)

WEB_SERVER_CONFIG_TEMPLATE = """
[server:${server_name}]
use = egg:Paste#http
port = ${port}
host = ${host}
use_threadpool = True
threadpool_kill_thread_limit = 10800
[app:main]
paste.app_factory = galaxy.web.buildapp:app_factory
static_dir = static/
"""

TOOL_CONF_TEMPLATE = """<toolbox>
  <tool file="data_source/upload.xml" />
  ${tool_definition}
</toolbox>
"""

SHED_TOOL_CONF_TEMPLATE = """<?xml version="1.0"?>
<toolbox tool_path="${shed_tool_path}">
</toolbox>
"""

SHED_DATA_MANAGER_CONF_TEMPLATE = """<?xml version="1.0"?>
<data_managers>
</data_managers>
"""

EMPTY_JOB_METRICS_TEMPLATE = """<?xml version="1.0"?>
<job_metrics>
</job_metrics>
"""

TOOL_SHEDS_CONF = """<tool_sheds>
  <tool_shed name="Target Shed" url="${shed_target_url}" />
</tool_sheds>
"""

JOB_CONFIG_LOCAL = """<job_conf>
    <plugins>
        <plugin id="planemo_runner" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
    </plugins>
    <handlers>
    </handlers>
    <destinations default="planemo_dest">
        <destination id="planemo_dest" runner="planemo_runner">
            <param id="require_container">${require_container}</param>
            <param id="docker_enabled">${docker_enable}</param>
            <param id="docker_sudo">${docker_sudo}</param>
            <param id="docker_sudo_cmd">${docker_sudo_cmd}</param>
            <param id="docker_cmd">${docker_cmd}</param>
            ${docker_host_param}
        </destination>
        <destination id="upload_dest" runner="planemo_runner">
            <param id="docker_enabled">false</param>
        </destination>
    </destinations>
    <tools>
        <tool id="upload1" destination="upload_dest" />
    </tools>
</job_conf>
"""

REFGENIE_CONFIG_TEMPLATE = """
config_version: %s
genome_folder: '%s'
genome_servers: ['http://refgenomes.databio.org']
genomes: null
"""

EMPTY_TOOL_CONF_TEMPLATE = """<toolbox></toolbox>"""
GX_TEST_TOOL_PATH = "$GALAXY_FUNCTIONAL_TEST_TOOLS"

DEFAULT_GALAXY_BRANCH = "master"
DEFAULT_GALAXY_SOURCE = "https://github.com/galaxyproject/galaxy"
CWL_GALAXY_SOURCE = "https://github.com/common-workflow-language/galaxy"

DATABASE_LOCATION_TEMPLATE = "sqlite:///%s?isolation_level=IMMEDIATE"

COMMAND_STARTUP_COMMAND = "./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}"

CLEANUP_IGNORE_ERRORS = True
DEFAULT_GALAXY_BRAND = "Configured by Planemo"
DEFAULT_TOOL_INSTALL_TIMEOUT = 60 * 60 * 1
UNINITIALIZED = object()


[docs]@contextlib.contextmanager def galaxy_config(ctx, runnables, **kwds): """Set up a ``GalaxyConfig`` in an auto-cleaned context.""" c = local_galaxy_config if kwds.get("dockerize", False): c = docker_galaxy_config elif kwds.get("external", False): c = external_galaxy_config log_thread = None e = threading.Event() try: with c(ctx, runnables, **kwds) as config: if kwds.get("daemon"): log_thread = threading.Thread(target=read_log, args=(ctx, config.log_file, e)) log_thread.daemon = True log_thread.start() yield config finally: if log_thread: e.set() log_thread.join(1)
def read_log(ctx, log_path, e: threading.Event): log_fh = None try: while not e.is_set(): if os.path.exists(log_path): if not log_fh: # Open in append so we start at the end of the log file log_fh = open(log_path, "a+") log_lines = log_fh.read() if log_lines: ctx.log(log_lines) e.wait(1) finally: if log_fh: log_fh.close() def simple_docker_volume(path): path = os.path.abspath(path) return DockerVolume(f"{path}:{path}:rw") @contextlib.contextmanager def docker_galaxy_config(ctx, runnables, for_tests=False, **kwds): """Set up a ``GalaxyConfig`` for Docker container.""" test_data_dir = _find_test_data(runnables, **kwds) with _config_directory(ctx, **kwds) as config_directory: def config_join(*args): return os.path.join(config_directory, *args) ensure_dependency_resolvers_conf_configured(ctx, kwds, os.path.join(config_directory, "resolvers_conf.xml")) _handle_job_metrics(config_directory, kwds) galaxy_root = kwds.get("galaxy_root") _handle_refgenie_config(config_directory, galaxy_root, kwds) shed_tool_conf = "config/shed_tool_conf.xml" all_tool_paths = _all_tool_paths(runnables, galaxy_root, kwds.get("extra_tools")) tool_directories = set() # Things to mount... for tool_path in all_tool_paths: directory = os.path.dirname(os.path.normpath(tool_path)) if os.path.exists(directory): tool_directories.add(directory) # TODO: remap these. tool_volumes = [] for tool_directory in tool_directories: volume = simple_docker_volume(tool_directory) tool_volumes.append(volume) empty_tool_conf = config_join("empty_tool_conf.xml") tool_conf = config_join("tool_conf.xml") shed_tool_path = kwds.get("shed_tool_path") or config_join("shed_tools") _ensure_directory(shed_tool_path) sheds_config_path = _configure_sheds_config_file(ctx, config_directory, **kwds) port = _get_port(kwds) properties = _shared_galaxy_properties(config_directory, kwds, for_tests=for_tests) _handle_container_resolution(ctx, kwds, properties) master_api_key = _get_master_api_key(kwds) template_args = dict( shed_tool_path=shed_tool_path, tool_conf=tool_conf, ) tool_config_file = f"{tool_conf},{shed_tool_conf}" _write_tool_conf(ctx, all_tool_paths, tool_conf) write_file(empty_tool_conf, EMPTY_TOOL_CONF_TEMPLATE) properties.update( dict( tool_config_file=tool_config_file, tool_sheds_config_file=sheds_config_path, migrated_tools_config=empty_tool_conf, ) ) server_name = f"planemo{random.randint(0, 100000)}" # Value substitutions in Galaxy properties - for consistency with # non-Dockerized version. template_args = dict() env = _build_env_for_galaxy(properties, template_args) env["NONUSE"] = "nodejs,proftp,reports" if ctx.verbose: env["GALAXY_LOGGING"] = "full" # TODO: setup FTP upload dir and disable FTP server in container. docker_target_kwds = docker_host_args(**kwds) volumes = tool_volumes + [simple_docker_volume(config_directory)] export_directory = kwds.get("export_directory", None) if export_directory is not None: volumes.append(DockerVolume(f"{export_directory}:/export:rw")) # TODO: Allow this to real Docker volumes and allow multiple. extra_volume = kwds.get("docker_extra_volume") if extra_volume: volumes.append(simple_docker_volume(extra_volume)) yield DockerGalaxyConfig( ctx, config_directory, env, test_data_dir, port, server_name, master_api_key, runnables, docker_target_kwds=docker_target_kwds, volumes=volumes, export_directory=export_directory, kwds=kwds, ) @contextlib.contextmanager def local_galaxy_config(ctx, runnables, for_tests=False, **kwds): """Set up a ``GalaxyConfig`` in an auto-cleaned context.""" test_data_dir = _find_test_data(runnables, **kwds) tool_data_tables = _find_tool_data_table(runnables, test_data_dir=test_data_dir, **kwds) data_manager_config_paths = [r.data_manager_conf_path for r in runnables if r.data_manager_conf_path] galaxy_root = _find_galaxy_root(ctx, **kwds) install_galaxy = kwds.get("install_galaxy", False) if galaxy_root is not None: if os.path.isdir(galaxy_root) and not os.listdir(galaxy_root): os.rmdir(galaxy_root) if os.path.isdir(galaxy_root) and install_galaxy: raise Exception(f"{galaxy_root} is an existing non-empty directory, cannot install Galaxy again") # Duplicate block in docker variant above. if kwds.get("mulled_containers", False): if not kwds.get("docker", False): if ctx.get_option_source("docker") != OptionSource.cli: kwds["docker"] = True else: raise Exception("Specified no docker and mulled containers together.") conda_default_options = ("conda_auto_init", "conda_auto_install") use_conda_options = ("dependency_resolution", "conda_use_local", "conda_prefix", "conda_exec") if not any(kwds.get(_) for _ in use_conda_options) and all( ctx.get_option_source(_) == OptionSource.default for _ in conda_default_options ): # If using mulled_containers and default conda options disable conda resolution kwds["no_dependency_resolution"] = kwds["no_conda_auto_init"] = True with _config_directory(ctx, **kwds) as config_directory: def config_join(*args): return os.path.join(config_directory, *args) install_env = {} if kwds.get("galaxy_skip_client_build", True): install_env["GALAXY_SKIP_CLIENT_BUILD"] = "1" if galaxy_root is None: galaxy_root = config_join("galaxy-dev") if not os.path.isdir(galaxy_root): _install_galaxy(ctx, galaxy_root, install_env, kwds) server_name = "main" # Once we don't have to support earlier than 18.01 - try putting these files # somewhere better than with Galaxy. log_file = f"{server_name}.log" pid_file = f"{server_name}.pid" ensure_dependency_resolvers_conf_configured(ctx, kwds, os.path.join(config_directory, "resolvers_conf.xml")) _handle_job_config_file(config_directory, server_name, kwds) _handle_job_metrics(config_directory, kwds) _handle_refgenie_config(config_directory, galaxy_root, kwds) file_path = kwds.get("file_path") or config_join("files") _ensure_directory(file_path) tool_dependency_dir = kwds.get("tool_dependency_dir") or config_join("deps") _ensure_directory(tool_dependency_dir) shed_tool_conf = kwds.get("shed_tool_conf") or config_join("shed_tools_conf.xml") all_tool_paths = _all_tool_paths(runnables, galaxy_root=galaxy_root, extra_tools=kwds.get("extra_tools")) empty_tool_conf = config_join("empty_tool_conf.xml") tool_conf = config_join("tool_conf.xml") shed_data_manager_config_file = config_join("shed_data_manager_conf.xml") shed_tool_path = kwds.get("shed_tool_path") or config_join("shed_tools") _ensure_directory(shed_tool_path) sheds_config_path = _configure_sheds_config_file(ctx, config_directory, **kwds) database_location = config_join("galaxy.sqlite") master_api_key = _get_master_api_key(kwds) dependency_dir = os.path.join(config_directory, "deps") _ensure_directory(shed_tool_path) port = _get_port(kwds) template_args = dict( port=port, host=kwds.get("host", "127.0.0.1"), server_name=server_name, temp_directory=config_directory, shed_tool_path=shed_tool_path, database_location=database_location, tool_conf=tool_conf, debug=kwds.get("debug", "true"), id_secret=kwds.get("id_secret", hashlib.md5(str(time.time()).encode("utf-8")).hexdigest()), log_level="DEBUG" if ctx.verbose else "INFO", ) tool_config_file = f"{tool_conf},{shed_tool_conf}" # Setup both galaxy_email and older test user test@bx.psu.edu # as admins for command_line, etc... properties = _shared_galaxy_properties(config_directory, kwds, for_tests=for_tests) properties.update( dict( server_name="main", ftp_upload_dir_template="${ftp_upload_dir}", ftp_upload_purge="False", ftp_upload_dir=test_data_dir or os.path.abspath("."), ftp_upload_site="Test Data", check_upload_content="False", tool_dependency_dir=dependency_dir, file_path=file_path, new_file_path="${temp_directory}/tmp", tool_config_file=tool_config_file, tool_sheds_config_file=sheds_config_path, manage_dependency_relationships="False", job_working_directory="${temp_directory}/job_working_directory", template_cache_path="${temp_directory}/compiled_templates", citation_cache_type="file", citation_cache_data_dir="${temp_directory}/citations/data", citation_cache_lock_dir="${temp_directory}/citations/lock", database_auto_migrate="True", enable_beta_tool_formats="True", id_secret="${id_secret}", log_level="${log_level}", debug="${debug}", watch_tools="auto", default_job_shell="/bin/bash", # For conda dependency resolution tool_data_table_config_path=",".join(tool_data_tables) if tool_data_tables else None, data_manager_config_file=",".join(data_manager_config_paths) or None, # without 'or None' may raise IOError in galaxy (see #946) integrated_tool_panel_config=("${temp_directory}/" "integrated_tool_panel_conf.xml"), migrated_tools_config=empty_tool_conf, test_data_dir=test_data_dir, # TODO: make gx respect this shed_data_manager_config_file=shed_data_manager_config_file, outputs_to_working_directory="True", # this makes Galaxy's files dir RO for dockerized testing ) ) _handle_container_resolution(ctx, kwds, properties) properties["database_connection"] = _database_connection(database_location, **kwds) if kwds.get("mulled_containers", False): properties["mulled_channels"] = kwds.get("conda_ensure_channels", "") _handle_kwd_overrides(properties, kwds) # TODO: consider following property # watch_tool = False # datatypes_config_file = config/datatypes_conf.xml # welcome_url = /static/welcome.html # logo_url = / # sanitize_all_html = True # serve_xss_vulnerable_mimetypes = False # track_jobs_in_database = None # retry_job_output_collection = 0 env = _build_env_for_galaxy(properties, template_args) env.update(install_env) env["GALAXY_DEVELOPMENT_ENVIRONMENT"] = "1" # Following are needed in 18.01 to prevent Galaxy from changing log and pid. # https://github.com/galaxyproject/planemo/issues/788 env["GALAXY_LOG"] = log_file env["GALAXY_PID"] = pid_file write_galaxy_config( galaxy_root=galaxy_root, properties=properties, env=env, kwds=kwds, template_args=template_args, config_join=config_join, ) _write_tool_conf(ctx, all_tool_paths, tool_conf) write_file(empty_tool_conf, EMPTY_TOOL_CONF_TEMPLATE) shed_tool_conf_contents = _sub(SHED_TOOL_CONF_TEMPLATE, template_args) # Write a new shed_tool_conf.xml if needed. write_file(shed_tool_conf, shed_tool_conf_contents, force=False) write_file(shed_data_manager_config_file, SHED_DATA_MANAGER_CONF_TEMPLATE) yield LocalGalaxyConfig( ctx, config_directory, env, test_data_dir, port, server_name, master_api_key, runnables, galaxy_root, kwds, ) def write_galaxy_config(galaxy_root, properties, env, kwds, template_args, config_join): if get_galaxy_major_version(galaxy_root) < parse_version("22.01"): # Legacy .ini setup env["GALAXY_CONFIG_FILE"] = config_join("galaxy.ini") web_config = _sub(WEB_SERVER_CONFIG_TEMPLATE, template_args) write_file(env["GALAXY_CONFIG_FILE"], web_config) else: env["GALAXY_CONFIG_FILE"] = config_join("galaxy.yml") env["GRAVITY_STATE_DIR"] = config_join("gravity") with NamedTemporaryFile(suffix=".sock", delete=True) as nt: env["SUPERVISORD_SOCKET"] = nt.name write_file( env["GALAXY_CONFIG_FILE"], json.dumps( { "galaxy": properties, "gravity": { "galaxy_root": galaxy_root, "gunicorn": {"bind": f"localhost:{template_args['port']}"}, "gx-it-proxy": { "enable": False, }, }, } ), ) def _expand_paths(galaxy_root: Optional[str], extra_tools: List[str]) -> List[str]: """Replace $GALAXY_FUNCTION_TEST_TOOLS with actual path.""" if galaxy_root: extra_tools = [ path if path != GX_TEST_TOOL_PATH else os.path.join(galaxy_root, "test/functional/tools") for path in extra_tools ] return extra_tools def get_galaxy_major_version(galaxy_root): spec = importlib.util.spec_from_file_location( "__galaxy_version", os.path.join(galaxy_root, "lib", "galaxy", "version.py") ) module = importlib.util.module_from_spec(spec) spec.loader.exec_module(module) return parse_version(module.VERSION_MAJOR) def get_refgenie_config(galaxy_root, refgenie_dir): config_version = 0.4 if galaxy_root: version_major = get_galaxy_major_version(galaxy_root=galaxy_root) if version_major < parse_version("21.09"): config_version = 0.3 return REFGENIE_CONFIG_TEMPLATE % (config_version, refgenie_dir) def _all_tool_paths( runnables: List["Runnable"], galaxy_root: Optional[str] = None, extra_tools: Optional[List[str]] = None ) -> Set[str]: extra_tools = extra_tools or [] all_tool_paths = {r.path for r in runnables if r.has_tools and not r.data_manager_conf_path} extra_tools = _expand_paths(galaxy_root, extra_tools=extra_tools) all_tool_paths.update(extra_tools) for runnable in runnables: if runnable.type.name == "galaxy_workflow": tool_ids = find_tool_ids(runnable.path) for tool_id in tool_ids: tool_paths = DISTRO_TOOLS_ID_TO_PATH.get(tool_id) if tool_paths: if isinstance(tool_paths, str): tool_paths = [tool_paths] all_tool_paths.update(tool_paths) return all_tool_paths def _shared_galaxy_properties(config_directory, kwds, for_tests): """Setup properties useful for local and Docker Galaxy instances. Most things related to paths, etc... are very different between Galaxy modalities and many taken care of internally to the container in that mode. But this method sets up API stuff, tool, and job stuff that can be shared. """ master_api_key = _get_master_api_key(kwds) user_email = _user_email(kwds) properties = { "master_api_key": master_api_key, "admin_users": f"{user_email},test@bx.psu.edu", "expose_dataset_path": "True", "collect_outputs_from": "job_working_directory", "allow_path_paste": "True", "check_migrate_tools": "False", "use_cached_dependency_manager": str(kwds.get("conda_auto_install", False)), "brand": kwds.get("galaxy_brand", DEFAULT_GALAXY_BRAND), "strict_cwl_validation": str(not kwds.get("non_strict_cwl", False)), } if kwds.get("no_cleanup", False): properties["cleanup_job"] = "never" else: properties["cleanup_job"] = "always" if kwds.get("galaxy_single_user", True): properties["single_user"] = user_email if for_tests: empty_dir = os.path.join(config_directory, "empty") _ensure_directory(empty_dir) properties["tour_config_dir"] = empty_dir properties["interactive_environment_plugins_directory"] = empty_dir properties["visualization_plugins_directory"] = empty_dir properties["refgenie_config_file"] = kwds.get("refgenie_config_file", "") return properties @contextlib.contextmanager def external_galaxy_config(ctx, runnables, for_tests=False, **kwds): yield BaseGalaxyConfig( ctx=ctx, galaxy_url=kwds.get("galaxy_url", None), master_api_key=_get_master_api_key(kwds), user_api_key=kwds.get("galaxy_user_key", None), runnables=runnables, kwds=kwds, ) def _get_master_api_key(kwds): master_api_key = kwds.get("galaxy_admin_key") or DEFAULT_ADMIN_API_KEY return master_api_key def _get_port(kwds): port = int(kwds.get("port", 9090)) return port def _user_email(kwds): user_email = kwds.get("galaxy_email") return user_email @contextlib.contextmanager def _config_directory(ctx, **kwds): config_directory = kwds.get("config_directory", None) created_config_directory = False if not config_directory: created_config_directory = True config_directory = os.path.realpath(mkdtemp()) ctx.vlog(f"Created directory for Galaxy configuration [{config_directory}]") try: yield config_directory finally: cleanup = not kwds.get("no_cleanup", False) if created_config_directory and cleanup: shutil.rmtree(config_directory, ignore_errors=True) class GalaxyInterface(metaclass=abc.ABCMeta): """Abstraction around a Galaxy instance. Description of a Galaxy instance and how to interact with it - this could potentially be a remote, already running instance or an instance Planemo manages to execute some task(s). """ @abc.abstractproperty def gi(self): """Return an admin bioblend Galaxy instance for API interactions.""" @abc.abstractproperty def user_gi(self): """Return a user-backed bioblend Galaxy instance for API interactions.""" @abc.abstractmethod def install_repo(self, *args, **kwds): """Install specified tool shed repository.""" @abc.abstractproperty def tool_shed_client(self): """Return a admin bioblend tool shed client.""" @abc.abstractmethod def wait_for_all_installed(self): """Wait for all queued up repositories installs to complete.""" @abc.abstractmethod def install_workflows(self): """Install all workflows configured with these planemo arguments.""" @abc.abstractmethod def workflow_id(self, path): """Get installed workflow API ID for input path.""" @abc.abstractproperty def version_major(self): """Return target Galaxy version.""" @abc.abstractproperty def user_api_config(self): """Return the API indicated configuration for user session. Calling .config.get_config() with admin GI session would yield a different object (admins have different view of Galaxy's configuration). """ @property def user_is_admin(self): return self.user_api_config["is_admin_user"] class GalaxyConfig(GalaxyInterface, metaclass=abc.ABCMeta): """Specialization of GalaxyInterface for Galaxy instances Planemo manages itself. This assumes more than an API connection is available - Planemo needs to be able to start and stop the Galaxy instance, recover logs, etc... There are currently two implementations - a locally executed Galaxy and one running inside a Docker containe """ @abc.abstractproperty def kill(self): """Stop the running instance.""" @abc.abstractmethod def startup_command(self, ctx, **kwds): """Return a shell command used to startup this instance. Among other common planmo kwds, this should respect the ``daemon`` keyword. """ @abc.abstractproperty def log_contents(self): """Retrieve text of log for running Galaxy instance.""" @abc.abstractmethod def cleanup(self): """Cleanup allocated resources to run this instance.""" @abc.abstractproperty def use_path_paste(self): """Use path paste to upload data. This will only be an option if the target user key is an admin user key. """ class BaseGalaxyConfig(GalaxyInterface): def __init__( self, ctx, galaxy_url, master_api_key, user_api_key, runnables, kwds, ): self._ctx = ctx self.galaxy_url = galaxy_url self.master_api_key = master_api_key self._user_api_key = user_api_key self.runnables = runnables self._kwds = kwds self._workflow_ids = {} self.installed_repos = {} self.updated_repos = {} self._target_version = UNINITIALIZED self._target_user_config = UNINITIALIZED @property def gi(self): assert self.galaxy_url return gi(url=self.galaxy_url, key=self.master_api_key) @property def user_gi(self): user_api_key = self.user_api_key assert user_api_key return self._gi_for_key(user_api_key) @property def user_api_key(self): # TODO: thread-safe if self._user_api_key is None: # TODO: respect --galaxy_email - seems like a real bug self._user_api_key = user_api_key(self.gi) return self._user_api_key def _gi_for_key(self, key): assert self.galaxy_url return gi(url=self.galaxy_url, key=key) def install_repo(self, *args, **kwds): self.tool_shed_client.install_repository_revision(*args, **kwds) @property def tool_shed_client(self): return self.gi.toolShed def wait_for_all_installed(self): def status_ready(repo): status = repo["status"] if status in ["Installing", "New"]: return None if status == "Installed": return True raise Exception(f"Error installing repo status is {status}") def ready(): repos = self.tool_shed_client.get_repositories() ready = all(map(status_ready, repos)) return ready or None wait_on(ready, "galaxy tool installation", timeout=DEFAULT_TOOL_INSTALL_TIMEOUT) def install_workflows(self): for runnable in self.runnables: if runnable.type.name in ["galaxy_workflow", "cwl_workflow"] and not runnable.is_remote_workflow_uri: self._install_workflow(runnable) def _install_workflow(self, runnable): if self._kwds.get("shed_install") and ( self._kwds.get("engine") != "external_galaxy" or self._kwds.get("galaxy_admin_key") ): workflow_repos = install_shed_repos( runnable, self.gi, self._kwds.get("ignore_dependency_problems", False), self._kwds.get("install_tool_dependencies", False), self._kwds.get("install_resolver_dependencies", True), self._kwds.get("install_repository_dependencies", True), self._kwds.get("install_most_recent_revision", False), ) self.installed_repos[runnable.path], self.updated_repos[runnable.path] = workflow_repos default_from_path = self._kwds.get("workflows_from_path", False) # TODO: Allow serialization so this doesn't need to assume a # shared filesystem with Galaxy server. from_path = default_from_path or (runnable.type.name == "cwl_workflow") workflow = import_workflow(runnable.path, admin_gi=self.gi, user_gi=self.user_gi, from_path=from_path) self._workflow_ids[runnable.path] = workflow["id"] def workflow_id_for_runnable(self, runnable): if runnable.is_remote_workflow_uri: workflow_id = remote_runnable_to_workflow_id(runnable) else: workflow_id = self.workflow_id(runnable.path) return workflow_id def workflow_id(self, path): return self._workflow_ids[path] @property def use_path_paste(self): option = self._kwds.get("paste_test_data_paths") if option is None: return self.default_use_path_paste else: return option @property def default_use_path_paste(self): return False @property def version_major(self) -> str: """Return target Galaxy version.""" if self._target_version is UNINITIALIZED: self._target_version = self.user_gi.config.get_version()["version_major"] return self._target_version @property def user_api_config(self): """Return the API indicated configuration for user session.""" if self._target_user_config is UNINITIALIZED: self._target_user_config = self.user_gi.config.get_config() return self._target_user_config class BaseManagedGalaxyConfig(BaseGalaxyConfig): def __init__( self, ctx, config_directory, env, test_data_dir, port, server_name, master_api_key, runnables, kwds, ): galaxy_url = f"http://localhost:{port}" super().__init__( ctx=ctx, galaxy_url=galaxy_url, master_api_key=master_api_key, user_api_key=None, runnables=runnables, kwds=kwds, ) self.config_directory = config_directory self.env = env self.test_data_dir = test_data_dir self.port = port self.server_name = server_name @property def log_file(self): """Log file used when planemo serves this Galaxy instance.""" file_name = f"{self.server_name}.log" return file_name class DockerGalaxyConfig(BaseManagedGalaxyConfig): """A :class:`GalaxyConfig` description of a Dockerized Galaxy instance.""" def __init__( self, ctx, config_directory, env, test_data_dir, port, server_name, master_api_key, runnables, docker_target_kwds, volumes, export_directory, kwds, ): super().__init__( ctx, config_directory, env, test_data_dir, port, server_name, master_api_key, runnables, kwds, ) self.docker_target_kwds = docker_target_kwds self.volumes = volumes self.export_directory = export_directory def kill(self): """Kill planemo container...""" kill_command = docker_util.kill_command(self.server_name, **self.docker_target_kwds) return shell(kill_command) def startup_command(self, ctx, **kwds): """Return a shell command used to startup this instance. Among other common planmo kwds, this should respect the ``daemon`` keyword. """ daemon = kwds.get("daemon", False) daemon_str = "" if not daemon else " -d" docker_run_extras = f"-p {self.port}:80{daemon_str}" env_directives = [f"{k}='{v}'" for k, v in self.env.items()] image = kwds.get("docker_galaxy_image", "bgruening/galaxy-stable") run_command = docker_util.build_docker_run_command( "", image, interactive=False, env_directives=env_directives, working_directory=None, name=self.server_name, run_extra_arguments=docker_run_extras, set_user=False, volumes=self.volumes, **self.docker_target_kwds, ) chmod_command = [ "chmod", "-R", "o+rwx", self.config_directory, ] if self.export_directory: chmod_command.append(self.export_directory) return shell_join( argv_to_str(chmod_command), run_command, ) @property def log_contents(self): logs_command = docker_util.logs_command(self.server_name, **self.docker_target_kwds) output, _ = communicate(logs_command) return output def cleanup(self): shutil.rmtree(self.config_directory, CLEANUP_IGNORE_ERRORS) class LocalGalaxyConfig(BaseManagedGalaxyConfig): """A local, non-containerized implementation of :class:`GalaxyConfig`.""" def __init__( self, ctx, config_directory, env, test_data_dir, port, server_name, master_api_key, runnables, galaxy_root, kwds, ): super().__init__( ctx, config_directory, env, test_data_dir, port, server_name, master_api_key, runnables, kwds, ) self.galaxy_root = galaxy_root self._virtual_env_dir = None @property def virtual_env_dir(self): virtual_env = self._virtual_env_dir or ".venv" if not os.path.isabs(virtual_env): virtual_env = os.path.join(self.galaxy_root, virtual_env) return virtual_env @property def gravity_state_dir(self): return self.env["GRAVITY_STATE_DIR"] def kill(self): if self._ctx.verbose: shell(["ps", "ax"]) exists = os.path.exists(self.pid_file) print(f"Killing pid file [{self.pid_file}]") print(f"pid_file exists? [{exists}]") if exists: with open(self.pid_file) as f: print(f"pid_file contents are [{f.read()}]") if self.env.get("GRAVITY_STATE_DIR"): stop_gravity(virtual_env=self.virtual_env_dir, gravity_state_dir=self.gravity_state_dir, env=self.env) kill_pid_file(self.pid_file) def startup_command(self, ctx, **kwds): """Return a shell command used to startup this instance. Among other common planemo kwds, this should respect the ``daemon`` keyword. """ daemon = kwds.get("daemon", False) # TODO: Allow running dockerized Galaxy here instead. setup_venv_command = setup_venv(ctx, kwds, self) run_script = f"{shlex.quote(os.path.join(self.galaxy_root, 'run.sh'))} $COMMON_STARTUP_ARGS" if daemon: run_script += " --daemon" else: run_script += f" --server-name {shlex.quote(self.server_name)}" cd_to_galaxy_command = ["cd", self.galaxy_root] return shell_join( cd_to_galaxy_command, setup_venv_command, run_script, ) @property def log_file(self): """Log file used when planemo serves this Galaxy instance.""" file_name = f"{self.server_name}.log" return os.path.join(self.galaxy_root, file_name) @property def pid_file(self): pid_file_name = f"{self.server_name}.pid" return os.path.join(self.galaxy_root, pid_file_name) @property def log_contents(self): if not os.path.exists(self.log_file): return "" with open(self.log_file) as f: return f.read() def cleanup(self): shutil.rmtree(self.config_directory, CLEANUP_IGNORE_ERRORS) @property def default_use_path_paste(self): # If Planemo started a local, native Galaxy instance assume files URLs can be # pasted. return self.user_is_admin def _database_connection(database_location, **kwds): default_connection = DATABASE_LOCATION_TEMPLATE % database_location database_connection = kwds.get("database_connection") or default_connection return database_connection def _find_galaxy_root(ctx, **kwds): root_prop = "galaxy_root" cwl = kwds.get("cwl", False) if cwl: root_prop = "cwl_galaxy_root" galaxy_root = kwds.get(root_prop, None) if galaxy_root: return galaxy_root else: par_dir = os.getcwd() while True: run = os.path.join(par_dir, "run.sh") config = os.path.join(par_dir, "config") if os.path.isfile(run) and os.path.isdir(config): return par_dir new_par_dir = os.path.dirname(par_dir) if new_par_dir == par_dir: break par_dir = new_par_dir return None def _find_test_data(runnables, **kwds): test_data_search_path = "." runnables = [r for r in runnables if r.has_tools] if len(runnables) > 0: test_data_search_path = runnables[0].test_data_search_path # Find test data directory associated with path. test_data = kwds.get("test_data", None) if test_data: return os.path.abspath(test_data) else: test_data = _search_tool_path_for(test_data_search_path, "test-data") if test_data: return test_data warn(NO_TEST_DATA_MESSAGE) return None def _find_tool_data_table(runnables, test_data_dir, **kwds) -> Optional[List[str]]: tool_data_search_path = "." runnables = [r for r in runnables if r.has_tools] if len(runnables) > 0: tool_data_search_path = runnables[0].tool_data_search_path tool_data_table = kwds.get("tool_data_table", None) if tool_data_table: return [os.path.abspath(table_path) for table_path in tool_data_table] else: extra_paths = [test_data_dir] if test_data_dir else [] tool_data_table = _search_tool_path_for( tool_data_search_path, "tool_data_table_conf.xml.test", extra_paths, ) or _search_tool_path_for( # if all else fails just use sample tool_data_search_path, "tool_data_table_conf.xml.sample" ) if tool_data_table: return [tool_data_table] return None def _search_tool_path_for(path, target, extra_paths=None): """Check for presence of a target in different artifact directories.""" if extra_paths is None: extra_paths = [] if not os.path.isdir(path): tool_dir = os.path.dirname(path) else: tool_dir = path possible_dirs = [tool_dir, "."] + extra_paths for possible_dir in possible_dirs: possible_path = os.path.join(possible_dir, target) if os.path.exists(possible_path): return os.path.abspath(possible_path) return None def _configure_sheds_config_file(ctx, config_directory, **kwds): if "shed_target" not in kwds: kwds = kwds.copy() kwds["shed_target"] = "toolshed" shed_target_url = tool_shed_url(ctx, **kwds) contents = _sub(TOOL_SHEDS_CONF, {"shed_target_url": shed_target_url}) tool_sheds_conf = os.path.join(config_directory, "tool_sheds_conf.xml") write_file(tool_sheds_conf, contents) return tool_sheds_conf def _tool_conf_entry_for(tool_paths): tool_definitions = "" for tool_path in tool_paths: if os.path.isdir(tool_path): tool_definitions += f"""<tool_dir dir="{tool_path}" />""" else: tool_definitions += f"""<tool file="{tool_path}" />""" return tool_definitions def _install_galaxy(ctx, galaxy_root, env, kwds): if not kwds.get("no_cache_galaxy", False): _install_galaxy_via_git(ctx, galaxy_root, env, kwds) else: _install_galaxy_via_download(ctx, galaxy_root, env, kwds) def _install_galaxy_via_download(ctx, galaxy_root, env, kwds): branch = _galaxy_branch(kwds) untar_to( "https://codeload.github.com/galaxyproject/galaxy/tar.gz/" + branch, tar_args=["-xvzf", "-", "galaxy-" + branch], dest_dir=galaxy_root, ) _install_with_command(ctx, galaxy_root, env, kwds) def _install_galaxy_via_git(ctx, galaxy_root, env, kwds): gx_repo = _ensure_galaxy_repository_available(ctx, kwds) branch = _galaxy_branch(kwds) command = git.command_clone(ctx, gx_repo, galaxy_root, branch=branch) exit_code = shell(command, env=env) if exit_code != 0: raise Exception("Failed to clone Galaxy via git") _install_with_command(ctx, galaxy_root, env, kwds) def _galaxy_branch(kwds): branch = kwds.get("galaxy_branch", None) if branch is None: cwl = kwds.get("cwl", False) branch = "cwl-1.0" if cwl else None if branch is None: branch = DEFAULT_GALAXY_BRANCH return branch def _galaxy_source(kwds): source = kwds.get("galaxy_source", None) if source is None: cwl = kwds.get("cwl", False) source = CWL_GALAXY_SOURCE if cwl else None if source is None: source = DEFAULT_GALAXY_SOURCE return source def _install_with_command(ctx, galaxy_root, env, kwds): setup_venv_command = setup_venv(ctx, kwds) install_cmd = shell_join( setup_venv_command, COMMAND_STARTUP_COMMAND, ) exit_code = shell(install_cmd, cwd=galaxy_root, env=env) if exit_code != 0: raise Exception(f"Failed to install Galaxy via command [{install_cmd}]") if not os.path.exists(galaxy_root): raise Exception(f"Failed to create Galaxy directory [{galaxy_root}]") if not os.path.exists(os.path.join(galaxy_root, "lib")): raise Exception(f"Failed to create Galaxy directory [{galaxy_root}], lib missing") def _ensure_galaxy_repository_available(ctx, kwds): workspace = ctx.workspace cwl = kwds.get("cwl", False) galaxy_source = kwds.get("galaxy_source") if galaxy_source and galaxy_source != DEFAULT_GALAXY_SOURCE: sanitized_repo_name = "".join(c if c.isalnum() else "_" for c in kwds["galaxy_source"]).rstrip()[:255] gx_repo = os.path.join(workspace, f"gx_repo_{sanitized_repo_name}") else: gx_repo = os.path.join(workspace, "gx_repo") if cwl: gx_repo += "_cwl" if os.path.exists(gx_repo): # Convert the git repository from bare to mirror, if needed shell(["git", "--git-dir", gx_repo, "config", "remote.origin.fetch", "+refs/*:refs/*"]) shell(["git", "--git-dir", gx_repo, "config", "remote.origin.mirror", "true"]) # Attempt remote update - but don't fail if not interweb, etc... shell(f"git --git-dir {gx_repo} remote update >/dev/null 2>&1") else: remote_repo = _galaxy_source(kwds) command = git.command_clone(ctx, remote_repo, gx_repo, mirror=True) shell(command) return gx_repo def _build_env_for_galaxy(properties, template_args): env = {} for key, value in properties.items(): if value is not None: # Do not override None with empty string var = f"GALAXY_CONFIG_OVERRIDE_{key.upper()}" value = _sub(value, template_args) env[var] = value return env def _handle_job_config_file(config_directory, server_name, kwds): job_config_file = kwds.get("job_config_file", None) if not job_config_file: template_str = JOB_CONFIG_LOCAL job_config_file = os.path.join( config_directory, "job_conf.xml", ) docker_enable = str(kwds.get("docker", False)) docker_host = kwds.get("docker_host", docker_util.DEFAULT_HOST) docker_host_param = "" if docker_host: docker_host_param = f"""<param id="docker_host">{docker_host}</param>""" conf_contents = Template(template_str).safe_substitute( { "server_name": server_name, "docker_enable": docker_enable, "require_container": "false", "docker_sudo": str(kwds.get("docker_sudo", False)), "docker_sudo_cmd": str(kwds.get("docker_sudo_cmd", docker_util.DEFAULT_SUDO_COMMAND)), "docker_cmd": str(kwds.get("docker_cmd", docker_util.DEFAULT_DOCKER_COMMAND)), "docker_host_param": docker_host_param, } ) write_file(job_config_file, conf_contents) kwds["job_config_file"] = job_config_file def _write_tool_conf(ctx, tool_paths, tool_conf_path): tool_definition = _tool_conf_entry_for(tool_paths) tool_conf_template_kwds = dict(tool_definition=tool_definition) tool_conf_contents = _sub(TOOL_CONF_TEMPLATE, tool_conf_template_kwds) write_file(tool_conf_path, tool_conf_contents) ctx.vlog( "Writing tool_conf to path %s with contents [%s]", tool_conf_path, tool_conf_contents, ) def _handle_container_resolution(ctx, kwds, galaxy_properties): if kwds.get("mulled_containers", False): galaxy_properties["enable_beta_mulled_containers"] = "True" involucro_context = build_involucro_context(ctx, **kwds) galaxy_properties["involucro_auto_init"] = "False" # Use planemo's galaxy_properties["involucro_path"] = involucro_context.involucro_bin def _handle_job_metrics(config_directory, kwds): metrics_conf = os.path.join(config_directory, "job_metrics_conf.xml") with open(metrics_conf, "w") as fh: fh.write(EMPTY_JOB_METRICS_TEMPLATE) kwds["job_metrics_config_file"] = metrics_conf def _handle_refgenie_config(config_directory, galaxy_root, kwds): refgenie_dir = os.path.join(config_directory, "refgenie") _ensure_directory(refgenie_dir) refgenie_config_file = os.path.join(refgenie_dir, "genome_config.yaml") refgenie_config = get_refgenie_config(galaxy_root=galaxy_root, refgenie_dir=refgenie_dir) with open(refgenie_config_file, "w") as fh: fh.write(refgenie_config) kwds["refgenie_config_file"] = refgenie_config_file def _handle_kwd_overrides(properties, kwds): kwds_gx_properties = [ "tool_data_path", "job_config_file", "job_metrics_config_file", "dependency_resolvers_config_file", ] for prop in kwds_gx_properties: val = kwds.get(prop, None) if val: properties[prop] = val def _sub(template, args): if template is None: return "" return Template(template).safe_substitute(args) def _ensure_directory(path): if path is not None and not os.path.exists(path): os.makedirs(path) __all__ = ( "DATABASE_LOCATION_TEMPLATE", "galaxy_config", )