set user dirs perms to allow read and write operations on jupyterlab

cowbird/handlers/impl/filesystem.py

@@ -204,12 +204,15 @@ def update_secure_data_proxy_path_perms(self, src_path: str, user_name: str) ->
         return access_allowed
 
     @staticmethod
-    def create_hardlink_path(src_path: str, hardlink_path: str, access_allowed: bool) -> None:
+    def create_hardlink_path(src_path: str, hardlink_path: str, access_allowed: bool, dir_perms: int = 0o775) -> None:
         """
         Creates a hardlink path from a source file, if the user has access rights.
         """
         if access_allowed:
-            os.makedirs(os.path.dirname(hardlink_path), exist_ok=True)
+            # set umask to allow all permissions, else, mode is ignored when making directories
+            previous_umask = os.umask(0)
+            os.makedirs(os.path.dirname(hardlink_path), mode=dir_perms, exist_ok=True)
+            os.umask(previous_umask)  # reset umask to default
             LOGGER.debug("Creating hardlink from file `%s` to the path `%s`", src_path, hardlink_path)
             try:
                 os.link(src_path, hardlink_path)
@@ -227,6 +230,9 @@ def _create_wpsoutputs_hardlink(self, src_path: str, overwrite: bool = False,
             if not process_user_files:
                 return
 
+            # User workspace directories require `rwx` permissions to allow file modifications via JupyterLab for
+            # files with write permissions
+            dir_perms = 0o777
             magpie_handler = HandlerFactory().get_handler("Magpie")
             user_name = magpie_handler.get_user_name_from_user_id(int(regex_match.group(2)))
             hardlink_path = self.get_user_hardlink(src_path=src_path,
@@ -243,6 +249,7 @@ def _create_wpsoutputs_hardlink(self, src_path: str, overwrite: bool = False,
         else:  # public files
             if not process_public_files:
                 return
+            dir_perms = 0o775
             hardlink_path = self._get_public_hardlink(src_path)
 
         if os.path.exists(hardlink_path):
@@ -254,7 +261,7 @@ def _create_wpsoutputs_hardlink(self, src_path: str, overwrite: bool = False,
                            "created file.", hardlink_path)
             os.remove(hardlink_path)
 
-        self.create_hardlink_path(src_path, hardlink_path, access_allowed)
+        self.create_hardlink_path(src_path, hardlink_path, access_allowed, dir_perms=dir_perms)
 
     def on_created(self, path: str) -> None:
         """
@@ -386,7 +393,7 @@ def _update_permissions_on_filesystem(self, permission: Permission) -> None:
                 # Resync hardlink path
                 if os.path.exists(hardlink_path):
                     os.remove(hardlink_path)
-                self.create_hardlink_path(user_path, hardlink_path, access_allowed)
+                self.create_hardlink_path(user_path, hardlink_path, access_allowed, dir_perms=0o777)
 
     def permission_created(self, permission: Permission) -> None:
         self._update_permissions_on_filesystem(permission)

tests/test_filesystem.py

@@ -17,7 +17,7 @@
 
 from cowbird.api.schemas import ValidOperations
 from cowbird.handlers import HandlerFactory
-from cowbird.handlers.impl.filesystem import NOTEBOOKS_DIR_NAME, SECURE_DATA_PROXY_NAME
+from cowbird.handlers.impl.filesystem import NOTEBOOKS_DIR_NAME, SECURE_DATA_PROXY_NAME, USER_WPS_OUTPUTS_USER_DIR_NAME
 from cowbird.typedefs import JSON
 from tests import test_magpie, utils
 
@@ -230,6 +230,9 @@ def test_public_wps_output_created(self):
 
         TestFileSystem.check_created_test_cases(output_file, hardlink_path)
 
+        # Check that the hardlink's parent directory have the right permissions
+        utils.check_path_permissions(os.path.join(filesystem_handler.get_wps_outputs_public_dir(), bird_name), 0o775)
+
         # A create event on a folder should not be processed (no corresponding target folder created)
         target_dir = os.path.join(filesystem_handler.get_wps_outputs_public_dir(), bird_name)
         shutil.rmtree(target_dir)
@@ -461,6 +464,12 @@ def test_user_wps_output_created(self):
 
         TestFileSystem.check_created_test_cases(self.output_file, self.hardlink_path)
 
+        # Check that the hardlink's parent directories have the right permissions
+        path_to_check = self.hardlink_path
+        while not path_to_check.endswith(USER_WPS_OUTPUTS_USER_DIR_NAME):
+            path_to_check = os.path.dirname(path_to_check)
+            utils.check_path_permissions(path_to_check, 0o777)
+
         # A create event on a folder should not be processed (no corresponding target folder created)
         src_dir = os.path.join(self.wpsoutputs_dir, f"{self.bird_name}/users/{self.user_id}/{self.job_id}")
         target_dir = os.path.join(self.wps_outputs_user_dir, f"{self.bird_name}/{self.job_id}")