feat: add rstudio subcommand

opensafely/__init__.py

@@ -22,6 +22,7 @@
  info,
  jupyter,
  pull,
+ rstudio,
  unzip,
  upgrade,
 )
@@ -136,6 +137,7 @@ def add_subcommand(cmd, module):
  add_subcommand("info", info)
  add_subcommand("exec", execute)
  add_subcommand("clean", clean)
+ add_subcommand("rstudio", rstudio)
 
  warn_if_updates_needed(sys.argv)
  args = parser.parse_args()

opensafely/rstudio.py

@@ -0,0 +1,137 @@
+import os
+import socket
+import sys
+import threading
+import time
+import webbrowser
+from pathlib import Path
+from sys import platform
+from urllib import request
+
+from opensafely import utils
+
+
+DESCRIPTION = "Run an RStudio Server session using the OpenSAFELY environment"
+
+
+# poor mans debugging because debugging threads on windows is hard
+if os.environ.get("DEBUG", False):
+
+ def debug(msg):
+ # threaded output for some reason needs the carriage return or else
+ # it doesn't reset the cursor.
+ sys.stderr.write("DEBUG: " + msg.replace("\n", "\r\n") + "\r\n")
+ sys.stderr.flush()
+
+else:
+
+ def debug(msg):
+ pass
+
+
+def add_arguments(parser):
+ parser.add_argument(
+ "--directory",
+ "-d",
+ default=os.getcwd(),
+ type=Path,
+ help="Directory to run the RStudio Server session in (default is current dir)",
+ )
+ parser.add_argument(
+ "--name",
+ help="Name of docker image (defaults to use directory name)",
+ default="rstudio",
+ )
+
+ parser.add_argument(
+ "--port",
+ "-p",
+ default=8787,
+ help="Port to run on",
+ )
+
+
+def open_browser(name, port):
+ try:
+ url = f"http://localhost:{port}"
+ debug(f"open_browser: url={url}")
+
+ # wait for port to be open
+ debug("open_browser: waiting for port")
+ start = time.time()
+ while time.time() - start < 60.0:
+ try:
+ response = request.urlopen(url, timeout=1)
+ except (request.URLError, OSError):
+ pass
+ else:
+ break
+
+ if not response:
+ debug("open_browser: open_browser: could not get response")
+ return
+
+ # open a webbrowser pointing to the docker container
+ debug("open_browser: open_browser: opening browser window")
+ webbrowser.open(url, new=2)
+
+ except Exception:
+ # reformat exception printing to work from thread
+ import traceback
+
+ sys.stderr.write("Error in open browser thread:\r\n")
+ tb = traceback.format_exc().replace("\n", "\r\n")
+ sys.stderr.write(tb)
+ sys.stderr.flush()
+
+
+def get_free_port():
+ sock = socket.socket()
+ sock.bind(("127.0.0.1", 0))
+ port = sock.getsockname()[1]
+ sock.close()
+ return port
+
+
+def main(directory, name, port):
+ if name is None:
+ name = f"os-rstudio-{directory.name}"
+
+ if port is None:
+ # this is a race condition, as something else could consume the socket
+ # before docker binds to it, but the chance of that on a user's
+ # personal machine is very small.
+ port = str(get_free_port())
+
+ # if not no_browser:
+ # start thread to open web browser
+ thread = threading.Thread(target=open_browser, args=(name, port), daemon=True)
+ thread.name = "browser thread"
+ debug("starting open_browser thread")
+ thread.start()
+
+ # Determine if on Linux, if so obtain user id
+ # And need to know in Windows win32 for text file line endings setting
+ if platform == "linux":
+ uid = os.getuid()
+ else:
+ uid = None
+
+ docker_args = [
+ "--platform=linux/amd64",
+ f"-p={port}:8787",
+ f"--name={name}",
+ f"--hostname={name}",
+ "--volume="
+ + os.path.join(os.path.expanduser("~"), ".gitconfig")
+ + ":/home/rstudio/local-gitconfig",
+ f"--env=HOSTPLATFORM={platform}",
+ f"--env=HOSTUID={uid}",
+ ]
+
+ debug("docker: " + " ".join(docker_args))
+ ps = utils.run_docker(
+ docker_args, "rstudio", "", interactive=True, user="0:0", directory=directory
+ )
+ # we want to exit with the same code that rstudio-server did
+ return ps.returncode

tests/test_rstudio.py

@@ -0,0 +1,38 @@
+import os
+import pathlib
+from sys import platform
+
+from opensafely import rstudio
+from tests.conftest import run_main
+
+
+def test_rstudio(run):
+ if platform == "linux":
+ uid = os.getuid()
+ else:
+ uid = None
+
+ run.expect(
+ [
+ "docker",
+ "run",
+ "--rm",
+ "--init",
+ "--label=opensafely",
+ "--interactive",
+ "--user=0:0",
+ f"--volume={pathlib.Path.cwd()}://workspace",
+ "--platform=linux/amd64",
+ "-p=8787:8787",
+ "--name=test_rstudio",
+ "--hostname=test_rstudio",
+ "--volume="
+ + os.path.join(os.path.expanduser("~"), ".gitconfig")
+ + ":/home/rstudio/local-gitconfig",
+ "--env=HOSTPLATFORM=" + platform,
+ f"--env=HOSTUID={uid}",
+ "ghcr.io/opensafely-core/rstudio",
+ ]
+ )
+
+ assert run_main(rstudio, "--port 8787 --name test_rstudio") == 0