remove deprecation warnings from argh (8132f766) · Commits · FNSO / I-FAIR IR / circe-server

circe/init.py

+13 −18

Original line number	Diff line number	Diff line
		@@ -4,10 +4,6 @@ import uuid
		import tarfile
		import zipfile
		from time import sleep

		version = "0.0.40"

		try:
		from uuid import uuid4
		import sanic.request
		import sanic.response
		@@ -15,7 +11,7 @@ try:
		from sanic import Sanic
		from .config import CONFIG
		from . import tasks
		from subprocess import call, Popen
		from subprocess import call
		from multiprocessing import Process
		import asyncio
		import sqlite3
		@@ -34,16 +30,9 @@ try:
		from pathlib import Path
		import re
		import aiofiles
		import logging
		import tempfile
		from pythonjsonlogger import jsonlogger
		except ModuleNotFoundError as e:
		sys.exit("Import error: {}. Please refer to the documentation.".format(e))
		import argh

		try:
		assert sys.version_info >= (3, 6)
		except AssertionError:
		sys.exit("Please update your python (>= 3.6)")
		version = "0.0.43"

		AUTH_DB_PATH = "{}/auth.db".format(CONFIG["CIRCE_WORKING_DIR"])

		@@ -201,7 +190,7 @@ async def index(request: sanic.request):


		@server.get("/version/")
		async def index(request: sanic.request):
		async def server_version(request: sanic.request):
		return sanic.response.text(version)


		@@ -473,10 +462,16 @@ def remove_api_access(app_uuid: str):
		conn.commit()


		@argh.arg(
		"--app_uuid",
		help="specify app uuid to change existing access. Ignore to create new access.",
		)
		@argh.arg("--title", help="Title of access (name of app).")
		@argh.arg("--out", help="output credentials in json format to given file")
		def make_api_access(
		app_uuid: "specify app uuid to change existing access. Ignore to create new access." = None,
		title: "Title of access (name of app)." = None,
		out: "output credentials in json format to given file" = None,
		app_uuid: str = None,
		title: str = None,
		out: str = None,
		):
		"""
		Create new app uuid / secret couple for api access.

circe/config.py

+9 −0

Original line number	Diff line number	Diff line
		@@ -21,6 +21,8 @@ CONFIG = {
		"CIRCE_WEB_UI_REMOVE_USER_FILES_DELAY": 7200,
		"CIRCE_TRANSFORMATIONS_MODULE": None,
		"CIRCE_UPDATE_NOTIFY_ROUTE": False,
		"CIRCE_TEMP_DIR": None,
		"ALLOWED_WEBHOOK_HOSTS": [],
		}

		for key in CONFIG.keys():
		@@ -37,6 +39,9 @@ for key in CONFIG.keys():
		CONFIG[key] = True if val == "1" else False
		elif key in ["CIRCE_PORT"]:
		CONFIG[key] = int(val)
		elif key == "ALLOWED_WEBHOOK_HOSTS":
		CONFIG[key] = val.split(",")
		pass
		else:
		CONFIG[key] = val
		except KeyError:
		@@ -54,10 +59,14 @@ if (
		if CONFIG["CIRCE_IMMEDIATE_MODE"]:
		CONFIG["CIRCE_WORKERS"] = 1

		if not CONFIG["CIRCE_TEMP_DIR"]:
		CONFIG["CIRCE_TEMP_DIR"] = "{}/tmp/".format(CONFIG["CIRCE_WORKING_DIR"])

		paths = [
		CONFIG["CIRCE_WORKING_DIR"],
		"{}/queue/".format(CONFIG["CIRCE_WORKING_DIR"]),
		"{}/done/".format(CONFIG["CIRCE_WORKING_DIR"]),
		CONFIG["CIRCE_TEMP_DIR"],
		]
		for path in paths:
		os.makedirs(path, exist_ok=True)

circe/tasks.py

+4 −5

Original line number	Diff line number	Diff line
		@@ -8,9 +8,7 @@ from uuid import uuid4
		import json
		import requests
		from requests.exceptions import ConnectionError, HTTPError
		import logging
		from inspect import getmembers, isfunction, isclass, signature
		import sys
		from pythonjsonlogger import jsonlogger
		import datetime
		import logging
		@@ -95,8 +93,7 @@ def remove_file(file_path):

		@huey.task()
		def do_transformations(uuid: uuid4, job_archive_path: str):
		with tempfile.TemporaryDirectory() as tmp_dir:

		with tempfile.TemporaryDirectory(dir=CONFIG["CIRCE_TEMP_DIR"]) as tmp_dir:
		handler: logging.FileHandler = logging.FileHandler("{}/out.log".format(tmp_dir))
		handler.setFormatter(
		CustomJsonFormatter("%(timestamp)s %(level)s %(name)s %(message)s")
		@@ -137,7 +134,9 @@ def do_transformations(uuid: uuid4, job_archive_path: str):
		"time": _stamp(),
		}
		)
		_, temp_zip_path = tempfile.mkstemp(suffix=".tar.gz")
		_, temp_zip_path = tempfile.mkstemp(
		suffix=".tar.gz", dir=CONFIG["CIRCE_TEMP_DIR"]
		)
		with tarfile.open(temp_zip_path, "w:gz") as destination_archive:
		destination_archive.add(tmp_dir, recursive=True, arcname="")
		final_archive_path = "{}/done/{}.tar.gz".format(

poetry.lock

+162 −199

File changed.

Preview size limit exceeded, changes collapsed.

pyproject.toml

+15 −13

Original line number	Diff line number	Diff line
		[tool.poetry]
		name = "circe-CERTIC"
		readme = "README.md"
		version = "0.0.40"
		version = "0.0.43"
		description = "Circe Server"
		authors = ["Mickaël Desfrênes <mickael.desfrenes@unicaen.fr>"]
		license = "CeCILL-B"
		@@ -10,20 +10,22 @@ packages = [
		]

		[tool.poetry.dependencies]
		python = "^3.9"
		requests = "^2.28.0"
		argh = "^0.26.2"
		sanic = "^22.3.2"
		huey = "^2.4.3"
		asyncio = "^3.4.3"
		itsdangerous = "^2.1.2"
		aiofiles = "^0.8.0"
		markdown2 = "^2.4.3"
		python-json-logger = "^2.0.2"
		python-dotenv = "^0.20.0"
		python = ">=3.9,<4"
		requests = ">=2.28.0"
		argh = ">=0.28.1"
		sanic = ">=22.3.2"
		huey = ">=2.4.3"
		asyncio = ">=3.4.3"
		itsdangerous = ">=2.1.2"
		aiofiles = ">=23.1.0"
		markdown2 = ">=2.4.3"
		python-json-logger = ">=2.0.2"
		python-dotenv = ">=1.0.0"

		[tool.poetry.dev-dependencies]
		black = "^22.3.0"
		black = "*"
		circe-client-CERTIC = "*"
		pytest = "*"

		[tool.poetry.scripts]
		circe = "circe.__main__:run_cli"