Corrected the job submission (and re-submission) to handle unique ID's (instead of grid ID's).

gridtk/sge.py

@@ -54,13 +54,14 @@ class JobManagerSGE(JobManager):
     jman = self.wrapper_script
     python = sys.executable
 
-    # remove duplicate dependencies
-    dependencies = sorted(list(set(dependencies)))
+    # get the grid id's for the dependencies and remove duplicates
+    dependent_jobs = self.get_jobs(dependencies)
+    deps = sorted(list(set([j.id for j in dependent_jobs])))
 
     # generate call to the wrapper script
     command = make_shell(python, [jman, '-d', self._database, 'run-job'])
     q_array = "%d-%d:%d" % array if array else None
-    grid_id = qsub(command, context=self.context, name=name, deps=dependencies, array=q_array, stdout=log_dir, stderr=log_dir, **kwargs)
+    grid_id = qsub(command, context=self.context, name=name, deps=deps, array=q_array, stdout=log_dir, stderr=log_dir, **kwargs)
 
     # get the result of qstat
     status = qstat(grid_id, context=self.context)
@@ -76,7 +77,7 @@ class JobManagerSGE(JobManager):
       logger.warn("This job will never be executed since the queue '%s' does not support multi-threading (pe_mth) -- use 'q1dm' or 'q1wm' instead." % kwargs['queue'] if 'queue' in kwargs else 'all.q')
 
     assert job.id == grid_id
-    return grid_id
+    return job.unique
 
 
   def submit(self, command_line, name = None, array = None, dependencies = [], log_dir = "logs", dry_run = False, stop_on_failure = False, **kwargs):
@@ -109,7 +110,7 @@ class JobManagerSGE(JobManager):
     jobs = self.get_jobs(job_ids)
     for job in jobs:
       job.refresh()
-      if job.status in ('queued', 'executing', 'waiting'):
+      if job.status in ('queued', 'executing', 'waiting') and job.queue_name != 'local':
         status = qstat(job.id, context=self.context)
         if len(status) == 0:
           job.status = 'failure'
@@ -147,7 +148,7 @@ class JobManagerSGE(JobManager):
         if job.queue_name == 'local' and 'queue' not in arguments:
           logger.warn("Re-submitting job '%s' locally (since no queue name is specified)." % job)
         else:
-          deps = [dep.id for dep in job.get_jobs_we_wait_for()]
+          deps = [dep.unique for dep in job.get_jobs_we_wait_for()]
           logger.debug("Re-submitting job '%s' with dependencies '%s' to the grid." % (job, deps))
           self._submit_to_grid(job, job.name, job.get_array(), deps, job.log_dir, **arguments)
 
@@ -159,8 +160,11 @@ class JobManagerSGE(JobManager):
     """Overwrites the run-job command from the manager to extract the correct job id before calling base class implementation."""
     # get the unique job id from the given grid id
     self.lock()
-    job = self.session.query(Job).filter(Job.id == job_id)
-    job_id = list(job)[0].unique
+    jobs = list(self.session.query(Job).filter(Job.id == job_id))
+    if len(jobs) != 1:
+      self.unlock()
+      raise ValueError("Could not find job id '%d' in the database'" % job_id)
+    job_id = jobs[0].unique
     self.unlock()
     # call base class implementation with the corrected job id
     return JobManager.run_job(self, job_id, array_id)