Corrected and standardised all occurrences of rsync subprocesses in murfey/client/*

Author: tieneupin

src/murfey/client/multigrid_control.py

@@ -1,5 +1,6 @@
 import json
 import logging
+import subprocess
 import threading
 from dataclasses import dataclass, field
 from datetime import datetime
@@ -8,10 +9,10 @@
 from typing import Dict, List, Optional
 from urllib.parse import urlparse
 
-import procrunner
 import requests
 
 import murfey.client.websocket
+from murfey.client import posix_path
 from murfey.client.analyser import Analyser
 from murfey.client.contexts.spa import SPAContext, SPAModularContext
 from murfey.client.contexts.tomo import TomographyContext
@@ -178,16 +179,23 @@ def _start_rsyncer(
         if self._environment:
             self._environment.default_destinations[source] = destination
             if self._environment.gain_ref and visit_path:
-                gain_rsync = procrunner.run(
-                    [
-                        "rsync",
-                        str(self._environment.gain_ref),
-                        f"{self._environment.url.hostname}::{visit_path}/processing",
-                    ]
-                )
+                # Set up rsync command
+                rsync_cmd = [
+                    "rsync",
+                    f"{posix_path(self._environment.gain_ref)!r}",  # '!r' will print strings in ''
+                    f"{self._environment.url.hostname}::{visit_path}/processing",
+                ]
+                # Wrap in bash shell
+                cmd = [
+                    "bash",
+                    "-c",
+                    " ".join(rsync_cmd),
+                ]
+                # Run rsync subprocess
+                gain_rsync = subprocess.run(cmd)
                 if gain_rsync.returncode:
                     log.warning(
-                        f"Gain reference file {self._environment.gain_ref} was not successfully transferred to {visit_path}/processing"
+                        f"Gain reference file {posix_path(self._environment.gain_ref)!r} was not successfully transferred to {visit_path}/processing"
                     )
         self.rsync_processes[source] = RSyncer(
             source,

src/murfey/client/rsync.py

@@ -440,46 +440,46 @@ def parse_stderr(line: str):
         success = True
         if rsync_stdin:
             # Wrap rsync command in a bash command
-            bash_cmd = [
+            cmd = [
                 "bash",
                 "-c",
                 # rsync command passed in as a single string
                 " ".join(rsync_cmd),
             ]
             result = subprocess.run(
-                bash_cmd,
+                cmd,
                 cwd=self._basepath,  # As-is Path is fine
                 capture_output=True,
                 input=rsync_stdin,
             )
             # Parse outputs
-            for line in result.stdout.decode("utf8", "replace").split("\n"):
+            for line in result.stdout.decode("utf-8", "replace").split("\n"):
                 parse_stdout(line)
-            for line in result.stderr.decode("utf8", "replace").split("\n"):
+            for line in result.stderr.decode("utf-8", "replace").split("\n"):
                 parse_stderr(line)
             success = result.returncode == 0
 
         # Remove files from source
         if rsync_stdin_remove:
-            # Insert flag file removal flag before locations
+            # Insert file removal flag before locations
             rsync_cmd.insert(-2, "--remove-source-files")
             # Wrap rsync command in a bash command
-            bash_cmd = [
+            cmd = [
                 "bash",
                 "-c",
                 # Pass rsync command as single string
                 " ".join(rsync_cmd),
             ]
             result = subprocess.run(
-                bash_cmd,
+                cmd,
                 cwd=self._basepath,
                 capture_output=True,
                 input=rsync_stdin_remove,
             )
             # Parse outputs
-            for line in result.stdout.decode("utf8", "replace").split("\n"):
+            for line in result.stdout.decode("utf-8", "replace").split("\n"):
                 parse_stdout(line)
-            for line in result.stderr.decode("utf8", "replace").split("\n"):
+            for line in result.stderr.decode("utf-8", "replace").split("\n"):
                 parse_stderr(line)
             # Leave it as a failure if the previous rsync subprocess failed
             if success:

src/murfey/client/tui/app.py

@@ -1,19 +1,20 @@
 from __future__ import annotations
 
 import logging
+import subprocess
 from datetime import datetime
 from functools import partial
 from pathlib import Path
 from queue import Queue
 from typing import Awaitable, Callable, Dict, List, OrderedDict, TypeVar
 from urllib.parse import urlparse
 
-import procrunner
 import requests
 from textual.app import App
 from textual.reactive import reactive
 from textual.widgets import Button, Input
 
+from murfey.client import posix_path
 from murfey.client.analyser import Analyser
 from murfey.client.contexts.spa import SPAContext, SPAModularContext
 from murfey.client.contexts.tomo import TomographyContext
@@ -203,16 +204,23 @@ def _start_rsyncer(
         if self._environment:
             self._environment.default_destinations[source] = destination
             if self._environment.gain_ref and visit_path:
-                gain_rsync = procrunner.run(
-                    [
-                        "rsync",
-                        str(self._environment.gain_ref),
-                        f"{self._url.hostname}::{visit_path}/processing",
-                    ]
-                )
+                # Set up rsync command
+                rsync_cmd = [
+                    "rsync",
+                    f"{posix_path(self._environment.gain_ref)!r}",
+                    f"{self._url.hostname}::{visit_path}/processing",
+                ]
+                # Encase in bash shell
+                cmd = [
+                    "bash",
+                    "-c",
+                    " ".join(rsync_cmd),
+                ]
+                # Run rsync subprocess
+                gain_rsync = subprocess.run(cmd)
                 if gain_rsync.returncode:
                     log.warning(
-                        f"Gain reference file {self._environment.gain_ref} was not successfully transferred to {visit_path}/processing"
+                        f"Gain reference file {posix_path(self._environment.gain_ref)!r} was not successfully transferred to {visit_path}/processing"
                     )
         self.rsync_processes[source] = RSyncer(
             source,

src/murfey/client/tui/screens.py

@@ -2,6 +2,7 @@
 
 # import contextlib
 import logging
+import subprocess
 from datetime import datetime
 from functools import partial
 from pathlib import Path
@@ -17,7 +18,6 @@
     TypeVar,
 )
 
-import procrunner
 import requests
 from pydantic import BaseModel, ValidationError
 from rich.box import SQUARE
@@ -46,6 +46,7 @@
 )
 from werkzeug.utils import secure_filename
 
+from murfey.client import posix_path
 from murfey.client.analyser import Analyser, spa_form_dependencies
 from murfey.client.contexts.spa import SPAContext, SPAModularContext
 from murfey.client.contexts.tomo import TomographyContext
@@ -838,18 +839,22 @@ def on_button_pressed(self, event):
             if event.button.id == "suggested-gain-ref":
                 self._dir_tree._gain_reference = self._gain_reference
             visit_path = f"data/{datetime.now().year}/{self.app._environment.visit}"
-            cmd = [
+            # Set up rsync command
+            rsync_cmd = [
                 "rsync",
-                str(self._dir_tree._gain_reference),
+                f"{posix_path(self._dir_tree._gain_reference)!r}",
                 f"{self.app._environment.url.hostname}::{visit_path}/processing/{secure_filename(self._dir_tree._gain_reference.name)}",
             ]
+            # Encase in bash shell
+            cmd = ["bash", "-c" " ".join(rsync_cmd)]
             if self.app._environment.demo:
                 log.info(f"Would perform {' '.join(cmd)}")
             else:
-                gain_rsync = procrunner.run(cmd)
+                # Run rsync subprocess
+                gain_rsync = subprocess.run(cmd)
                 if gain_rsync.returncode:
                     log.warning(
-                        f"Gain reference file {self._dir_tree._gain_reference} was not successfully transferred to {visit_path}/processing"
+                        f"Gain reference file {posix_path(self._dir_tree._gain_reference)!r} was not successfully transferred to {visit_path}/processing"
                     )
             process_gain_response = requests.post(
                 url=f"{str(self.app._environment.url.geturl())}/sessions/{self.app._environment.murfey_session}/process_gain",