Merge branch 'main' into allow_user_to_update_fields

Author: brichet

README.md

@@ -47,8 +47,10 @@ If you are interested in contributing to the project, see [`CONTRIBUTING.rst`](C
 ## Team Meetings and Roadmap
 
 - When: Thursdays [8:00am, Pacific time](https://www.thetimezoneconverter.com/?t=8%3A00%20am&tz=San%20Francisco&)
-- Where: [Jovyan Zoom](https://zoom.us/my/jovyan?pwd=c0JZTHlNdS9Sek9vdzR3aTJ4SzFTQT09)
-- What: [Meeting notes](https://github.com/jupyter-server/team-compass/issues/45)
+- Where: [Jovyan Zoom](https://zoom.us/j/95228013874?pwd=Ep7HIk8t9JP6VToxt1Wj4P7K5PshC0.1)
+- What:
+  - [Meeting notes](https://github.com/jupyter-server/team-compass/issues?q=is%3Aissue%20%20Meeting%20Notes%20)
+  - [Agenda](https://hackmd.io/Wmz_wjrLRHuUbgWphjwRWw)
 
 See our tentative [roadmap here](https://github.com/jupyter/jupyter_server/issues/127).
 

jupyter_server/extension/serverextension.py

@@ -259,9 +259,23 @@ def toggle_server_extension(self, import_name: str) -> None:
             self.log.info(f"- Writing config: {config_dir}")
             # Validate the server extension.
             self.log.info(f"    - Validating {import_name}...")
+            config = extension_manager.config_manager
+            enabled = False
+            if config:
+                jpserver_extensions = config.get_jpserver_extensions()
+                if import_name not in jpserver_extensions:
+                    msg = (
+                        f"The module '{import_name}' could not be found. Are you "
+                        "sure the extension is installed?"
+                    )
+                    raise ValueError(msg)
+                enabled = jpserver_extensions[import_name]
+
             # Interface with the Extension Package and validate.
-            extpkg = ExtensionPackage(name=import_name)
-            extpkg.validate()
+            extpkg = ExtensionPackage(name=import_name, enabled=enabled)
+            if not extpkg.validate():
+                msg = "validation failed"
+                raise ValueError(msg)
             version = extpkg.version
             self.log.info(f"      {import_name} {version} {GREEN_OK}")
 

jupyter_server/services/contents/filecheckpoints.py

@@ -4,6 +4,7 @@
 
 import os
 import shutil
+import tempfile
 
 from anyio.to_thread import run_sync
 from jupyter_core.utils import ensure_dir_exists
@@ -111,6 +112,10 @@ def checkpoint_path(self, checkpoint_id, path):
         filename = f"{basename}-{checkpoint_id}{ext}"
         os_path = self._get_os_path(path=parent)
         cp_dir = os.path.join(os_path, self.checkpoint_dir)
+        # If parent directory isn't writable, use system temp
+        if not os.access(os.path.dirname(cp_dir), os.W_OK):
+            rel = os.path.relpath(os_path, start=self.root_dir)
+            cp_dir = os.path.join(tempfile.gettempdir(), "jupyter_checkpoints", rel)
         with self.perm_to_403():
             ensure_dir_exists(cp_dir)
         cp_path = os.path.join(cp_dir, filename)

jupyter_server/services/contents/fileio.py

@@ -39,6 +39,12 @@ def copy2_safe(src, dst, log=None):
 
     like shutil.copy2, but log errors in copystat instead of raising
     """
+    # if src file is not writable, avoid creating a back-up
+    if not os.access(src, os.W_OK):
+        if log:
+            log.debug("Source file, %s, is not writable", src, exc_info=True)
+        raise PermissionError(errno.EACCES, f"File is not writable: {src}")
+
     shutil.copyfile(src, dst)
     try:
         shutil.copystat(src, dst)
@@ -52,6 +58,11 @@ async def async_copy2_safe(src, dst, log=None):
 
     like shutil.copy2, but log errors in copystat instead of raising
     """
+    if not os.access(src, os.W_OK):
+        if log:
+            log.debug("Source file, %s, is not writable", src, exc_info=True)
+        raise PermissionError(errno.EACCES, f"File is not writable: {src}")
+
     await run_sync(shutil.copyfile, src, dst)
     try:
         await run_sync(shutil.copystat, src, dst)
@@ -101,6 +112,21 @@ def atomic_writing(path, text=True, encoding="utf-8", log=None, **kwargs):
     if os.path.islink(path):
         path = os.path.join(os.path.dirname(path), os.readlink(path))
 
+    # Fall back to direct write for existing file in a non-writable dir
+    dirpath = os.path.dirname(path) or os.getcwd()
+    if os.path.isfile(path) and not os.access(dirpath, os.W_OK) and os.access(path, os.W_OK):
+        mode = "w" if text else "wb"
+        # direct open on the target file
+        if text:
+            fileobj = open(path, mode, encoding=encoding, **kwargs)  # noqa: SIM115
+        else:
+            fileobj = open(path, mode, **kwargs)  # noqa: SIM115
+        try:
+            yield fileobj
+        finally:
+            fileobj.close()
+        return
+
     tmp_path = path_to_intermediate(path)
 
     if os.path.isfile(path):

tests/extension/test_serverextension.py

@@ -134,3 +134,11 @@ def test_server_extension_apps(jp_env_config_path, jp_extension_environ):
 def test_server_extension_app():
     app = ServerExtensionApp()
     app.launch_instance(["list"])
+
+
+def test_toggle_missing_server_extension(jp_env_config_path, capsys):
+    app = ToggleServerExtensionApp()
+    app.extra_args = ["missingextension"]
+    app.start()
+    captured = capsys.readouterr()
+    assert "Validation failed: The module 'missingextension' could not be found." in captured.err

tests/services/contents/test_fileio.py

@@ -136,6 +136,26 @@ def test_path_to_invalid(tmpdir):
     assert path_to_invalid(tmpdir) == str(tmpdir) + ".invalid"
 
 
+@pytest.mark.skipif(sys.platform.startswith("win"), reason="requires POSIX directory perms")
+def test_atomic_writing_in_readonly_dir(tmp_path):
+    # Setup: non-writable dir but a writable file inside
+    nonw = tmp_path / "nonwritable"
+    nonw.mkdir()
+    f = nonw / "file.txt"
+    f.write_text("original content")
+    os.chmod(str(nonw), 0o500)
+    os.chmod(str(f), 0o700)
+
+    # direct write fallback succeeds
+    with atomic_writing(str(f)) as ff:
+        ff.write("new content")
+    assert f.read_text() == "new content"
+
+    # dir perms unchanged
+    mode = stat.S_IMODE(os.stat(str(nonw)).st_mode)
+    assert mode == 0o500
+
+
 @pytest.mark.skipif(os.name == "nt", reason="test fails on Windows")
 def test_file_manager_mixin(tmp_path):
     mixin = FileManagerMixin()