<commit_before>from multiprocessing import Pool
from multiprocessing import Process
import sys
import os
import argparse
from CPAC.pipeline import cpac_pipeline


def get_vectors(strat):

    paths = []
    def dfs(val_list, path):

        if val_list == []:
            paths.append(path)

        else:
            vals = val_list.pop()
            for val in vals:
                if path == '':
                    dfs(list(val_list), str(val))
                else:
                    dfs(list(val_list), str(val) + '#' + path)


    val_list = []

    for key in sorted(strat.keys()):
        val_list.append(strat[key])

    dfs(val_list, '')

    print paths
    return paths


def make_enteries(paths, path_iterables):

    enteries = []
    idx = 1
    for path in sorted(paths):

        sub_enteries = []
        values = path.split('#')

        indx = 0
        for value in values:

            if '[' or '(' in value:

                value = value.strip('[]')
                value = value.strip('()')

            if ',' in value:
                import re
                value = re.sub(r',', '.', value)
                value = re.sub(r' ', '', value)
            sub_enteries.append(path_iterables[indx] + '_' + value)
            indx += 1


        enteries.append(sub_enteries)

    return enteries



def build_strategies(configuration):

    import collections

    path_iterables = ['_gm_threshold', '_wm_threshold', '_csf_threshold', '_threshold', '_compcor', '_target_angle_deg']
    non_strategy_iterables = ['_fwhm', '_hp', '_lp', '_bandpass_freqs']

    proper_names = {'_threshold':'Scrubbing Threshold = ', '_csf_threshold':'Cerebral Spinal Fluid Threshold = ',
                    '_gm_threshold':'Gray Matter Threshold = ',
                    'nc':'Compcor: Number Of Components = ', '_compcor':'Nuisance Signal Corrections = ',
                    '_target_angle_deg':'Median Angle Correction: Traget Angle in Degree = ', '_wm_threshold':'White Matter Threshold = '}


    config_iterables = {'_gm_threshold': eval('configuration.grayMatterThreshold'), '_wm_threshold': eval('configuration.whiteMatterThreshold'), '_csf_threshold': eval('configuration.cerebralSpinalFluidThreshold'), '_threshold': eval('configuration.scrubbingThreshold'), '_compcor': eval('configuration.Corrections'), '_target_angle_deg': eval('configuration.targetAngleDeg')}


    ### This is really dirty code and ordering of corrections in 
    ### in output directory is dependant on the nuisance workflow
    ### when the workflow is changed , change this section as well
    corrections_order = ['pc1', 'linear', 'wm', 'global', 'motion', 'quadratic', 'gm', 'compcor', 'csf']


    corrections_dict_list = config_iterables['_compcor']


    print corrections_dict_list

    main_all_options = []
    for corrections_dict in corrections_dict_list:
        string = ""
        for correction in corrections_order:

            string += correction + str(corrections_dict[correction]) + '.'

        string = string[0:len(string) -1]



        cmpcor_components = eval('configuration.nComponents')


        all_options = []
        for comp in cmpcor_components:

            all_options.append('ncomponents_%d' %comp + '_selector_' + string)

        main_all_options.append(str(str(all_options).strip('[]')).strip('\'\''))


    config_iterables['_compcor'] = main_all_options


    ############

    paths = get_vectors(config_iterables)

    strategy_enteries = make_enteries(paths, sorted(path_iterables))

    return strategy_enteries




def run_sge_jobs(c, config_file, strategies_file, subject_list_file):


    import commands
    import pickle
    from time import strftime

    path, fname = os.path.split(os.path.realpath(subject_list_file))
    sys.path.append(path)
    s = __import__(fname.split('.')[0])

    sublist = s.subjects_list

    shell = commands.getoutput('echo $SHELL')

    temp_files_dir = os.path.join(os.getcwd(), 'cluster_temp_files')
    subject_bash_file = os.path.join(temp_files_dir, 'submit_%s.sge' % str(strftime("%Y_%m_%d_%H_%M_%S")))
    f = open(subject_bash_file, 'w')
    print >>f, '#! %s' % shell
    print >>f, '#$ -cwd'
    print >>f, '#$ -S %s' % shell
    print >>f, '#$ -V'
    print >>f, '#$ -t 1-%d' % len(sublist)
    print >>f, '#$ -q %s' % c.queue
    print >>f, '#$ -pe %s %d' % (c.parallelEnvironment, c.numCoresPerSubject)
    print >>f, '#$ -e %s' % os.path.join(temp_files_dir, 'c-pac_%s.err' % str(strftime("%Y_%m_%d_%H_%M_%S")))
    print >>f, '#$ -o %s' % os.path.join(temp_files_dir, 'c-pac_%s.out' % str(strftime("%Y_%m_%d_%H_%M_%S")))
    print >>f, 'source ~/.bashrc'

#    print >>f, "python CPAC.pipeline.cpac_pipeline.py -c ", str(config_file), " -s ", subject_list_file, " -indx $SGE_TASK_ID  -strategies ", strategies_file
    print >>f, "python -c \"import CPAC; CPAC.pipeline.cpac_pipeline.run('%s','%s',$SGE_TASK_ID,'%s') \" " % (str(config_file), subject_list_file, strategies_file)

    f.close()

    commands.getoutput('chmod +x %s' % subject_bash_file )
    print commands.getoutput('qsub  %s ' % (subject_bash_file))


def run_pbs_jobs(c, config_file, strategies_file, subject_list_file):



    import commands
    import pickle<commit_msg>attempting sge with cpac_pipeline path from package installed<commit_after>from multiprocessing import Pool
from multiprocessing import Process
import sys
import os
import argparse
from CPAC.pipeline import cpac_pipeline


def get_vectors(strat):

    paths = []
    def dfs(val_list, path):

        if val_list == []:
            paths.append(path)

        else:
            vals = val_list.pop()
            for val in vals:
                if path == '':
                    dfs(list(val_list), str(val))
                else:
                    dfs(list(val_list), str(val) + '#' + path)


    val_list = []

    for key in sorted(strat.keys()):
        val_list.append(strat[key])

    dfs(val_list, '')

    print paths
    return paths


def make_enteries(paths, path_iterables):

    enteries = []
    idx = 1
    for path in sorted(paths):

        sub_enteries = []
        values = path.split('#')

        indx = 0
        for value in values:

            if '[' or '(' in value:

                value = value.strip('[]')
                value = value.strip('()')

            if ',' in value:
                import re
                value = re.sub(r',', '.', value)
                value = re.sub(r' ', '', value)
            sub_enteries.append(path_iterables[indx] + '_' + value)
            indx += 1


        enteries.append(sub_enteries)

    return enteries



def build_strategies(configuration):

    import collections

    path_iterables = ['_gm_threshold', '_wm_threshold', '_csf_threshold', '_threshold', '_compcor', '_target_angle_deg']
    non_strategy_iterables = ['_fwhm', '_hp', '_lp', '_bandpass_freqs']

    proper_names = {'_threshold':'Scrubbing Threshold = ', '_csf_threshold':'Cerebral Spinal Fluid Threshold = ',
                    '_gm_threshold':'Gray Matter Threshold = ',
                    'nc':'Compcor: Number Of Components = ', '_compcor':'Nuisance Signal Corrections = ',
                    '_target_angle_deg':'Median Angle Correction: Traget Angle in Degree = ', '_wm_threshold':'White Matter Threshold = '}


    config_iterables = {'_gm_threshold': eval('configuration.grayMatterThreshold'), '_wm_threshold': eval('configuration.whiteMatterThreshold'), '_csf_threshold': eval('configuration.cerebralSpinalFluidThreshold'), '_threshold': eval('configuration.scrubbingThreshold'), '_compcor': eval('configuration.Corrections'), '_target_angle_deg': eval('configuration.targetAngleDeg')}


    ### This is really dirty code and ordering of corrections in 
    ### in output directory is dependant on the nuisance workflow
    ### when the workflow is changed , change this section as well
    corrections_order = ['pc1', 'linear', 'wm', 'global', 'motion', 'quadratic', 'gm', 'compcor', 'csf']


    corrections_dict_list = config_iterables['_compcor']


    print corrections_dict_list

    main_all_options = []
    for corrections_dict in corrections_dict_list:
        string = ""
        for correction in corrections_order:

            string += correction + str(corrections_dict[correction]) + '.'

        string = string[0:len(string) -1]



        cmpcor_components = eval('configuration.nComponents')


        all_options = []
        for comp in cmpcor_components:

            all_options.append('ncomponents_%d' %comp + '_selector_' + string)

        main_all_options.append(str(str(all_options).strip('[]')).strip('\'\''))


    config_iterables['_compcor'] = main_all_options


    ############

    paths = get_vectors(config_iterables)

    strategy_enteries = make_enteries(paths, sorted(path_iterables))

    return strategy_enteries




def run_sge_jobs(c, config_file, strategies_file, subject_list_file):


    import commands
    import pickle
    from time import strftime

    path, fname = os.path.split(os.path.realpath(subject_list_file))
    sys.path.append(path)
    s = __import__(fname.split('.')[0])

    sublist = s.subjects_list

    shell = commands.getoutput('echo $SHELL')

    temp_files_dir = os.path.join(os.getcwd(), 'cluster_temp_files')
    subject_bash_file = os.path.join(temp_files_dir, 'submit_%s.sge' % str(strftime("%Y_%m_%d_%H_%M_%S")))
    f = open(subject_bash_file, 'w')
    print >>f, '#! %s' % shell
    print >>f, '#$ -cwd'
    print >>f, '#$ -S %s' % shell
    print >>f, '#$ -V'
    print >>f, '#$ -t 1-%d' % len(sublist)
    print >>f, '#$ -q %s' % c.queue
    print >>f, '#$ -pe %s %d' % (c.parallelEnvironment, c.numCoresPerSubject)
    print >>f, '#$ -e %s' % os.path.join(temp_files_dir, 'c-pac_%s.err' % str(strftime("%Y_%m_%d_%H_%M_%S")))
    print >>f, '#$ -o %s' % os.path.join(temp_files_dir, 'c-pac_%s.out' % str(strftime("%Y_%m_%d_%H_%M_%S")))
    print >>f, 'source ~/.bashrc'

#    print >>f, "python CPAC.pipeline.cpac_pipeline.py -c ", str(config_file), " -s ", subject_list_file, " -indx $SGE_TASK_ID  -strategies ", strategies_file
    print >>f, "python -c \"import CPAC; CPAC.pipeline.cpac_pipeline.run(\"%s\" , \"%s\", str($SGE_TASK_ID) , \"%s\") \" " % (str(config_file), subject_list_file, strategies_file)

    f.close()

    commands.getoutput('chmod +x %s' % subject_bash_file )
    print commands.getoutput('qsub  %s ' % (subject_bash_file))


def run_pbs_jobs(c, config_file, strategies_file, subject_list_file):



    import commands
    import pickle
{'fraction_non_alphanumeric': 0.14494403339024853, 'fraction_numerical': 0.0015177385695313982, 'mean_word_length': 3.044112006137323, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 51, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '4011147', 'n_tokens_mistral': 3616, 'n_tokens_neox': 3384, 'n_words': 725}