apply patch from #96

{{cookiecutter.profile_name}}/slurm-sidecar.py

@@ -1,9 +1,9 @@
 #!/usr/bin/env python3
 """Run a Snakemake v7+ sidecar process for Slurm
 
-This sidecar process will poll ``squeue --user [user] --format='%i,%T'``
-every 60 seconds by default (use environment variable
-``SNAKEMAKE_SLURM_SQUEUE_WAIT`` for adjusting this).
+This sidecar process will poll ``squeue --me --format='%i,%T'`` every 60
+seconds by default (use environment variable ``SNAKEMAKE_SLURM_SQUEUE_WAIT``
+for adjusting this).
 
 Note that you have to adjust the value to fit to your ``MinJobAge`` Slurm
 configuration.  Jobs remain at least ``MinJobAge`` seconds known to the
@@ -63,7 +63,7 @@ def __init__(
         squeue_cmd,
         squeue_timeout=2,
         sleep_time=0.01,
-        max_tries=3,
+        max_tries=10,
         *args,
         **kwargs
     ):
@@ -103,7 +103,10 @@ def get_state(self, jobid):
         """Return the job state for the given jobid."""
         jobid = str(jobid)
         if jobid not in self.states:
-            self.states[jobid] = self._get_state_sacct(jobid)
+            try:
+                self.states[jobid] = self._get_state_sacct(jobid)
+            except:
+                return "__not_seen_yet__"
         return self.states.get(jobid, "__not_seen_yet__")
 
     def register_job(self, jobid):
@@ -122,17 +125,22 @@ def _get_state_sacct(self, jobid):
             try:
                 logger.debug("Calling %s (try %d)", cmd, try_num)
                 output = subprocess.check_output(cmd, timeout=self.squeue_timeout, text=True)
-                break
             except subprocess.TimeoutExpired as e:
-                logger.debug("Call to %s timed out (try %d of %d)", cmd, try_num, self.max_tries)
+                logger.warning("Call to %s timed out (try %d of %d)", cmd, try_num, self.max_tries)
+                continue
             except subprocess.CalledProcessError as e:
-                logger.debug("Call to %s failed (try %d of %d)", cmd, try_num, self.max_tries)
-        if try_num >= self.max_tries:
-            raise Exception("Problem with call to %s" % cmd)
-        else:
-            parsed = {x.split("|")[0]: x.split("|")[1] for x in output.strip().split("\n")}
-            logger.debug("Returning state of %s as %s", jobid, parsed[jobid])
-            return parsed[jobid]
+                logger.warning("Call to %s failed (try %d of %d)", cmd, try_num, self.max_tries)
+                continue
+            try:
+                parsed = {x.split("|")[0]: x.split("|")[1] for x in output.strip().split("\n")}
+                logger.debug("Returning state of %s as %s", jobid, parsed[jobid])
+                return parsed[jobid]
+            except IndexError:
+                logger.warning("Could not parse %s (try %d of %d)", repr(output), try_num, self.max_tries)
+            secs = try_num / 2.0
+            loger.info("Sleeping %f seconds", secs)
+            time.sleep(secs)
+        raise Exception("Problem with call to %s" % cmd)
 
     def stop(self):
         """Flag thread to stop execution"""
@@ -143,7 +151,7 @@ def _call_squeue(self, allow_failure=True):
         """Run the call to ``squeue``"""
         cluster = CookieCutter.get_cluster_option()
         try_num = 0
-        cmd = [SQUEUE_CMD, "--user={}".format(os.environ.get("USER")), "--format=%i,%T", "--state=all"]
+        cmd = [SQUEUE_CMD, "--me", "--format=%i,%T", "--state=all"]
         if cluster:
             cmd.append(cluster)
         while try_num < self.max_tries:
@@ -209,6 +217,12 @@ def do_GET(self):
             return
         # Otherwise, query job ID status
         job_id = self.path[len("/job/status/") :]
+        try:
+            logger.debug("CLEMENS:")
+            logger.debug(job_id)
+            job_id=job_id.split("%20")[3]
+        except IndexError:
+            pass
         logger.debug("Querying for job ID %s" % repr(job_id))
         status = self.server.poll_thread.get_state(job_id)
         logger.debug("Status: %s" % status)
@@ -286,8 +300,8 @@ def main():
     poll_thread = PollSqueueThread(SQUEUE_WAIT, SQUEUE_CMD, name="poll-squeue")
     poll_thread.start()
 
-    # Initialize HTTP server that makes available the output of ``squeue --user [user]``
-    # in a controlled fashion.
+    # Initialize HTTP server that makes available the output of ``squeue --me`` in a
+    # controlled fashion.
     http_server = JobStateHttpServer(poll_thread)
     http_thread = threading.Thread(name="http-server", target=http_server.serve_forever)
     http_thread.start()