# Path: diagnostic_primers/sge_jobs.py
# class JobGroup(object):
# 
#     """Class that stores a group of jobs, permitting parameter sweeps."""
# 
#     def __init__(self, name, command, queue=None, arguments=None):
#         """ Instantiate a JobGroup object.  JobGroups allow for the use of
#         combinatorial parameter sweeps by using the 'command' and 'arguments'
#         arguments.
# 
#         - name              String, the JobGroup name
#         - command           String, the command to be run, with arguments
#                             specified
#         - queue             String, the queue for SGE to use
#         - arguments         Dictionary, the values for each parameter as
#                             lists of strings, keyed by an identifier for
#                             the command string
# 
#         For example, to use a command 'my_cmd' with the arguments
#         '-foo' and '-bar' having values 1, 2, 3, 4 and 'a', 'b', 'c', 'd' in
#         all combinations, respectively, you would pass
#         command='my_cmd $SGE_TASK_ID -foo $fooargs -bar $barargs'
#         arguments='{'fooargs': ['1','2','3','4'],
#                     'barargs': ['a','b','c','d']}
#         """
#         self.name = name  # Set JobQueue name
#         self.queue = queue  # Set SGE queue to request
#         self.command = command  # Set command string
#         self.dependencies = []  # Create empty list for dependencies
#         self.submitted = True  # Set submitted Boolean
#         if arguments is None:
#             self.arguments = dict()  # Dictionary of arguments for command
#         else:
#             self.arguments = arguments
#         self.generate_script()  # Make SGE script
# 
#     def generate_script(self):
#         """Create the SGE script that will run the jobs in the JobGroup, with the
#         passed arguments.
#         """
#         self.script = ""  # Holds the script string
#         total = 1  # total number of jobs in this group
# 
#         # for now, SGE_TASK_ID becomes TASK_ID, but we base it at zero
#         self.script += """let "TASK_ID=$SGE_TASK_ID - 1"\n"""
# 
#         # build the array definitions
#         for key in self.arguments.keys():
#             values = self.arguments[key]
#             line = "%s_ARRAY=( " % (key)
#             for value in values:
#                 line += value
#                 line += " "
#             line += " )\n"
#             self.script += line
#             total *= len(values)
#         self.script += "\n"
# 
#         # now, build the decoding logic in the script
#         for key in self.arguments.keys():
#             count = len(self.arguments[key])
#             self.script += """let "%s_INDEX=$TASK_ID %% %d"\n""" % (key, count)
#             self.script += """%s=${%s_ARRAY[$%s_INDEX]}\n""" % (key, key, key)
#             self.script += """let "TASK_ID=$TASK_ID / %d"\n""" % (count)
# 
#         # now, add the command to run the job
#         self.script += "\n"
#         self.script += self.command
#         self.script += "\n"
# 
#         # set the number of tasks in this group
#         self.tasks = total
# 
#     def add_dependency(self, job):
#         """Add the passed job to the dependency list for this JobGroup.  This
#         JobGroup should not execute until all dependent jobs are completed
# 
#         - job         Job, job to be added to the JobGroup's dependency list
#         """
#         self.dependencies.append(job)
# 
#     def remove_dependency(self, job):
#         """ Remove the passed job from this JobGroup's dependency list
# 
#         - job         Job, job to be removed from the JobGroup's dependency list
#         """
#         self.dependencies.remove(job)
# 
#     def wait(self, interval=SGE_WAIT):
#         """Wait for a defined period."""
#         finished = False
#         while not finished:
#             time.sleep(interval)
#             interval = min(2 * interval, 60)
#             cmd = "qstat -j {}".format(self.name)
#             args = [shlex.quote(_) for _ in cmd.split()]
#             result = subprocess.run(args, stdout=subprocess.DEVNULL)  # nosec
#             finished = result.returncode  # 1 if job does not exist


import itertools
import os
import shlex
import subprocess
from collections import defaultdict
from diagnostic_primers.sge_jobs import JobGroup
        unsatisfied = sum([(subjob.submitted is False) for subjob in job.dependencies])
        if 0 == unsatisfied:
            submittable.add(job)
    return list(submittable)


def submit_safe_jobs(root_dir, jobs, sgeargs=None):
    """Submit the passed list of jobs to the Grid Engine server, using the passed
    directory as the root for scheduler output.

    - root_dir      Path to output directory
    - jobs          Iterable of Job objects
    """
    # Loop over each job, constructing SGE command-line
    for job in jobs:
        job.out = os.path.join(root_dir, "stdout")
        job.err = os.path.join(root_dir, "stderr")

        # Add job name, current working directory, SGE stdout and stderr
        # directories to the SGE command line
        args = " -N %s " % (job.name)
        args += " -cwd "
        args += " -o %s -e %s " % (job.out, job.err)

        # If a queue is specified, add this to the SGE command line
        # if job.queue is not None and job.queue in local_queues:
        #    args += local_queues[job.queue]
        #    #args += "-q %s " % job.queue

        # If the job is actually a JobGroup, add the task numbering argument

# Path: diagnostic_primers/sge_jobs.py
# class JobGroup(object):
# 
#     """Class that stores a group of jobs, permitting parameter sweeps."""
# 
#     def __init__(self, name, command, queue=None, arguments=None):
#         """ Instantiate a JobGroup object.  JobGroups allow for the use of
#         combinatorial parameter sweeps by using the 'command' and 'arguments'
#         arguments.
# 
#         - name              String, the JobGroup name
#         - command           String, the command to be run, with arguments
#                             specified
#         - queue             String, the queue for SGE to use
#         - arguments         Dictionary, the values for each parameter as
#                             lists of strings, keyed by an identifier for
#                             the command string
# 
#         For example, to use a command 'my_cmd' with the arguments
#         '-foo' and '-bar' having values 1, 2, 3, 4 and 'a', 'b', 'c', 'd' in
#         all combinations, respectively, you would pass
#         command='my_cmd $SGE_TASK_ID -foo $fooargs -bar $barargs'
#         arguments='{'fooargs': ['1','2','3','4'],
#                     'barargs': ['a','b','c','d']}
#         """
#         self.name = name  # Set JobQueue name
#         self.queue = queue  # Set SGE queue to request
#         self.command = command  # Set command string
#         self.dependencies = []  # Create empty list for dependencies
#         self.submitted = True  # Set submitted Boolean
#         if arguments is None:
#             self.arguments = dict()  # Dictionary of arguments for command
#         else:
#             self.arguments = arguments
#         self.generate_script()  # Make SGE script
# 
#     def generate_script(self):
#         """Create the SGE script that will run the jobs in the JobGroup, with the
#         passed arguments.
#         """
#         self.script = ""  # Holds the script string
#         total = 1  # total number of jobs in this group
# 
#         # for now, SGE_TASK_ID becomes TASK_ID, but we base it at zero
#         self.script += """let "TASK_ID=$SGE_TASK_ID - 1"\n"""
# 
#         # build the array definitions
#         for key in self.arguments.keys():
#             values = self.arguments[key]
#             line = "%s_ARRAY=( " % (key)
#             for value in values:
#                 line += value
#                 line += " "
#             line += " )\n"
#             self.script += line
#             total *= len(values)
#         self.script += "\n"
# 
#         # now, build the decoding logic in the script
#         for key in self.arguments.keys():
#             count = len(self.arguments[key])
#             self.script += """let "%s_INDEX=$TASK_ID %% %d"\n""" % (key, count)
#             self.script += """%s=${%s_ARRAY[$%s_INDEX]}\n""" % (key, key, key)
#             self.script += """let "TASK_ID=$TASK_ID / %d"\n""" % (count)
# 
#         # now, add the command to run the job
#         self.script += "\n"
#         self.script += self.command
#         self.script += "\n"
# 
#         # set the number of tasks in this group
#         self.tasks = total
# 
#     def add_dependency(self, job):
#         """Add the passed job to the dependency list for this JobGroup.  This
#         JobGroup should not execute until all dependent jobs are completed
# 
#         - job         Job, job to be added to the JobGroup's dependency list
#         """
#         self.dependencies.append(job)
# 
#     def remove_dependency(self, job):
#         """ Remove the passed job from this JobGroup's dependency list
# 
#         - job         Job, job to be removed from the JobGroup's dependency list
#         """
#         self.dependencies.remove(job)
# 
#     def wait(self, interval=SGE_WAIT):
#         """Wait for a defined period."""
#         finished = False
#         while not finished:
#             time.sleep(interval)
#             interval = min(2 * interval, 60)
#             cmd = "qstat -j {}".format(self.name)
#             args = [shlex.quote(_) for _ in cmd.split()]
#             result = subprocess.run(args, stdout=subprocess.DEVNULL)  # nosec
#             finished = result.returncode  # 1 if job does not exist


# Path: diagnostic_primers/sge.py
import itertools
import os
import shlex
import subprocess
from collections import defaultdict
from diagnostic_primers.sge_jobs import JobGroup

        unsatisfied = sum([(subjob.submitted is False) for subjob in job.dependencies])
        if 0 == unsatisfied:
            submittable.add(job)
    return list(submittable)


def submit_safe_jobs(root_dir, jobs, sgeargs=None):
    """Submit the passed list of jobs to the Grid Engine server, using the passed
    directory as the root for scheduler output.

    - root_dir      Path to output directory
    - jobs          Iterable of Job objects
    """
    # Loop over each job, constructing SGE command-line
    for job in jobs:
        job.out = os.path.join(root_dir, "stdout")
        job.err = os.path.join(root_dir, "stderr")

        # Add job name, current working directory, SGE stdout and stderr
        # directories to the SGE command line
        args = " -N %s " % (job.name)
        args += " -cwd "
        args += " -o %s -e %s " % (job.out, job.err)

        # If a queue is specified, add this to the SGE command line
        # if job.queue is not None and job.queue in local_queues:
        #    args += local_queues[job.queue]
        #    #args += "-q %s " % job.queue

        # If the job is actually a JobGroup, add the task numbering argument

        if isinstance(job, JobGroup):