import argparse
import logging
import logging.config
import os
import pathlib
import shutil
import sys
from typing import cast
import django
from django.conf import settings
from django.core.management import execute_from_command_line
from gpf_instance.gpf_instance import WGPFInstance
from dae import __version__ # type: ignore
from dae.annotation.reannotate_instance import ReannotateInstanceTool
from dae.pheno.build_pheno_browser import main as build_pheno_browser
from dae.utils.verbosity_configuration import VerbosityConfiguration
logger = logging.getLogger("wgpf")
def _add_gpf_instance_path(parser: argparse.ArgumentParser) -> None:
parser.add_argument(
"--gpf-instance", "--gpf", type=str,
default=None,
help="Path to GPF instance configuration file. If None, the tool "
"will check the environment for a 'DAE_DB_DIR' environment variable "
"and if the variable is set it will use it as a GPF instance dictory. "
"If 'DAE_DB_DIR' environment variable is not set, then the current "
"directory and all its parents will be searched for a GPF instance "
"configuration file `gpf_instance.yaml`")
def _configure_init_subparser(subparsers: argparse._SubParsersAction) -> None:
parser = subparsers.add_parser(
"init",
help="Initialize a GPF Development Web Server for a GPF instance")
_add_gpf_instance_path(parser)
parser.add_argument(
"-f", "--force", default=False,
action="store_true",
help="ingore the state of the instance and re-init.")
def _add_host_port_group(parser: argparse.ArgumentParser) -> None:
group = parser.add_argument_group(
title="Specify GPF development server host and port")
group.add_argument(
"-H", "--host", type=str,
default="0.0.0.0", # noqa: S104
help="The host IP address on which the GPF development server will "
"listen for incoming connections.")
group.add_argument(
"-P", "--port", type=int,
default=8000,
help="The port on which the GPF development server will listen "
"for incomming connections.")
def _configure_run_subparser(subparsers: argparse._SubParsersAction) -> None:
parser = subparsers.add_parser(
"run",
help="Run a GPF Development Web Server for a GPF instance")
_add_host_port_group(parser)
_add_gpf_instance_path(parser)
def _init_flag(wgpf_instance: WGPFInstance) -> pathlib.Path:
return pathlib.Path(wgpf_instance.dae_dir) / ".wgpf_init.flag"
def _check_is_initialized(wgpf_instance: WGPFInstance) -> bool:
if not os.path.exists(wgpf_instance.dae_dir):
return False
return _init_flag(wgpf_instance).exists()
def _run_init_command(
wgpf_instance: WGPFInstance, **kwargs: str | bool) -> None:
force = cast(bool, kwargs.pop("force", False))
if _check_is_initialized(wgpf_instance) and not force:
logger.error(
"GPF instance %s already initialized. If you need to re-init "
"please use '--force' flag.", wgpf_instance.dae_dir)
sys.exit(0)
try:
try:
execute_from_command_line([
"wgpf", "migrate",
"--skip-checks",
])
except SystemExit:
if not force:
raise
try:
execute_from_command_line([
"wgpf", "createapplication",
"public", "authorization-code",
"--client-id", "gpfjs",
"--name", "GPF development server",
"--redirect-uris", "http://localhost:8000/datasets",
"--skip-checks",
])
except SystemExit:
if not force:
raise
finally:
_init_flag(wgpf_instance).touch()
[docs]
def collect_outdated_phenotype_studies(
wgpf_instance: WGPFInstance,
) -> list[str]:
"""Collect a list of phenotype IDs with outdated or missing browsers."""
collected_ids = []
for phenotype_data_id in wgpf_instance.get_phenotype_data_ids():
phenotype_data = wgpf_instance.get_phenotype_data(phenotype_data_id)
browser = phenotype_data.browser
if browser is None:
collected_ids.append(phenotype_data_id)
continue
if phenotype_data.is_browser_outdated(browser):
collected_ids.append(phenotype_data_id)
return collected_ids
def _run_run_command(
wgpf_instance: WGPFInstance, **kwargs: bool | str) -> None:
if not _check_is_initialized(wgpf_instance):
logger.info(
"GPF instance %s should be initialized first. "
"Running `wgpf init`...",
wgpf_instance.dae_dir)
_run_init_command(wgpf_instance, **kwargs)
host = kwargs.get("host")
port = kwargs.get("port")
work_dir = os.path.join(
wgpf_instance.dae_dir, ".reannotate-instance")
shutil.rmtree(work_dir, ignore_errors=True)
reannotation_tool = ReannotateInstanceTool(
["--work-dir", work_dir], wgpf_instance)
reannotation_tool.run()
try:
execute_from_command_line([
"wgpf", "runserver", f"{host}:{port}",
"--skip-checks",
])
finally:
pass
[docs]
def cli(argv: list[str] | None = None) -> None:
"""Provide CLI for development GPF web server management."""
if argv is None:
argv = sys.argv[:]
desc = "GPF Development Web Server Management Tool"
parser = argparse.ArgumentParser(description=desc)
parser.add_argument(
"--version", action="store_true", default=False,
help="Prints GPF version and exists.")
VerbosityConfiguration.set_arguments(parser)
commands_parser = parser.add_subparsers(
dest="command", help="Command to execute")
_configure_init_subparser(commands_parser)
_configure_run_subparser(commands_parser)
args = parser.parse_args(argv[1:])
if args.version:
print(f"GPF version: {__version__}")
sys.exit(0)
command = args.command
if command is None:
logger.error("missing wgpf subcommand")
parser.print_help()
sys.exit(1)
build_pheno_browser([
"--gpf-instance",
args.gpf_instance,
"--no-cache",
])
os.environ.setdefault("DJANGO_SETTINGS_MODULE", "wdae.wgpf_settings")
django.setup()
settings.DISABLE_PERMISSIONS = True
settings.STUDIES_EAGER_LOADING = True
# pylint: disable=import-outside-toplevel
from gpf_instance import gpf_instance
wgpf_instance = gpf_instance.get_wgpf_instance(args.gpf_instance)
logger.info("using GPF instance at %s", wgpf_instance.dae_dir)
if command not in {"init", "run"}:
logger.error("unknown subcommand %s used in `wgpf`", command)
sys.exit(1)
settings.DEFAULT_WDAE_DIR = os.path.join(
wgpf_instance.dae_dir, "wdae")
os.makedirs(settings.DEFAULT_WDAE_DIR, exist_ok=True)
if args.verbose > 0:
settings.LOGGING["handlers"]["console"]["level"] = logging.DEBUG
logging.config.dictConfig(settings.LOGGING)
logger.info("using wdae directory: %s", settings.DEFAULT_WDAE_DIR)
if command == "init":
_run_init_command(wgpf_instance, **vars(args))
elif command == "run":
_run_run_command(wgpf_instance, **vars(args))