#!/usr/bin/env python

# Copyright INRA (Institut National de la Recherche Agronomique)
# http://www.inra.fr
# http://urgi.versailles.inra.fr
#
# This software is governed by the CeCILL license under French law and
# abiding by the rules of distribution of free software.  You can  use, 
# modify and/ or redistribute the software under the terms of the CeCILL
# license as circulated by CEA, CNRS and INRIA at the following URL
# "http://www.cecill.info". 
#
# As a counterpart to the access to the source code and  rights to copy,
# modify and redistribute granted by the license, users are provided only
# with a limited warranty  and the software's author,  the holder of the
# economic rights,  and the successive licensors  have only  limited
# liability. 
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# In this respect, the user's attention is drawn to the risks associated
# with loading,  using,  modifying and/or developing or reproducing the
# software by the user in light of its specific status of free software,
# that may mean  that it is complicated to manipulate,  and  that  also
# therefore means  that it is reserved for developers  and  experienced
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import os
import sys
from ConfigParser import NoSectionError, NoOptionError
from commons.core.checker.CheckerUtils import CheckerUtils
from commons.core.checker.CheckerException import CheckerException
from commons.core.utils.FileUtils import FileUtils
from commons.core.seq.FastaUtils import FastaUtils

class PrepareBatches(object):
    
    def __init__(self, pipelineName, projectDir, projectName, iConfig, verbose):
        self._pipelineName = pipelineName
        self._projectDir = projectDir
        self._projectName = projectName
        self._iConfig = iConfig
        self._verbose = verbose
        
    def run(self):
        if self._verbose > 0:
            print "beginning of step 1"
            sys.stdout.flush()
        if FileUtils.isRessourceExists("%s_db" % self._projectName):
            print "ERROR: directory '%s_db' already exists" % self._projectName
            sys.exit(1)
        
        os.mkdir("%s_db" % self._projectName)
        os.chdir("%s_db" % self._projectName)
        genomeFastaFileName = "%s.fa" % self._projectName
        os.symlink("../%s" % genomeFastaFileName, genomeFastaFileName)
        sectionName = "prepare_batches"
        self._checkConfig(sectionName)  
        
        separator = "\n"
        inGenomeFileHandler = open(genomeFastaFileName, "r")
        try:
            CheckerUtils.checkHeaders(inGenomeFileHandler)
        except CheckerException, e:
            print "Error in file %s. Wrong headers are :" % genomeFastaFileName
            print separator.join(e.messages)
            print "Authorized characters are : a-z A-Z 0-9 - . : _\n"
            inGenomeFileHandler.close()
            sys.exit(1)
        inGenomeFileHandler.close()

        doClean = False
        if self._iConfig.get(sectionName, "clean") == "yes":
            doClean = True
        chunkFilePrefix = "%s_chunks" % self._projectName
        chunkLength = int(self._iConfig.get(sectionName, "chunk_length"))
        chunkOverlap = int(self._iConfig.get(sectionName, "chunk_overlap"))
        FastaUtils.dbChunks(genomeFastaFileName, chunkLength, chunkOverlap, 0, chunkFilePrefix, doClean, self._verbose)
        
        nbSeq = int(self._iConfig.get(sectionName, "nb_seq_per_batch"))
        FastaUtils.splitFastaFileInBatches("%s.fa" % chunkFilePrefix, nbSeq * chunkLength)

        if self._iConfig.get(sectionName, "clean") == "yes":
            FileUtils.removeFilesByPattern("%s.fa*" % self._projectName)
            
        os.chdir( ".." )
        if self._verbose > 0:
            print "step 1 finished successfully"
            sys.stdout.flush()

    def _checkConfig(self, sectionName):
        try:
            CheckerUtils.checkSectionInConfigFile(self._iConfig, sectionName)
        except NoSectionError:
            print "ERROR: the section %s must be in your configuration file" % sectionName
            sys.exit(1)
        try:
            CheckerUtils.checkOptionInSectionInConfigFile(self._iConfig, sectionName, "chunk_length")
        except NoOptionError:
            print "ERROR: the option 'chunk_length' must be defined in %s in your configuration file" % sectionName
            sys.exit(1)
        try:
            CheckerUtils.checkOptionInSectionInConfigFile(self._iConfig, sectionName, "chunk_overlap")
        except NoOptionError:
            print "ERROR: the option 'chunk_overlap' must be defined in %s in your configuration file" % sectionName
            sys.exit(1)
        try:
            CheckerUtils.checkOptionInSectionInConfigFile(self._iConfig, sectionName, "nb_seq_per_batch")
        except NoOptionError:
            print "ERROR: the option 'nb_seq_per_batch' must be defined in %s in your configuration file" % sectionName
            sys.exit(1)
        try:
            CheckerUtils.checkOptionInSectionInConfigFile(self._iConfig, sectionName, "resources")
        except NoOptionError:
            print "ERROR: the option 'resources' must be defined in %s in your configuration file" % sectionName
            sys.exit(1)
        try:
            CheckerUtils.checkOptionInSectionInConfigFile(self._iConfig, sectionName, "tmpDir")
        except NoOptionError:
            print "ERROR: the option 'tmpDir' must be defined in %s in your configuration file" % sectionName
            sys.exit(1)