From 6af885f148dd3f2bec5ee66f90706b07c39ffd56 Mon Sep 17 00:00:00 2001
From: Benoit Seignovert <benoit.seignovert@univ-nantes.fr>
Date: Mon, 18 Mar 2024 17:57:20 +0100
Subject: [PATCH] Add explicit path to spawner and singleuser commands

---
 src/glicid_spawner/spawner.py | 18 ++++++++++++++++++
 tests/test_spawner.py         | 11 ++++++++++-
 2 files changed, 28 insertions(+), 1 deletion(-)

diff --git a/src/glicid_spawner/spawner.py b/src/glicid_spawner/spawner.py
index 65ccbf7..12f8339 100644
--- a/src/glicid_spawner/spawner.py
+++ b/src/glicid_spawner/spawner.py
@@ -2,6 +2,8 @@
 
 import asyncio
 import re
+import sys
+from pathlib import Path
 
 from batchspawner import JobStatus, SlurmSpawner
 from traitlets import Bool, Integer, Unicode, default
@@ -11,6 +13,8 @@ from .micromamba import MAMBA_EXE, MAMBA_ROOT_PREFIX
 from .progress import ElapseTime, get_progress
 from .templates import get_template_src
 
+SPAWNER_BIN = Path(sys.exec_prefix) / 'bin'
+
 
 class GlicidSpawner(SlurmSpawner):
     """Glicid SLURM Spawner."""
@@ -60,6 +64,20 @@ class GlicidSpawner(SlurmSpawner):
         """The URL the single-user server should start in."""
         return '/lab/tree' + self.user_options.get('workdir', '/home/{username}') + '?reset'
 
+    def cmd_formatted_for_batch(self):
+        """The command which is substituted inside of the batch script.
+
+        Here we need the absolute path to the spawner and singleuser commands.
+
+        """
+        return ' '.join(
+            [
+                str(SPAWNER_BIN / self.batchspawner_singleuser_cmd),
+                str(SPAWNER_BIN / self.cmd[0]),
+                *self.get_args(),
+            ]
+        )
+
     slurm_job_id_re = Unicode(r'(\d+)(?:;(\w+))?').tag(config=True)
 
     def parse_job_id(self, output):
diff --git a/tests/test_spawner.py b/tests/test_spawner.py
index 9dc2a4e..e6e430e 100644
--- a/tests/test_spawner.py
+++ b/tests/test_spawner.py
@@ -1,5 +1,6 @@
 """Test GLiCID spawner module."""
 
+import re
 from collections import namedtuple
 from itertools import repeat
 
@@ -22,6 +23,10 @@ def test_spawner_config():
 
     assert spawner.batchspawner_singleuser_cmd == 'glicid-spawner-singleuser'
 
+    cmd = spawner.cmd_formatted_for_batch()
+    assert 'bin/glicid-spawner-singleuser' in cmd
+    assert 'bin/jupyterhub-singleuser' in cmd
+
     assert spawner.req_mamba_root_prefix == '/micromamba/operator'
     assert spawner.req_mamba_exe == '/micromamba/operator/bin/micromamba'
     assert spawner.req_job_name == 'jupyterhub_glicid'
@@ -49,7 +54,9 @@ def test_spawner_batch_script(monkeypatch):
     )
 
     script = format_template(
-        spawner.batch_script, **(spawner.get_req_subvars() | spawner.user_options)
+        spawner.batch_script,
+        cmd=spawner.cmd_formatted_for_batch(),
+        **(spawner.get_req_subvars() | spawner.user_options),
     )
 
     assert '#SBATCH --job-name=jupyterhub_glicid' in script
@@ -65,6 +72,8 @@ def test_spawner_batch_script(monkeypatch):
     assert 'export MAMBA_ROOT_PREFIX=/micromamba/operator;' in script
     assert 'micromamba activate /micromamba/john-doe/envs/foo;' in script
 
+    assert re.search(r'.*/bin/glicid-spawner-singleuser .*/bin/jupyterhub-singleuser', script)
+
 
 def test_spawner_parse_job_id():
     """Test spawner job id parser."""