"""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 (
Any,
Dict,
Iterable,
List,
Optional,
Set,
TYPE_CHECKING,
)
from galaxy.tool_util.deps import docker_util
from galaxy.tool_util.deps.container_volumes import DockerVolume
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>
"""
FILE_SOURCES_TEMPLATE = """
- type: posix
root: '${test_data_dir}'
id: test_data_dir
label: Test data directory
doc: Test data directory for the runnables being tested
"""
TOOL_SHEDS_CONF = """<tool_sheds>
<tool_shed name="Target Shed" url="${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">${docker_cmd}</param>
<param id="docker_volumes">${docker_volumes}</param>
<param id="docker_run_extra_arguments"><![CDATA[${docker_run_extra_arguments}]]></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 create_docker_volumes(paths: Iterable[str]) -> Iterable[DockerVolume]:
"""
Creates string of the format "host_path:target_path:mode" and deduplicates overlapping mounts.
"""
docker_volumes: Dict[str, DockerVolume] = {}
for path in paths:
docker_volume = DockerVolume.from_str(path)
if docker_volume.path in docker_volumes:
# volume has been specified already, make sure we use "rw" if any of the modes are "rw"
if docker_volume.mode == "rw" or docker_volumes[docker_volume.path].mode == "rw":
docker_volumes[docker_volume.path].mode = "rw"
else:
docker_volumes[docker_volume.path] = docker_volume
return docker_volumes.values()
@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)
volumes = []
for tool_directory in tool_directories:
volumes.append(tool_directory)
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.append(config_directory)
export_directory = kwds.get("export_directory", None)
if export_directory is not None:
volumes.append(f"{export_directory}:/export:rw")
# TODO: Allow this to real Docker volumes and allow multiple.
extra_volumes = kwds.get("docker_extra_volume") or []
volumes.extend(extra_volumes)
docker_volumes = create_docker_volumes(volumes)
yield DockerGalaxyConfig(
ctx,
config_directory,
env,
test_data_dir,
port,
server_name,
master_api_key,
runnables,
docker_target_kwds=docker_target_kwds,
volumes=docker_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"))
all_tool_paths = _all_tool_paths(runnables, galaxy_root=galaxy_root, extra_tools=kwds.get("extra_tools"))
_handle_job_config_file(config_directory, server_name, test_data_dir, all_tool_paths, kwds)
_handle_job_metrics(config_directory, kwds)
_handle_file_sources(config_directory, test_data_dir, 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")
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
object_store_store_by="uuid",
)
)
_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"{kwds.get('host', '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_locs = []
@property
def virtual_env_dir(self):
loc = None
for loc in self._virtual_env_locs:
if not os.path.isabs(loc):
loc = os.path.join(self.galaxy_root, loc)
if os.path.isdir(loc):
break
return loc
@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 or os.path.join(self.galaxy_root, ".venv"),
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)
source = _galaxy_source(kwds)
if source.startswith("https://github.com/"):
source = source[len("https://github.com/") :]
untar_to(
f"https://codeload.github.com/{source}/tar.gz/{branch}",
tar_args=["--strip-components", "1", "-xvzf", "-", "galaxy-" + branch.replace("/", "-")],
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, depth=1)
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: str,
server_name: str,
test_data_dir: Optional[str],
all_tool_paths: Set[str],
kwds: Dict[str, Any],
):
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>"""
volumes = list(kwds.get("docker_extra_volume") or [])
if test_data_dir:
volumes.append(f"{test_data_dir}:ro")
docker_volumes_str = "$defaults"
if volumes:
# exclude tool directories, these are mounted :ro by $defaults
all_tool_dirs = {os.path.dirname(tool_path) for tool_path in all_tool_paths}
extra_volumes_str = ",".join(str(v) for v in create_docker_volumes(volumes) if v.path not in all_tool_dirs)
docker_volumes_str = f"{docker_volumes_str},{extra_volumes_str}"
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,
"docker_volumes": docker_volumes_str,
"docker_run_extra_arguments": kwds.get("docker_run_extra_arguments", ""),
}
)
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_file_sources(config_directory, test_data_dir, kwds):
file_sources_conf = os.path.join(config_directory, "file_sources_conf.yml")
file_sources_conf_contents = _sub(FILE_SOURCES_TEMPLATE, {"test_data_dir": test_data_dir})
write_file(file_sources_conf, file_sources_conf_contents)
kwds["file_sources_config_file"] = file_sources_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",
)