# Copyright 2013, Institute for Bioninformatics and Evolutionary Studies
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#    http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# See the License for the specific language governing permissions and
# limitations under the License.
import os
import time
import sys
import traceback
# from copy import deepcopy
from ARC import exceptions
from ARC import logger
from ARC.runners import Base
from ARC.runners import Finisher
# from ARC.runner import AssemblyChecker
class AssemblyChecker(Base):
    Checks for "finished" files in each of the assembly folders. Set values of params['assemblies'] to True for
    all finished assemblies. If all assemblies are finished, kick off the finisher process.
    required params:
        'targets': dictionary, keys are paths, values are boolean
    def message(self):
        return 'Starting AssemblyChecker for sample %s' % self.params['sample']
    def start(self):
        """ run through list of targets, check any that haven't finished already """
        sample = self.params['sample']
        completed = sum(self.params['targets'].values())
        logger.info("Sample: %s AssemblyChecker started with %s of %s targets completed" % (sample, completed, len(self.params['targets'])))
        for target_folder in self.params['targets']:
            if not self.params['targets'][target_folder]:
                f = os.path.join(target_folder, 'finished')
                if os.path.exists(f):
                    self.params['targets'][target_folder] = True
                    logger.info("%s exists" % f)
                    completed += 1
        #Now check whether all have finished, if not, add a new AssemblyChecker to the queue
        if len(self.params['targets']) > sum(self.params['targets'].values()):
            #some jobs haven't completed yet
            checker_params = {}
            for k in self.params:
                checker_params[k] = self.params[k]
            #checker_params = deepcopy(self.params)
            # checker = AssemblyChecker(checker_params)
            time.sleep(5)  # sleep 5 seconds before putting a checker back on the job_q
            logger.info("Sample: %s Assemblies not finished: %s of %s targets completed" % (sample, completed, len(self.params['targets'])))
            params = {}
            for k in self.params:
                params[k] = self.params[k]
            # params = deepcopy(self.params)
            # finisher = Finisher(params)
            logger.debug("Sample: %s, iteration %s, Submitting finisher job to queue." % (sample, self.params['iteration']))
            logger.info("Sample: %s Assemblies finished: %s of %s targets completed" % (sample, completed, len(self.params['targets'])))