Suppress Slurm job listing and polling output from debug logs (#4493)

src/toil/batchSystems/slurm.py

@@ -41,7 +41,7 @@ def getRunningJobIDs(self):
             # -h for no header
             # --format to get jobid i, state %t and time days-hours:minutes:seconds
 
-            lines = call_command(['squeue', '-h', '--format', '%i %t %M']).split('\n')
+            lines = call_command(['squeue', '-h', '--format', '%i %t %M'], quiet=True).split('\n')
             for line in lines:
                 values = line.split()
                 if len(values) < 3:
@@ -165,7 +165,7 @@ def _getJobDetailsFromSacct(self, job_id_list: list) -> dict:
                     '--format', 'JobIDRaw,State,ExitCode',  # specify output columns
                     '-P',  # separate columns with pipes
                     '-S', '1970-01-01']  # override start time limit
-            stdout = call_command(args)
+            stdout = call_command(args, quiet=True)
 
             # Collect the job statuses in a dict; key is the job-id, value is a tuple containing
             # job state and exit status. Initialize dict before processing output of `sacct`.
@@ -174,7 +174,6 @@ def _getJobDetailsFromSacct(self, job_id_list: list) -> dict:
                 job_statuses[job_id] = (None, None)
 
             for line in stdout.splitlines():
-                #logger.debug("%s output %s", args[0], line)
                 values = line.strip().split('|')
                 if len(values) < 3:
                     continue
@@ -210,7 +209,7 @@ def _getJobDetailsFromScontrol(self, job_id_list: list) -> dict:
             if len(job_id_list) == 1:
                 args.append(str(job_id_list[0]))
 
-            stdout = call_command(args)
+            stdout = call_command(args, quiet=True)
 
             # Job records are separated by a blank line.
             if isinstance(stdout, str):
@@ -233,7 +232,6 @@ def _getJobDetailsFromScontrol(self, job_id_list: list) -> dict:
                 job = {}
                 for line in record.splitlines():
                     for item in line.split():
-                        #logger.debug("%s output %s", args[0], item)
                         # Output is in the form of many key=value pairs, multiple pairs on each line
                         # and multiple lines in the output. Each pair is pulled out of each line and
                         # added to a dictionary.

src/toil/lib/misc.py

@@ -109,14 +109,24 @@ def __str__(self) -> str:
 
 
 def call_command(cmd: List[str], *args: str, input: Optional[str] = None, timeout: Optional[float] = None,
-                useCLocale: bool = True, env: Optional[typing.Dict[str, str]] = None) -> str:
-    """Simplified calling of external commands.  This always returns
-    stdout and uses utf- encode8.  If process fails, CalledProcessErrorStderr
-    is raised.  The captured stderr is always printed, regardless of
-    if an expect occurs, so it can be logged.  At the debug log level, the
-    command and captured out are always used.  With useCLocale, C locale
-    is force to prevent failures that occurred in some batch systems
-    with UTF-8 locale.
+                useCLocale: bool = True, env: Optional[typing.Dict[str, str]] = None, quiet: Optional[bool] = False) -> str:
+    """
+    Simplified calling of external commands.
+
+    If the process fails, CalledProcessErrorStderr is raised.
+
+    The captured stderr is always printed, regardless of
+    if an exception occurs, so it can be logged.
+
+    Always logs the command at debug log level.
+
+    :param quiet: If True, do not log the command output. If False (the
+           default), do log the command output at debug log level.
+
+    :param useCLocale: If True, C locale is forced, to prevent failures that
+           can occur in some batch systems when using UTF-8 locale.
+
+    :returns: Command standard output, decoded as utf-8.
     """
 
     # using non-C locales can cause GridEngine commands, maybe other to
@@ -136,5 +146,5 @@ def call_command(cmd: List[str], *args: str, input: Optional[str] = None, timeou
     if proc.returncode != 0:
         logger.debug("command failed in {}s: {}: {}".format(runtime, " ".join(cmd), stderr.rstrip()))
         raise CalledProcessErrorStderr(proc.returncode, cmd, output=stdout, stderr=stderr)
-    logger.debug("command succeeded in {}s: {}: {}".format(runtime, " ".join(cmd), stdout.rstrip()))
+    logger.debug("command succeeded in {}s: {}{}".format(runtime, " ".join(cmd), (': ' + stdout.rstrip()) if not quiet else ''))
     return stdout