Feature/logging (#85)

* added log method in class Generator for storing information about command line arguments, date, time, user and hostname in generatemc.log

* added loging current working directory

* fixed pep8 issues without changing some lines

* merged save_logs and log methods and minor esthetical changes

* changed logging using python logging feature

* some fixes in logging

* changed imports order in generator.py according to imports formating guidelines

* changed logger naming

* changed logger naming

* added some formatting for logging batch system output

mcpartools/generator.py

@@ -1,13 +1,20 @@
-import os
+import getpass
 import logging
+import os
 import shutil
+import socket
+import sys
 import time
 
 from mcpartools.mcengine.common import EngineDiscover
 from mcpartools.scheduler.common import SchedulerDiscover
 
 logger = logging.getLogger(__name__)
 
+file_logger = logging.getLogger('file_logger')
+file_logger.setLevel(logging.INFO)
+file_logger.propagate = False
+
 
 class Options:
 
@@ -139,7 +146,7 @@ def run(self):
         # make symlinks to external files found
         self.symlink_external_files()
 
-        # save logs
+        # store information about command line arguments, date, time, user and hostname into generatemc.log
         self.save_logs()
 
         return 0
@@ -159,6 +166,8 @@ def generate_main_dir(self):
         os.mkdir(dir_path)
         self.main_dir = dir_path
 
+        file_logger.addHandler(logging.FileHandler(os.path.join(dir_path, "generatemc.log"), mode='w+'))
+
     def generate_workspace(self):
         wspdir_name = 'workspace'
         wspdir_path = os.path.join(self.main_dir, wspdir_name)
@@ -225,4 +234,7 @@ def symlink_external_files(self):
                 os.symlink(abs_path, os.path.join(jobdir_path, os.path.split(abs_path)[-1]))
 
     def save_logs(self):
-        pass
+        file_logger.info('Executed command: ' + ' '.join(sys.argv))
+        file_logger.info('Date and time: ' + time.strftime("%Y-%m-%d %H:%M:%S"))
+        file_logger.info('username@hostname: ' + getpass.getuser() + '@' + socket.gethostname())
+        file_logger.info('Current working directory: ' + os.getcwd())

mcpartools/scheduler/common.py

@@ -1,6 +1,5 @@
 import logging
-import os
-from subprocess import check_call, CalledProcessError
+from subprocess import check_output, CalledProcessError
 
 from mcpartools.scheduler.slurm import Slurm
 from mcpartools.scheduler.torque import Torque
@@ -16,17 +15,19 @@ def __init__(self):
 
     @classmethod
     def get_scheduler(cls, scheduler_options, log_location):
-        with open(os.path.join(log_location, "generatemc.log"), 'w+') as LOG_FILE:
-            try:
-                check_call(['srun --version'], stdout=LOG_FILE, stderr=LOG_FILE, shell=True)
-                logger.debug("Discovered job scheduler SLURM")
-                return Slurm(scheduler_options)
-            except CalledProcessError as e:
-                logger.debug("Slurm not found: %s", e)
-            try:
-                check_call(['qsub --version'], stdout=LOG_FILE, stderr=LOG_FILE, shell=True)
-                logger.debug("Discovered job scheduler Torque")
-                return Torque(scheduler_options)
-            except CalledProcessError as e:
-                logger.debug("Torque not found: %s", e)
+        file_logger = logging.getLogger('file_logger')
+        try:
+            srun_output = check_output(['srun --version'], shell=True)
+            file_logger.info("srun output: {}".format(srun_output[:-1]))
+            logger.debug("Discovered job scheduler SLURM")
+            return Slurm(scheduler_options)
+        except CalledProcessError as e:
+            logger.debug("Slurm not found: %s", e)
+        try:
+            qsub_output = check_output(['qsub --version'], shell=True)
+            file_logger.info("qsub output: {}".format(qsub_output[:-1]))
+            logger.debug("Discovered job scheduler Torque")
+            return Torque(scheduler_options)
+        except CalledProcessError as e:
+            logger.debug("Torque not found: %s", e)
         raise SystemError("No known batch system found!")