Migrate client-side utility functions to a separate module

src/murfey/client/__init__.py

@@ -2,8 +2,6 @@
 
 import argparse
 import configparser
-
-# import json
 import logging
 import os
 import platform
@@ -12,57 +10,26 @@
 import time
 import webbrowser
 from datetime import datetime
-from functools import partial
 from pathlib import Path
 from queue import Queue
 from typing import List, Literal
 from urllib.parse import ParseResult, urlparse
 
 import requests
-
-# from multiprocessing import Process, Queue
 from rich.prompt import Confirm
 
-import murfey.client.rsync
 import murfey.client.update
 import murfey.client.watchdir
 import murfey.client.websocket
 from murfey.client.customlogging import CustomHandler, DirectableRichHandler
 from murfey.client.instance_environment import MurfeyInstanceEnvironment
 from murfey.client.tui.app import MurfeyTUI
 from murfey.client.tui.status_bar import StatusBar
-from murfey.util import _get_visit_list
-
-# from asyncio import Queue
-
-
-# from rich.prompt import Prompt
-
+from murfey.util.client import _get_visit_list, authorised_requests, read_config
 
 log = logging.getLogger("murfey.client")
 
-
-def read_config() -> configparser.ConfigParser:
-    config = configparser.ConfigParser()
-    try:
-        mcch = os.environ.get("MURFEY_CLIENT_CONFIG_HOME")
-        murfey_client_config_home = Path(mcch) if mcch else Path.home()
-        with open(murfey_client_config_home / ".murfey") as configfile:
-            config.read_file(configfile)
-    except FileNotFoundError:
-        log.warning(
-            f"Murfey client configuration file {murfey_client_config_home / '.murfey'} not found"
-        )
-    if "Murfey" not in config:
-        config["Murfey"] = {}
-    return config
-
-
-token = read_config()["Murfey"].get("token", "")
-
-requests.get = partial(requests.get, headers={"Authorization": f"Bearer {token}"})
-requests.post = partial(requests.post, headers={"Authorization": f"Bearer {token}"})
-requests.delete = partial(requests.delete, headers={"Authorization": f"Bearer {token}"})
+requests.get, requests.post, requests.put, requests.delete = authorised_requests()
 
 
 def write_config(config: configparser.ConfigParser):

src/murfey/client/analyser.py

@@ -22,7 +22,8 @@
 from murfey.client.instance_environment import MurfeyInstanceEnvironment
 from murfey.client.rsync import RSyncerUpdate, TransferResult
 from murfey.client.tui.forms import FormDependency
-from murfey.util import Observer, get_machine_config_client
+from murfey.util import Observer
+from murfey.util.client import get_machine_config_client
 from murfey.util.mdoc import get_block
 from murfey.util.models import PreprocessingParametersTomo, ProcessingParametersSPA
 

src/murfey/client/contexts/clem.py

@@ -14,7 +14,7 @@
 
 from murfey.client.context import Context
 from murfey.client.instance_environment import MurfeyInstanceEnvironment
-from murfey.util import capture_post, get_machine_config_client
+from murfey.util.client import capture_post, get_machine_config_client
 
 # Create logger object
 logger = logging.getLogger("murfey.client.contexts.clem")

src/murfey/client/contexts/fib.py

@@ -10,7 +10,7 @@
 
 from murfey.client.context import Context
 from murfey.client.instance_environment import MurfeyInstanceEnvironment
-from murfey.util import authorised_requests
+from murfey.util.client import authorised_requests
 
 logger = logging.getLogger("murfey.client.contexts.fib")
 

src/murfey/client/contexts/spa.py

@@ -15,7 +15,7 @@
     MurfeyID,
     MurfeyInstanceEnvironment,
 )
-from murfey.util import (
+from murfey.util.client import (
     authorised_requests,
     capture_get,
     capture_post,

src/murfey/client/contexts/spa_metadata.py

@@ -8,7 +8,11 @@
 from murfey.client.context import Context
 from murfey.client.contexts.spa import _file_transferred_to, _get_source
 from murfey.client.instance_environment import MurfeyInstanceEnvironment, SampleInfo
-from murfey.util import authorised_requests, capture_post, get_machine_config_client
+from murfey.util.client import (
+    authorised_requests,
+    capture_post,
+    get_machine_config_client,
+)
 from murfey.util.spa_metadata import (
     FoilHoleInfo,
     get_grid_square_atlas_positions,

src/murfey/client/contexts/tomo.py

@@ -17,7 +17,11 @@
     MurfeyID,
     MurfeyInstanceEnvironment,
 )
-from murfey.util import authorised_requests, capture_post, get_machine_config_client
+from murfey.util.client import (
+    authorised_requests,
+    capture_post,
+    get_machine_config_client,
+)
 from murfey.util.mdoc import get_block, get_global_data, get_num_blocks
 from murfey.util.tomo import midpoint
 

src/murfey/client/multigrid_control.py

@@ -20,7 +20,8 @@
 from murfey.client.rsync import RSyncer, RSyncerUpdate, TransferResult
 from murfey.client.tui.screens import determine_default_destination
 from murfey.client.watchdir import DirWatcher
-from murfey.util import capture_post, get_machine_config_client, posix_path
+from murfey.util import posix_path
+from murfey.util.client import capture_post, get_machine_config_client
 
 log = logging.getLogger("murfey.client.mutligrid_control")
 

src/murfey/client/tui/app.py

@@ -33,10 +33,10 @@
 from murfey.client.tui.status_bar import StatusBar
 from murfey.client.watchdir import DirWatcher
 from murfey.client.watchdir_multigrid import MultigridDirWatcher
-from murfey.util import (
+from murfey.util import posix_path
+from murfey.util.client import (
     capture_post,
     get_machine_config_client,
-    posix_path,
     read_config,
     set_default_acquisition_output,
 )

src/murfey/client/tui/screens.py

@@ -56,7 +56,8 @@
 )
 from murfey.client.rsync import RSyncer
 from murfey.client.tui.forms import FormDependency
-from murfey.util import capture_post, get_machine_config_client, posix_path, read_config
+from murfey.util import posix_path
+from murfey.util.client import capture_post, get_machine_config_client, read_config
 from murfey.util.models import PreprocessingParametersTomo, ProcessingParametersSPA
 
 log = logging.getLogger("murfey.tui.screens")

src/murfey/instrument_server/__init__.py

@@ -5,9 +5,9 @@
 from rich.logging import RichHandler
 
 import murfey
-from murfey.client import read_config
 from murfey.client.customlogging import CustomHandler
 from murfey.util import LogFilter
+from murfey.util.client import read_config
 
 logger = logging.getLogger("murfey.instrument_server")
 

src/murfey/instrument_server/api.py

@@ -17,11 +17,11 @@
 from pydantic import BaseModel
 from werkzeug.utils import secure_filename
 
-from murfey.client import read_config
 from murfey.client.multigrid_control import MultigridController
 from murfey.client.rsync import RSyncer
 from murfey.client.watchdir_multigrid import MultigridDirWatcher
 from murfey.util import posix_path, sanitise, sanitise_nonpath, secure_path
+from murfey.util.client import read_config
 from murfey.util.instrument_models import MultigridWatcherSpec
 from murfey.util.models import File, Token
 

src/murfey/util/__init__.py

@@ -1,67 +1,19 @@
 from __future__ import annotations
 
 import asyncio
-import configparser
-import copy
 import inspect
-import json
 import logging
-import os
-import shutil
-from functools import lru_cache, partial
 from pathlib import Path
 from queue import Queue
 from threading import Thread
-from typing import Awaitable, Callable, Dict, List, Optional, Tuple, Union
-from urllib.parse import ParseResult, urlparse, urlunparse
+from typing import Awaitable, Callable, Optional
 from uuid import uuid4
 
-import requests
 from werkzeug.utils import secure_filename
 
-from murfey.util.models import Visit
-
 logger = logging.getLogger("murfey.util")
 
 
-def read_config() -> configparser.ConfigParser:
-    config = configparser.ConfigParser()
-    try:
-        mcch = os.environ.get("MURFEY_CLIENT_CONFIG_HOME")
-        murfey_client_config_home = Path(mcch) if mcch else Path.home()
-        with open(murfey_client_config_home / ".murfey") as configfile:
-            config.read_file(configfile)
-    except FileNotFoundError:
-        logger.warning(
-            f"Murfey client configuration file {murfey_client_config_home / '.murfey'} not found"
-        )
-    if "Murfey" not in config:
-        config["Murfey"] = {}
-    return config
-
-
-@lru_cache(maxsize=1)
-def get_machine_config_client(
-    url: str, instrument_name: str = "", demo: bool = False
-) -> dict:
-    _instrument_name: str | None = instrument_name or os.getenv("BEAMLINE")
-    if not _instrument_name:
-        return {}
-    return requests.get(f"{url}/instruments/{_instrument_name}/machine").json()
-
-
-def authorised_requests() -> Tuple[Callable, Callable, Callable, Callable]:
-    token = read_config()["Murfey"].get("token", "")
-    _get = partial(requests.get, headers={"Authorization": f"Bearer {token}"})
-    _post = partial(requests.post, headers={"Authorization": f"Bearer {token}"})
-    _put = partial(requests.put, headers={"Authorization": f"Bearer {token}"})
-    _delete = partial(requests.delete, headers={"Authorization": f"Bearer {token}"})
-    return _get, _post, _put, _delete
-
-
-requests.get, requests.post, requests.put, requests.delete = authorised_requests()
-
-
 def sanitise(in_string: str) -> str:
     return in_string.replace("\r\n", "").replace("\n", "")
 
@@ -113,106 +65,6 @@ def posix_path(path: Path) -> str:
     return str(path)
 
 
-def _get_visit_list(api_base: ParseResult, instrument_name: str):
-    get_visits_url = api_base._replace(
-        path=f"/instruments/{instrument_name}/visits_raw"
-    )
-    server_reply = requests.get(get_visits_url.geturl())
-    if server_reply.status_code != 200:
-        raise ValueError(f"Server unreachable ({server_reply.status_code})")
-    return [Visit.parse_obj(v) for v in server_reply.json()]
-
-
-def capture_post(url: str, json: dict | list = {}) -> requests.Response | None:
-    try:
-        response = requests.post(url, json=json)
-    except Exception as e:
-        logger.error(f"Exception encountered in post to {url}: {e}")
-        response = requests.Response()
-    if response.status_code != 200:
-        logger.warning(
-            f"Response to post to {url} with data {json} had status code "
-            f"{response.status_code}. The reason given was {response.reason}"
-        )
-        split_url = urlparse(url)
-        client_config = read_config()
-        failure_url = urlunparse(
-            split_url._replace(
-                path=f"/instruments/{client_config['Murfey']['instrument_name']}/failed_client_post"
-            )
-        )
-        try:
-            resend_response = requests.post(
-                failure_url, json={"url": url, "data": json}
-            )
-        except Exception as e:
-            logger.error(f"Exception encountered in post to {failure_url}: {e}")
-            resend_response = requests.Response()
-        if resend_response.status_code != 200:
-            logger.warning(
-                f"Response to post to {failure_url} failed with {resend_response.reason}"
-            )
-
-    return response
-
-
-def capture_get(url: str) -> requests.Response | None:
-    try:
-        response = requests.get(url)
-    except Exception as e:
-        logger.error(f"Exception encountered in get from {url}: {e}")
-        response = None
-    if response and response.status_code != 200:
-        logger.warning(
-            f"Response to get from {url} had status code {response.status_code}. "
-            f"The reason given was {response.reason}"
-        )
-    return response
-
-
-def set_default_acquisition_output(
-    new_output_dir: Path,
-    software_settings_output_directories: Dict[str, List[str]],
-    safe: bool = True,
-):
-    for p, keys in software_settings_output_directories.items():
-        if safe:
-            settings_copy_path = Path(p)
-            settings_copy_path = settings_copy_path.parent / (
-                "_murfey_" + settings_copy_path.name
-            )
-            shutil.copy(p, str(settings_copy_path))
-        with open(p, "r") as for_parsing:
-            settings = json.load(for_parsing)
-        # for safety
-        settings_copy = copy.deepcopy(settings)
-
-        def _set(d: dict, keys_list: List[str], value: str) -> dict:
-            if len(keys_list) > 1:
-                tmp_value: Union[dict, str] = _set(
-                    d[keys_list[0]], keys_list[1:], value
-                )
-            else:
-                tmp_value = value
-            return {_k: tmp_value if _k == keys_list[0] else _v for _k, _v in d.items()}
-
-        settings_copy = _set(settings_copy, keys, str(new_output_dir))
-
-        def _check_dict_structure(d1: dict, d2: dict) -> bool:
-            if set(d1.keys()) != set(d2.keys()):
-                return False
-            for k in d1.keys():
-                if isinstance(d1[k], dict):
-                    if not isinstance(d2[k], dict):
-                        return False
-                    _check_dict_structure(d1[k], d2[k])
-            return True
-
-        if _check_dict_structure(settings, settings_copy):
-            with open(p, "w") as sf:
-                json.dump(settings_copy, sf)
-
-
 class Observer:
     """
     A helper class implementing the observer pattern supporting both