Merge branch 'resubmit-log-delete' into 'master'

Do not delete the logs of the jobs that are not resubmitted

Closes #29

See merge request !25

gridtk/local.py

@@ -62,7 +62,7 @@ class JobManagerLocal(JobManager):
     return job_id
 
 
-  def resubmit(self, job_ids = None, also_success = False, running_jobs = False, new_command=None, **kwargs):
+  def resubmit(self, job_ids = None, also_success = False, running_jobs = False, new_command=None, keep_logs=False, **kwargs):
     """Re-submit jobs automatically"""
     self.lock()
     # iterate over all jobs
@@ -81,6 +81,8 @@ class JobManagerLocal(JobManager):
         else:
           # re-submit job to the grid
           logger.info("Re-submitted job '%s' to the database", job)
+          if not keep_logs:
+            self.delete_logs(job)
           job.submit('local')
 
     self.session.commit()

gridtk/manager.py

@@ -325,6 +325,14 @@ class JobManager:
 
     self.unlock()
 
+  def delete_logs(self, job):
+    out_file, err_file = job.std_out_file(), job.std_err_file()
+    if out_file and os.path.exists(out_file):
+      os.remove(out_file)
+      logger.debug("Removed output log file '%s'" % out_file)
+    if err_file and os.path.exists(err_file):
+      os.remove(err_file)
+      logger.debug("Removed error log file '%s'" % err_file)
 
   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."""
@@ -336,13 +344,7 @@ class JobManager:
     def _delete(job, try_to_delete_dir=False):
       # delete the job from the database
       if delete_logs:
-        out_file, err_file = job.std_out_file(), job.std_err_file()
-        if out_file and os.path.exists(out_file):
-          os.remove(out_file)
-          logger.debug("Removed output log file '%s'" % out_file)
-        if err_file and os.path.exists(err_file):
-          os.remove(err_file)
-          logger.debug("Removed error log file '%s'" % err_file)
+        self.delete_logs(job)
         if try_to_delete_dir:
           _delete_dir_if_empty(job.log_dir)
       if delete_jobs:

gridtk/script/jman.py

@@ -161,8 +161,6 @@ def submit(args):
 def resubmit(args):
   """Re-submits the jobs with the given ids."""
   jm = setup(args)
-  if not args.keep_logs:
-    jm.delete(job_ids=get_ids(args.job_ids), delete_jobs=False)
 
   kwargs = {
       'cwd': True,
@@ -184,8 +182,7 @@ def resubmit(args):
   if args.no_io_big:
     kwargs['io_big'] = False
 
-
-  jm.resubmit(get_ids(args.job_ids), args.also_success, args.running_jobs, args.overwrite_command, **kwargs)
+  jm.resubmit(get_ids(args.job_ids), args.also_success, args.running_jobs, args.overwrite_command, keep_logs=args.keep_logs, **kwargs)
 
 
 def run_scheduler(args):

gridtk/sge.py

@@ -132,7 +132,7 @@ class JobManagerSGE(JobManager):
     self.unlock()
 
 
-  def resubmit(self, job_ids = None, also_success = False, running_jobs = False, new_command=None, verbosity=0, **kwargs):
+  def resubmit(self, job_ids = None, also_success = False, running_jobs = False, new_command=None, verbosity=0, keep_logs=False, **kwargs):
     """Re-submit jobs automatically"""
     self.lock()
     # iterate over all jobs
@@ -159,6 +159,8 @@ class JobManagerSGE(JobManager):
               del arguments[arg]
         job.set_arguments(kwargs=arguments)
         # delete old status and result of the job
+        if not keep_logs:
+          self.delete_logs(job)
         job.submit()
         if job.queue_name == 'local' and 'queue' not in arguments:
           logger.warn("Re-submitting job '%s' locally (since no queue name is specified)." % job)