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 +1,131 @@
+import os
+import socket
+import sys
+import threading
+import time
+import webbrowser
+from pathlib import Path
+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 nt=windows or posix=Linux/Darwin/Unix
+    osname = os.name
+
+    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=HOST={osname}",
+    ]
+
+    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 +1,31 @@
+import os
+import pathlib
+
+from opensafely import rstudio
+from tests.conftest import run_main
+
+
+def test_rstudio(run):
+    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=HOST=" + os.name,
+            "ghcr.io/opensafely-core/rstudio",
+        ]
+    )
+
+    assert run_main(rstudio, "--port 8787 --name test_rstudio") == 0