Replace instances of common.exec_subproc

Author: Pierre-siddall

Coupled_Drivers/common.py

@@ -228,73 +228,6 @@ def setup_runtime(common_env):
 
     return runlen_sec
 
-def exec_subproc_timeout(cmd, timeout_sec=10):
-    '''
-    Execute a given shell command with a timeout. Takes a list containing
-    the commands to be run, and an integer timeout_sec for how long to
-    wait for the command to run. Returns the return code from the process
-    and the standard out from the command or 'None' if the command times out.
-    '''
-    process = subprocess.Popen(cmd, shell=False,
-                               stdin=subprocess.PIPE,
-                               stdout=subprocess.PIPE,
-                               stderr=subprocess.PIPE)
-    timer = threading.Timer(timeout_sec, process.kill)
-    try:
-        timer.start()
-        stdout, err = process.communicate()
-        if err:
-            sys.stderr.write('[SUBPROCESS ERROR] %s\n' % error)
-        rcode = process.returncode
-    finally:
-        timer.cancel()
-    if sys.version_info[0] >= 3:
-        output = stdout.decode()
-    else:
-        output = stdout
-    return rcode, output
-
-
-def exec_subproc(cmd, verbose=True):
-    '''
-    Execute given shell command. Takes a list containing the commands to be
-    run, and a logical verbose which if set to true will write the output of
-    the command to stdout.
-    '''
-    process = subprocess.Popen(cmd, shell=False,
-                               stdin=subprocess.PIPE,
-                               stdout=subprocess.PIPE,
-                               stderr=subprocess.PIPE)
-    output, err = process.communicate()
-    if verbose and output:
-        sys.stdout.write('[SUBPROCESS OUTPUT] %s\n' % output)
-    if err:
-        sys.stderr.write('[SUBPROCESS ERROR] %s\n' % error)
-    if sys.version_info[0] >= 3:
-        output = output.decode()
-    return process.returncode, output
-
-
-def __exec_subproc_true_shell(cmd, verbose=True):
-    '''
-    Execute given shell command, with shell=True. Only use this function if
-    exec_subproc does not work correctly. Takes a list containing the commands
-    to be run, and a logical verbose which if set to true will write the
-    output of the command to stdout.
-    '''
-    process = subprocess.Popen(cmd, shell=True,
-                               stdin=subprocess.PIPE,
-                               stdout=subprocess.PIPE,
-                               stderr=subprocess.PIPE)
-    output, err = process.communicate()
-    if verbose and output:
-        sys.stdout.write('[SUBPROCESS OUTPUT] %s\n' % output)
-    if err:
-        sys.stderr.write('[SUBPROCESS ERROR] %s\n' % error)
-    if sys.version_info[0] >= 3:
-        output = output.decode()
-    return process.returncode, output
-
 
 def _calculate_ppn_values(nproc, nodes):
     '''

Postprocessing/common/utils.py

@@ -23,7 +23,7 @@
 import os
 import errno
 import shutil
-import subprocess
+import shellout
 import timer
 
 
@@ -153,61 +153,13 @@ def finalcycle():
     return fcycle
 
 
-@timer.run_timer
-def exec_subproc(cmd, verbose=True, cwd=os.getcwd()):
-    '''
-    Execute given shell command.
-    'cmd' input should be in the form of either a:
-      string        - "cd DIR; command arg1 arg2"
-      list of words - ["command", "arg1", "arg2"]
-    Optional arguments:
-      verbose = False: only reproduce the command std.out upon
-                failure of the command
-                True: reproduce std.out regardless of outcome
-      cwd     = Directory in which to execute the command
-    '''
-    import shlex
-
-    cmd_array = [cmd]
-    if not isinstance(cmd, list):
-        cmd_array = cmd.split(';')
-        for i, cmd in enumerate(cmd_array):
-            # Use shlex.split to cope with arguments that contain whitespace
-            cmd_array[i] = shlex.split(cmd)
-
-    # Initialise rcode, in the event there is no command
-    rcode = 99
-    output = 'No command provided'
-
-    for cmd in cmd_array:
-        try:
-            output = subprocess.check_output(cmd,
-                                             stderr=subprocess.STDOUT,
-                                             universal_newlines=True, cwd=cwd)
-            rcode = 0
-            if verbose:
-                log_msg('[SUBPROCESS]: ' + str(output))
-        except subprocess.CalledProcessError as exc:
-            output = exc.output
-            rcode = exc.returncode
-        except OSError as exc:
-            output = exc.strerror
-            rcode = exc.errno
-        if rcode != 0:
-            msg = '[SUBPROCESS]: Command: {}\n[SUBPROCESS]: Error = {}:\n\t{}'
-            log_msg(msg.format(' '.join(cmd), rcode, output), level='WARN')
-            break
-
-    return rcode, output
-
-
 def get_utility_avail(utility):
     '''Return True/False if shell command is available'''
     try:
         status = shutil.which(utility)
     except AttributeError:
         # subprocess.getstatusoutput does not exist at Python2.7
-         status, _ = utils.exec_subproc(utility + ' --help', verbose=False)
+         status, _ = shellout.exec_subprocess(utility + ' --help')
 
     return bool(status)
 
@@ -496,7 +448,7 @@ def _mod_all_calendars_date(indate, delta, cal):
                 cmd = '{} {} --calendar {} --offset {} --print-format ' \
                     '%Y,%m,%d,%H,%M'.format(datecmd, dateinput, cal, offset)
 
-                rcode, output = exec_subproc(cmd, verbose=False)
+                rcode, output = shellout._exec_subprocess(cmd)
             else:
                 log_msg('add_period_to_date: Invalid date for conversion to '
                         'ISO 8601 date representation: ' + str(outdate),

Utilities/lib/shellout.py

@@ -6,7 +6,7 @@
 
 
 @timer.run_timer
-def _exec_subprocess(cmd, verbose=True, current_working_directory=os.getcwd()):
+def _exec_subprocess(cmd, verbose=False, current_working_directory=os.getcwd()):
     """
     Execute a given shell command
 
@@ -44,4 +44,4 @@ def _exec_subprocess(cmd, verbose=True, current_working_directory=os.getcwd()):
         output = exc.strerror
         rcode = exc.errno
 
-    return output, rcode
+    return rcode, output