Added possibility to resubmit job with new command line; few bug fixes.

gridtk/local.py

@@ -62,11 +62,16 @@ class JobManagerLocal(JobManager):
     return job_id
 
 
-  def resubmit(self, job_ids = None, also_success = False, running_jobs = False, **kwargs):
+  def resubmit(self, job_ids = None, also_success = False, running_jobs = False, new_command=None, **kwargs):
     """Re-submit jobs automatically"""
     self.lock()
     # iterate over all jobs
     jobs = self.get_jobs(job_ids)
+    if new_command is not None:
+      if len(jobs) == 1:
+        jobs[0].set_command_line(new_command)
+      else:
+        logger.warn("Ignoring new command since no single job id was specified")
     accepted_old_status = ('success', 'failure') if also_success else ('failure',)
     for job in jobs:
       # check if this job needs re-submission

gridtk/manager.py

@@ -249,7 +249,7 @@ class JobManager:
     def _write_array_jobs(array_jobs):
       for array_job in array_jobs:
         if unfinished or array_job.status in accepted_status:
-          print("Array Job", str(array_job.id), ":")
+          print("Array Job", str(array_job.id), ("(%s) :"%array_job.machine_name if array_job.machine_name is not None else ":"))
           _write_contents(array_job)
 
     self.lock()
@@ -314,7 +314,7 @@ class JobManager:
         for array_job in array_jobs:
           if array_job.status in status:
             if delete_jobs:
-              logger.debug("Deleting array job '%d' of job '%d' from the database." % array_job.id, job.unique)
+              logger.debug("Deleting array job '%d' of job '%d' from the database." % (array_job.id, job.unique))
             _delete(array_job)
         if not job.array:
           if job.status in status:

gridtk/models.py

@@ -203,6 +203,11 @@ class Job(Base):
     # In python 3, the command line is bytes, which can be pickled directly
     return loads(self.command_line) if isinstance(self.command_line, bytes) else loads(str(self.command_line))
 
+  def set_command_line(self, command_line):
+    """Sets / overwrites the command line for the job."""
+    self.command_line = dumps(command_line)
+
+
   def get_array(self):
     """Returns the array arguments for the job; usually a string."""
     # In python 2, the command line is unicode, which needs to be converted to string before pickling;

gridtk/script/jman.py

@@ -155,7 +155,7 @@ def resubmit(args):
     kwargs['io_big'] = False
 
 
-  jm.resubmit(get_ids(args.job_ids), args.also_success, args.running_jobs, **kwargs)
+  jm.resubmit(get_ids(args.job_ids), args.also_success, args.running_jobs, args.overwrite_command, **kwargs)
 
 
 def run_scheduler(args):
@@ -296,6 +296,7 @@ def main(command_line_options = None):
   resubmit_parser.add_argument('-k', '--keep-logs', action='store_true', help='Do not clean the log files of the old job before re-submitting.')
   resubmit_parser.add_argument('-s', '--also-success', action='store_true', help='Re-submit also jobs that have finished successfully.')
   resubmit_parser.add_argument('-a', '--running-jobs', action='store_true', help='Re-submit even jobs that are running or waiting (use this flag with care).')
+  resubmit_parser.add_argument('-o', '--overwrite-command', nargs=argparse.REMAINDER, help = "Overwrite the command line (of a single job) that should be executed (useful to keep job dependencies).")
   resubmit_parser.set_defaults(func=resubmit)
 
   # subcommand 'stop'

gridtk/sge.py

@@ -126,11 +126,16 @@ class JobManagerSGE(JobManager):
     self.unlock()
 
 
-  def resubmit(self, job_ids = None, also_success = False, running_jobs = False, **kwargs):
+  def resubmit(self, job_ids = None, also_success = False, running_jobs = False, new_command=None, **kwargs):
     """Re-submit jobs automatically"""
     self.lock()
     # iterate over all jobs
     jobs = self.get_jobs(job_ids)
+    if new_command is not None:
+      if len(jobs) == 1:
+        jobs[0].set_command_line(new_command)
+      else:
+        logger.warn("Ignoring new command since no single job id was specified")
     accepted_old_status = ('submitted', 'success', 'failure') if also_success else ('submitted', 'failure',)
     for job in jobs:
       # check if this job needs re-submission

gridtk/tests/__init__.py

@@ -106,7 +106,7 @@ class GridTKTest(unittest.TestCase):
 
 
       # reset the job 1
-      jman.main(['./bin/jman', '--local', '--database', self.database, 'resubmit', '--job-id', '1', '--running-jobs'])
+      jman.main(['./bin/jman', '--local', '--database', self.database, 'resubmit', '--job-id', '1', '--running-jobs', '--overwrite-command', script_1])
 
       # now, start the local execution of the job in a parallel job
       self.scheduler_job = subprocess.Popen(['./bin/jman', '--local', '--database', self.database, 'run-scheduler', '--sleep-time', '5', '--parallel', '2'])

setup.py

@@ -9,7 +9,7 @@ if sys.version_info[:2] < (2, 7) or ((3,0) <= sys.version_info[:2] < (3,2)):
 
 setup(
     name='gridtk',
-    version='1.1.6a0',
+    version='1.1.7a0',
     description='SGE Grid and Local Submission and Monitoring Tools for Idiap',
 
     url='http://github.com/idiap/gridtk',