fix: quote jobid passed to status script to support multi-cluster Slurm setup

snakemake/executors/__init__.py

@@ -1215,7 +1215,7 @@ def job_status(job, valid_returns=["running", "success", "failed"]):
                     if self.sidecar_vars:
                         env["SNAKEMAKE_CLUSTER_SIDECAR_VARS"] = self.sidecar_vars
                     ret = subprocess.check_output(
-                        "{statuscmd} {jobid}".format(
+                        "{statuscmd} '{jobid}'".format(
                             jobid=job.jobid, statuscmd=self.statuscmd
                         ),
                         shell=True,

tests/test_cluster_statusscript_multi/Snakefile.nonstandard

@@ -0,0 +1,13 @@
+from snakemake import shell
+
+envvars:
+    "TESTVAR"
+
+
+
+rule all:
+	input: 'output.txt'
+
+rule compute:
+	output: 'output.txt'
+	shell: 'touch {output}'

tests/test_cluster_statusscript_multi/sbatch

@@ -0,0 +1,8 @@
+#!/bin/bash
+echo `date` >> sbatch.log
+tail -n1 $1 >> sbatch.log
+# simulate printing of job id by a random number plus the name
+# of the cluster
+echo "$RANDOM;name-of-cluster"
+cat $1 >> sbatch.log
+sh $1

tests/test_cluster_statusscript_multi/status.sh

@@ -0,0 +1,9 @@
+#!/bin/bash
+
+# The argument passed from sbatch is "jobid;cluster_name"
+
+arg="$1"
+jobid="${arg%%;*}"
+cluster="${arg##*;}"
+
+echo success

tests/tests.py

@@ -166,6 +166,17 @@ def test_cluster_cancelscript_nargs1():
     assert len(scancel_lines[1].split(" ")) == 2
 
 
+@skip_on_windows
+def test_cluster_statusscript_multi():
+    os.environ["TESTVAR"] = "test"
+    run(
+        dpath("test_cluster_statusscript_multi"),
+        snakefile="Snakefile.nonstandard",
+        cluster="./sbatch",
+        cluster_status="./status.sh",
+    )
+
+
 def test15():
     run(dpath("test15"))