fix some syntax errors

src/run-submit-pol-job.py

@@ -15,6 +15,7 @@ def parse_args():
     parser = argparse.ArgumentParser(description=description,
                                      formatter_class=argparse.RawTextHelpFormatter
                                      )
+    
     parser.add_argument('-o','--outdir', type=str,
                         help="Directory to store the policy output in",
                         default='/data/rc/gpfs-policy/data')
@@ -24,6 +25,7 @@ def parse_args():
                              "file name will have the policy type, the job ID, and the run date tagged on the end")
     parser.add_argument('--with-dirs', action='store_true',
                         help="Include directories as entries in the policy output (Default: false)")
+    
     sbatch = parser.add_argument_group('sbatch parameters')
     sbatch.add_argument('-N','--nodes',type=int,default=1,
                         help='Number of nodes to run job across')
@@ -35,10 +37,11 @@ def parse_args():
                         help='Time limit for job formatted as [D-]HH:MM:SS')
     sbatch.add_argument('-m','--mem-per-cpu',type=str,default='8G',
                         help='Amount of RAM to allocate per core')
+    
     parser.add_argument('device',type=str,
                         help="GPFS fileset/directory apply the policy to. Can be specified as either the name of the"
                              "fileset or the full path to the directory. (Examples: scratch, /data/user/[username])')")
-    args = parser.parse_args()
+    args = vars(parser.parse_args())
     return args
 
 # Validate that the string supplied to 'device' is either the name of a valid, predefined fileset (only 'scratch' 
@@ -62,14 +65,14 @@ def validate_device(device):
     if p.exists() and any([parent in p.parents for parent in valid_parents]):
         return p
     else:
-        raise InvalidDeviceError('The path or fileset must be within /data or /scratch')
+        raise InvalidDeviceError(f'The path or fileset {device} does not exist within /data or /scratch')
 
 def validate_time(time):
     if not re.match(r'^(?:[0-6]-\d{2}|\d{1,3}):\d{2}:\d{2}$',time):
         raise ValueError("Time must have format [[H]H]H:MM:SS or D-HH:MM:SS")
     
 def validate_mem(mem):
-    if not re.match(r'[\d]+[GM]?', mem):
+    if not re.fullmatch(r'^[\d]+[GM]?$', mem):
         raise ValueError("Mem per CPU must be an integer. May be followed by M or G to denote units")
 
 def validate_partition(partition):
@@ -77,11 +80,11 @@ def validate_partition(partition):
         raise ValueError("Multiple partitions should be given as a comma-separated list")
     
     partition = re.sub(r'\s',r'',partition)
-    partitions = [partition.split(r',')]
+    partitions = partition.split(r',')
     cmd=r'sinfo -h -o "%R"'
-    avail_partitions=subprocess.run(cmd, shell=True, stdout=subprocess.PIPE, text=True).stdout.splitlines()
+    avail_partitions=subprocess.run(cmd, shell=True, stdout=subprocess.PIPE).stdout.decode('utf-8').splitlines()
 
-    if ([p for p in partitions if p not in avail_partitions]):
+    if any([p for p in partitions if p not in avail_partitions]):
         incorrect = [p for p in partitions if p not in avail_partitions]
         raise ValueError(f"The following partition(s) do not exist: {', '.join(incorrect)}. To see a list of valid partitions, visit https://rc.uab.edu/")
 
@@ -95,14 +98,6 @@ def validate_ntasks(n):
     if not isinstance(n,int) and n >= 1 and n <= 48:
         raise ValueError('Ntasks must be an integer between 1 and 48')
 
-def validate_sbatch_options(args):
-    validate_nodes(args['nodes'])
-    validate_ntasks(args['ntasks'])
-    validate_mem(args['mem_per_cpu'])
-    validate_time(args['time'])
-    args['partition'] = validate_partition(args['partition'])
-    return args
-
 # Need to validate that the output directory exists. This will not create a directory that does not already exist.
 def validate_output_directory(outdir):
     p = Path(outdir).resolve()
@@ -120,20 +115,24 @@ def create_default_outfile(device):
 
 def main():
     args = parse_args()
-    args_dict = vars(args)
-
     args['device'] = validate_device(args['device'])
 
-    sbatch_args = {(k,v) for k,v in args_dict.items() if k in ['nodes','ntasks','partition','time','mem_per_cpu'] and v is not None}
-    sbatch_args = validate_sbatch_options(sbatch_args)
+    validate_nodes(args['nodes'])
+    validate_ntasks(args['ntasks'])
+    validate_mem(args['mem_per_cpu'])
+    validate_time(args['time'])
+    args['partition'] = validate_partition(args['partition'])
 
     args['outdir'] = validate_output_directory(args['outdir'])
 
-    if 'outfile' not in args.keys():
+    if args['outfile'] is None:
         args['outfile'] = create_default_outfile(args['device'])
 
-    cmd = f"./submit-pol-job "
+    cmd = "./submit-pol-job -o {outdir} -f {outfile} -N {nodes} -n {ntasks} -p {partition} -t {time} -m {mem_per_cpu} {device}".format(**args)
+    if args['with_dirs']:
+        cmd = f'{cmd} --with-dirs'
 
+    print(cmd)
     exit()
 
 if __name__ == '__main__':