models.py 15.5 KB
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import sqlalchemy
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from sqlalchemy import Table, Column, Integer, DateTime, String, Boolean, ForeignKey
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from sqlalchemy.orm import backref
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from sqlalchemy.ext.declarative import declarative_base
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from .tools import Enum, relationship
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import os
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import sys
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from datetime import datetime
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if sys.version_info[0] >= 3:
  from pickle import dumps, loads
else:
  from cPickle import dumps, loads
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from .tools import logger
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Base = declarative_base()

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Status = ('submitted', 'queued', 'waiting', 'executing', 'success', 'failure')
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class ArrayJob(Base):
  """This class defines one element of an array job."""
  __tablename__ = 'ArrayJob'

  unique = Column(Integer, primary_key = True)
  id = Column(Integer)
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  job_id = Column(Integer, ForeignKey('Job.unique'))
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  status = Column(Enum(*Status))
  result = Column(Integer)
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  machine_name = Column(String(10))
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  submit_time = Column(DateTime)
  start_time = Column(DateTime)
  finish_time = Column(DateTime)

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  job = relationship("Job", backref='array', order_by=id)

  def __init__(self, id, job_id):
    self.id = id
    self.job_id = job_id
    self.status = Status[0]
    self.result = None
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    self.machine_name = None # will be set later, by the Job class
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    self.submit_time = datetime.now()
    self.start_time = None
    self.finish_time = None


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  def std_out_file(self):
    return self.job.std_out_file() + "." + str(self.id) if self.job.log_dir else None

  def std_err_file(self):
    return self.job.std_err_file() + "." + str(self.id) if self.job.log_dir else None

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  def __str__(self):
    n = "<ArrayJob %d> of <Job %d>" % (self.id, self.job.id)
    if self.result is not None: r = "%s (%d)" % (self.status, self.result)
    else: r = "%s" % self.status
    return "%s : %s" % (n, r)

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  def format(self, format):
    """Formats the current job into a nicer string to fit into a table."""

    job_id = "%d - %d" % (self.job.id, self.id)
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    queue = self.job.queue_name if self.machine_name is None else self.machine_name
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    status = "%s" % self.status + (" (%d)" % self.result if self.result is not None else "" )

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    return format.format("", job_id, queue, status)
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class Job(Base):
  """This class defines one Job that was submitted to the Job Manager."""
  __tablename__ = 'Job'

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  unique = Column(Integer, primary_key = True) # The unique ID of the job (not corresponding to the grid ID)
  command_line = Column(String(255))           # The command line to execute, converted to one string
  name = Column(String(20))                    # A hand-chosen name for the task
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  queue_name = Column(String(20))              # The name of the queue
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  machine_name = Column(String(10))            # The name of the machine in which the job is run
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  grid_arguments = Column(String(255))         # The kwargs arguments for the job submission (e.g. in the grid)
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  id = Column(Integer)                         # The ID of the job as given from the grid
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  exec_dir = Column(String(255))               # The directory in which the command should be executed
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  log_dir = Column(String(255))                # The directory where the log files will be put to
  array_string = Column(String(255))           # The array string (only needed for re-submission)
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  stop_on_failure = Column(Boolean)            # An indicator whether to stop depending jobs when this job finishes with an error
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  submit_time = Column(DateTime)
  start_time = Column(DateTime)
  finish_time = Column(DateTime)


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  status = Column(Enum(*Status))
  result = Column(Integer)

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  def __init__(self, command_line, name = None, exec_dir = None, log_dir = None, array_string = None, queue_name = 'local', machine_name = None, stop_on_failure = False, **kwargs):
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    """Constructs a Job object without an ID (needs to be set later)."""
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    self.command_line = dumps(command_line)
    self.name = name
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    self.queue_name = queue_name   # will be set during the queue command later
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    self.machine_name = machine_name   # will be set during the execute command later
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    self.grid_arguments = dumps(kwargs)
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    self.exec_dir = exec_dir
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    self.log_dir = log_dir
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    self.stop_on_failure = stop_on_failure
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    self.array_string = dumps(array_string)
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    self.submit()


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  def submit(self, new_queue = None):
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    """Sets the status of this job to 'submitted'."""
    self.status = 'submitted'
    self.result = None
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    self.machine_name = None
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    if new_queue is not None:
      self.queue_name = new_queue
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    for array_job in self.array:
      array_job.status = 'submitted'
      array_job.result = None
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      array_job.machine_name = None
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    self.submit_time = datetime.now()
    self.start_time = None
    self.finish_time = None
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  def queue(self, new_job_id = None, new_job_name = None, queue_name = None):
    """Sets the status of this job to 'queued' or 'waiting'."""
    # update the job id (i.e., when the job is executed in the grid)
    if new_job_id is not None:
      self.id = new_job_id

    if new_job_name is not None:
      self.name = new_job_name

    if queue_name is not None:
      self.queue_name = queue_name

    new_status = 'queued'
    self.result = None
    # check if we have to wait for another job to finish
    for job in self.get_jobs_we_wait_for():
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      if job.status not in ('success', 'failure'):
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        new_status = 'waiting'
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      elif self.stop_on_failure and job.status == 'failure':
        new_status = 'failure'
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    # reset the queued jobs that depend on us to waiting status
    for job in self.get_jobs_waiting_for_us():
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      if job.status == 'queued':
        job.status = 'failure' if new_status == 'failure' else 'waiting'
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    self.status = new_status
    for array_job in self.array:
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      if array_job.status not in ('success', 'failure'):
        array_job.status = new_status
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  def execute(self, array_id = None, machine_name = None):
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    """Sets the status of this job to 'executing'."""
    self.status = 'executing'
    if array_id is not None:
      for array_job in self.array:
        if array_job.id == array_id:
          array_job.status = 'executing'
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          if machine_name is not None:
            array_job.machine_name = machine_name
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            array_job.start_time = datetime.now()
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    elif machine_name is not None:
      self.machine_name = machine_name
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    if self.start_time is None:
      self.start_time = datetime.now()
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    # sometimes, the 'finish' command did not work for array jobs,
    # so check if any old job still has the 'executing' flag set
    for job in self.get_jobs_we_wait_for():
      if job.array and job.status == 'executing':
        job.finish(0, -1)


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  def finish(self, result, array_id = None):
    """Sets the status of this job to 'success' or 'failure'."""
    # check if there is any array job still running
    new_status = 'success' if result == 0 else 'failure'
    new_result = result
    finished = True
    if array_id is not None:
      for array_job in self.array:
        if array_job.id == array_id:
          array_job.status = new_status
          array_job.result = result
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          array_job.finish_time = datetime.now()
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        if array_job.status not in ('success', 'failure'):
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          finished = False
        elif new_result == 0:
          new_result = array_job.result

    if finished:
      # There was no array job, or all array jobs finished
      self.status = 'success' if new_result == 0 else 'failure'
      self.result = new_result
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      self.finish_time = datetime.now()
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      # update all waiting jobs
      for job in self.get_jobs_waiting_for_us():
        if job.status == 'waiting':
          job.queue()

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  def refresh(self):
    """Refreshes the status information."""
    if self.status == 'executing' and self.array:
      new_result = 0
      for array_job in self.array:
        if array_job.status == 'failure' and new_result is not None:
          new_result = array_job.result
        elif array_job.status not in ('success', 'failure'):
          new_result = None
      if new_result is not None:
        self.status = 'success' if new_result == 0 else 'failure'
        self.result = new_result


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  def get_command_line(self):
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    """Returns the command line for the job."""
    # In python 2, the command line is unicode, which needs to be converted to string before pickling;
    # In python 3, the command line is bytes, which can be pickled directly
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    return loads(self.command_line) if isinstance(self.command_line, bytes) else loads(self.command_line.encode())
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  def set_command_line(self, command_line):
    """Sets / overwrites the command line for the job."""
    self.command_line = dumps(command_line)

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  def get_exec_dir(self):
    """Returns the command line for the job."""
    # In python 2, the command line is unicode, which needs to be converted to string before pickling;
    # In python 3, the command line is bytes, which can be pickled directly
    return str(os.path.realpath(self.exec_dir)) if self.exec_dir is not None else None


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  def get_array(self):
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    """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;
    # In python 3, the command line is bytes, which can be pickled directly
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    return loads(self.array_string) if isinstance(self.array_string, bytes) else loads(self.array_string.encode())
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  def get_arguments(self):
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    """Returns the additional options for the grid (such as the queue, memory requirements, ...)."""
    # In python 2, the command line is unicode, which needs to be converted to string before pickling;
    # In python 3, the command line is bytes, which can be pickled directly
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    args = loads(self.grid_arguments)['kwargs'] if isinstance(self.grid_arguments, bytes) else loads(self.grid_arguments.encode())['kwargs']
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    # in any case, the commands have to be converted to str
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    retval = {}
    if 'pe_opt' in args:
      retval['pe_opt'] = args['pe_opt']
    if 'memfree' in args and args['memfree'] is not None:
      retval['memfree'] = args['memfree']
    if 'hvmem' in args and args['hvmem'] is not None:
      retval['hvmem'] = args['hvmem']
    if 'env' in args and len(args['env']) > 0:
      retval['env'] = args['env']
    if 'io_big' in args and args['io_big']:
      retval['io_big'] = True

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    # also add the queue
    if self.queue_name is not None:
      retval['queue'] = str(self.queue_name)

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    return retval

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  def set_arguments(self, **kwargs):
    self.grid_arguments = dumps(kwargs)
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  def get_jobs_we_wait_for(self):
    return [j.waited_for_job for j in self.jobs_we_have_to_wait_for if j.waited_for_job is not None]

  def get_jobs_waiting_for_us(self):
    return [j.waiting_job for j in self.jobs_that_wait_for_us if j.waiting_job is not None]


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  def std_out_file(self, array_id = None):
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    return os.path.join(self.log_dir, (self.name if self.name else 'job') + ".o" + str(self.id)) if self.log_dir else None
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  def std_err_file(self, array_id = None):
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    return os.path.join(self.log_dir, (self.name if self.name else 'job') + ".e" + str(self.id)) if self.log_dir else None
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  def _cmdline(self):
    cmdline = self.get_command_line()
    c = ""
    for cmd in cmdline:
      if cmd[0] == '-':
        c += "%s " % cmd
      else:
        c += "'%s' " % cmd
    return c

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  def __str__(self):
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    id = "%d (%d)" % (self.unique, self.id)
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    if self.machine_name: m = "%s - %s" % (self.queue_name, self.machine_name)
    else: m = self.queue_name
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    if self.array: a = "[%d-%d:%d]" % self.get_array()
    else: a = ""
    if self.name is not None: n = "<Job: %s %s - '%s'>" % (id, a, self.name)
    else: n = "<Job: %s>" % id
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    if self.result is not None: r = "%s (%d)" % (self.status, self.result)
    else: r = "%s" % self.status
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    return "%s | %s : %s -- %s" % (n, m, r, self._cmdline())
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  def format(self, format, dependencies = 0, limit_command_line = None):
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    """Formats the current job into a nicer string to fit into a table."""
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    command_line = self._cmdline()
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    if limit_command_line is not None and len(command_line) > limit_command_line:
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      command_line = command_line[:limit_command_line-3] + '...'

    job_id = "%d" % self.id + (" [%d-%d:%d]" % self.get_array() if self.array else "")
    status = "%s" % self.status + (" (%d)" % self.result if self.result is not None else "" )
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    queue = self.queue_name if self.machine_name is None else self.machine_name
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    if limit_command_line is None:
      grid_opt = self.get_arguments()
      if grid_opt:
        # add additional information about the job at the end
André Anjos's avatar
André Anjos committed
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        command_line = "<" + ",".join(["%s=%s" % (key,value) for key,value in grid_opt.items()]) + ">: " + command_line
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      if self.exec_dir is not None:
        command_line += "; [Executed in directory: '%s']" % self.exec_dir
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    if dependencies:
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      deps = str(sorted(list(set([dep.unique for dep in self.get_jobs_we_wait_for()]))))
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      if dependencies < len(deps):
        deps = deps[:dependencies-3] + '...'
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      return format.format(self.unique, job_id, queue[:12], status, self.name, deps, command_line)
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    else:
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      return format.format(self.unique, job_id, queue[:12], status, self.name, command_line)
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class JobDependence(Base):
  """This table defines a many-to-many relationship between Jobs."""
  __tablename__ = 'JobDependence'
  id = Column(Integer, primary_key=True)
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  waiting_job_id = Column(Integer, ForeignKey('Job.unique')) # The ID of the waiting job
  waited_for_job_id = Column(Integer, ForeignKey('Job.unique')) # The ID of the job to wait for
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  # This is twisted: The 'jobs_we_have_to_wait_for' field in the Job class needs to be joined with the waiting job id, so that jobs_we_have_to_wait_for.waiting_job is correct
  # Honestly, I am lost but it seems to work...
  waiting_job = relationship('Job', backref = 'jobs_we_have_to_wait_for', primaryjoin=(Job.unique == waiting_job_id), order_by=id) # The job that is waited for
  waited_for_job = relationship('Job', backref = 'jobs_that_wait_for_us', primaryjoin=(Job.unique == waited_for_job_id), order_by=id) # The job that waits
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  def __init__(self, waiting_job_id, waited_for_job_id):
    self.waiting_job_id = waiting_job_id
    self.waited_for_job_id = waited_for_job_id
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def add_job(session, command_line, name = 'job', dependencies = [], array = None, exec_dir=None, log_dir = None, stop_on_failure = False, **kwargs):
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  """Helper function to create a job, add the dependencies and the array jobs."""
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  job = Job(command_line=command_line, name=name, exec_dir=exec_dir, log_dir=log_dir, array_string=array, stop_on_failure=stop_on_failure, kwargs=kwargs)
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  session.add(job)
  session.flush()
  session.refresh(job)

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  # by default id and unique id are identical, but the id might be overwritten later on
  job.id = job.unique
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  for d in dependencies:
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    if d == job.unique:
      logger.warn("Adding self-dependency of job %d is not allowed" % d)
      continue
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    depending = list(session.query(Job).filter(Job.unique == d))
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    if len(depending):
      session.add(JobDependence(job.unique, depending[0].unique))
    else:
      logger.warn("Could not find dependent job with id %d in database" % d)

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  if array:
    (start, stop, step) = array
    # add array jobs
    for i in range(start, stop+1, step):
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      session.add(ArrayJob(i, job.unique))
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  session.commit()

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  return job
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def times(job):
  """Returns a string containing timing information for teh given job, which might be a :py:class:`Job` or an :py:class:`ArrayJob`."""
  timing = "Submitted: %s" % job.submit_time.ctime()
  if job.start_time is not None:
    timing += "\nStarted  : %s \t Job waited  : %s" % (job.start_time.ctime(), job.start_time - job.submit_time)
  if job.finish_time is not None:
    timing += "\nFinished : %s \t Job executed: %s" % (job.finish_time.ctime(), job.finish_time - job.start_time)
  return timing