Improved behavior of 'jman ls' and 'jman del' commands; added more informative...

Improved behavior of 'jman ls' and 'jman del' commands; added more informative output during scheduler run.

gridtk/local.py

@@ -121,13 +121,13 @@ class JobManagerLocal(JobManager):
     # generate call to the wrapper script
     command = [self.wrapper_script, '-ld', self._database, 'run-job']
 
-    logger.info("Started execution of Job '%s'" % self._format_log(job_id, array_id))
+    job = self.get_jobs((job_id,))[0]
+    logger.info("Starting execution of Job '%s': '%s'" % (self._format_log(job_id, array_id), job.name))
 
     # return the subprocess pipe to the process
     try:
       return subprocess.Popen(command, env=environ, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
     except OSError as e:
-      job = self.get_jobs((job_id,))[0]
       logger.error("Could not execute job '%s' locally,\nreason:\t%s,\ncommand_line\t%s:" % (self._format_log(job_id, array_id), e, job.get_command_line()))
       job.finish(117, array_id) # ASCII 'O'
       return None

gridtk/manager.py

@@ -3,7 +3,7 @@ from __future__ import print_function
 
 import os
 import subprocess
-from .models import Base, Job, ArrayJob
+from .models import Base, Job, ArrayJob, Status
 from .tools import logger
 
 import sqlalchemy
@@ -201,12 +201,13 @@ class JobManager:
 
     def _write_array_jobs(array_jobs):
       for array_job in array_jobs:
-        if unfinished or array_job.status in ('success', 'failure'):
+        if unfinished or array_job.status in accepted_status:
           print("Array Job", str(array_job.id), ":")
           _write_contents(array_job)
 
     self.lock()
 
+    accepted_status = ('failure',) if error and not output else ('success', 'failure')
     # check if an array job should be reported
     if array_ids:
       if len(job_ids) != 1: logger.error("If array ids are specified exactly one job id must be given.")
@@ -219,20 +220,20 @@ class JobManager:
       jobs = self.get_jobs(job_ids)
       for job in jobs:
         if job.array:
-          if (unfinished or job.status in ('success', 'failure', 'executing')):
+          if unfinished or job.status in accepted_status or job.status == 'executing':
             print(job)
             _write_array_jobs(job.array)
         else:
-          if unfinished or job.status in ('success', 'failure'):
+          if unfinished or job.status in accepted_status:
             print(job)
             _write_contents(job)
-        if job.log_dir is not None:
+        if job.log_dir is not None and job.status in accepted_status:
           print("-"*60)
 
     self.unlock()
 
 
-  def delete(self, job_ids, array_ids = None, delete_logs = True, delete_log_dir = False, delete_jobs = True):
+  def delete(self, job_ids, array_ids = None, delete_logs = True, delete_log_dir = False, status = Status, delete_jobs = True):
     """Deletes the jobs with the given ids from the database."""
     def _delete_dir_if_empty(log_dir):
       if log_dir and delete_log_dir and os.path.isdir(log_dir) and not os.listdir(log_dir):
@@ -264,11 +265,13 @@ class JobManager:
       if array_jobs:
         job = array_jobs[0].job
         for array_job in array_jobs:
-          logger.debug("Deleting array job '%d' of job '%d' from the database." % array_job.id, job.id)
-          _delete(array_job)
+          if array_job.status in status:
+            logger.debug("Deleting array job '%d' of job '%d' from the database." % array_job.id, job.id)
+            _delete(array_job)
         if not job.array:
-          logger.info("Deleting job '%d' from the database." % job.id)
-          _delete(job, True)
+          if job.status in status:
+            logger.info("Deleting job '%d' from the database." % job.id)
+            _delete(job, True)
 
     else:
       # iterate over all jobs
@@ -277,11 +280,13 @@ class JobManager:
         # delete all array jobs
         if job.array:
           for array_job in job.array:
-            logger.debug("Deleting array job '%d' of job '%d' from the database." % (array_job.id, job.id))
-            _delete(array_job)
+            if array_job.status in status:
+              logger.debug("Deleting array job '%d' of job '%d' from the database." % (array_job.id, job.id))
+              _delete(array_job)
         # delete this job
-        logger.info("Deleting job '%d' from the database." % job.id)
-        _delete(job, True)
+        if job.status in status:
+          logger.info("Deleting job '%d' from the database." % job.id)
+          _delete(job, True)
 
     self.session.commit()
     self.unlock()

gridtk/script/jman.py

@@ -21,6 +21,7 @@ import logging
 
 from ..tools import make_shell, logger
 from .. import local, sge
+from ..models import Status
 
 def setup(args):
   """Returns the JobManager and sets up the basic infrastructure"""
@@ -149,10 +150,10 @@ def delete(args):
   """Deletes the jobs from the job manager. If the jobs are still running in the grid, they are stopped."""
   jm = setup(args)
   # first, stop the jobs if they are running in the grid
-  if not args.local:
+  if not args.local and 'executing' in args.status:
     stop(args)
   # then, delete them from the database
-  jm.delete(job_ids=args.job_ids, array_ids=args.array_ids, delete_logs=not args.keep_logs, delete_log_dir=not args.keep_log_dir)
+  jm.delete(job_ids=args.job_ids, array_ids=args.array_ids, delete_logs=not args.keep_logs, delete_log_dir=not args.keep_log_dir, status=args.status)
 
 
 def run_job(args):
@@ -275,6 +276,7 @@ def main(command_line_options = None):
   delete_parser.add_argument('-a', '--array-ids', metavar='ID', nargs='*', type=int, help='Delete only the jobs with the given array ids. If specified, a single job-id must be given as well. Note that the whole job including all array jobs will be removed from the SGE queue.')
   delete_parser.add_argument('-r', '--keep-logs', action='store_true', help='If set, the log files will NOT be removed.')
   delete_parser.add_argument('-R', '--keep-log-dir', action='store_true', help='When removing the logs, keep the log directory.')
+  delete_parser.add_argument('-s', '--status', nargs='+', choices = Status, default = Status, help='Delete only jobs that have the given stati; by default all jobs are deleted.')
   delete_parser.set_defaults(func=delete)
 
   # subcommand 'run_scheduler'

gridtk/tools.py

@@ -9,7 +9,6 @@ probing.
 
 import os
 import re
-import sys
 import six
 import hashlib
 import random