fix: when the database is read-only

It can happen that the database could be read-only but running commands like gridtk list should still work.

Author: 183amir

src/gridtk/cli.py

@@ -142,14 +142,14 @@ def _job_filters_decorator(function):
     "--database",
     help="Path to the database file.",
     default=Path("jobs.sql3"),
-    type=click.Path(path_type=Path, file_okay=True, dir_okay=False, writable=True),
+    type=click.Path(path_type=Path, file_okay=True, dir_okay=False),
 )
 @click.option(
     "-l",
     "--logs-dir",
     help="Path to the logs directory.",
     default=Path("logs"),
-    type=click.Path(path_type=Path, file_okay=False, dir_okay=True, writable=True),
+    type=click.Path(path_type=Path, file_okay=False, dir_okay=True),
 )
 @click.pass_context
 def cli(ctx, database, logs_dir):

src/gridtk/manager.py

@@ -25,7 +25,7 @@
 
 from collections.abc import Iterable
 from pathlib import Path
-from typing import Any
+from typing import Any, Optional
 
 import sqlalchemy
 
@@ -98,15 +98,26 @@ def get_dependent_jobs_recursive(jobs: Iterable[Job]) -> list[Job]:
 class JobManager:
     """Implements a job manager for Slurm."""
 
-    def __init__(self, database: Path, logs_dir: Path) -> None:
+    def __init__(
+        self, database: Path, logs_dir: Path, read_only: Optional[bool] = None
+    ) -> None:
         self.database = Path(database)
+        # check if database exists and is read-only
+        if (
+            read_only is None
+            and self.database.exists()
+            and not os.access(self.database, os.W_OK)
+        ):
+            read_only = True
+        self.read_only = read_only
         self.engine = create_engine(f"sqlite:///{self.database}", echo=False)
         self.logs_dir = Path(logs_dir)
         self.logs_dir.mkdir(exist_ok=True)
 
     def __enter__(self):
         # opens a new session and returns it
-        Base.metadata.create_all(self.engine)
+        if not self.read_only:
+            Base.metadata.create_all(self.engine)
         self._session = Session(self.engine)
         self._session.begin()
         return self._session
@@ -165,6 +176,8 @@ def submit_job(self, name, command, array, dependencies):
 
     def update_jobs(self) -> None:
         """Update the status of all jobs."""
+        if self.read_only:
+            return
         jobs_by_grid_id: dict[int, Job] = dict()
         query = self.session.query(Job)
         for job in query.all():

tests/test_gridtk.py

@@ -4,8 +4,10 @@
 # SPDX-License-Identifier: GPL-3.0-or-later
 
 import json
+import stat
 import traceback
 
+from pathlib import Path
 from unittest.mock import Mock, patch
 
 import pytest
@@ -240,6 +242,23 @@ def test_list_jobs(mock_check_output, runner):
         )
 
 
+@patch("subprocess.check_output")
+def test_list_jobs_readonly_database(mock_check_output, runner):
+    with runner.isolated_filesystem():
+        submit_job_id = 9876543
+        _submit_job(
+            runner=runner, mock_check_output=mock_check_output, job_id=submit_job_id
+        )
+        # Simulate a readonly database
+        mock_check_output.side_effect = []
+        Path("jobs.sql3").chmod(stat.S_IREAD)
+        result = runner.invoke(cli, ["list"])
+        assert_click_runner_result(result)
+        # The job should be UNKNOWN because we can't query the slurm when the
+        # database is read-only
+        assert "UNKNOWN" in result.output
+
+
 @patch("subprocess.check_output")
 def test_report_job(mock_check_output, runner):
     with runner.isolated_filesystem():