#!/usr/bin/env python

#Copyright (C) 2009-2011 by Benedict Paten (benedictpaten@gmail.com)
#
#Released under the MIT license, see LICENSE.txt
import unittest
import sys
import os
from sonLib.bioio import logger
from cactus.shared.test import parseCactusSuiteTestOptions
from sonLib.bioio import TestStatus
from sonLib.bioio import system
from sonLib.bioio import getTempDirectory
from sonLib.bioio import getLogLevelString

from cactus.shared.test import getCactusInputs_random
from cactus.shared.test import getCactusWorkflowExperimentForTest

from cactus.shared.common import runCactusSetup
from cactus.shared.common import runCactusAligner


class TestCase(unittest.TestCase):

    def setUp(self):
        self.testNo = TestStatus.getTestSetup(1,5, 50, 0)
        unittest.TestCase.setUp(self)
       
    def testCactusAligner(self):
        """Tests cactus aligner, using the dummy aligner.
        """
        for test in xrange(self.testNo): 
            runAligner()
            
    def testCactusAlignerWithBatchBlast(self):
        """Tests cactus aligner, using the dummy aligner.
        """
        for test in xrange(self.testNo): 
            runAligner(useDummy=False)
    
def runAligner(useDummy=True):       
    ##########################################
    #Make inputs
    ##########################################
    
    tempDir = getTempDirectory(".")
    tempAlignmentFile = os.path.join(tempDir, "tempAlignment.cigar")
    
    sequenceDirs, newickTreeString = getCactusInputs_random(tempDir=getTempDirectory(tempDir))
    outputDir = getTempDirectory(tempDir)
    
    experiment = getCactusWorkflowExperimentForTest(sequenceDirs, newickTreeString, outputDir)
    cactusDiskDatabaseString = experiment.getDatabaseString()
    
    runCactusSetup(cactusDiskDatabaseString, sequenceDirs, newickTreeString)
    logger.info("Setup the test, running cactus aligner")
    
    ##########################################
    #Do actual run
    ##########################################
    
    runCactusAligner(cactusDiskDatabaseString, tempAlignmentFile, 
                     tempDir=getTempDirectory(tempDir), useDummy=useDummy)
    runCactusAligner(cactusDiskDatabaseString, tempAlignmentFile, \
                     tempDir=getTempDirectory(tempDir), useDummy=useDummy) #Run it twice to check blockicity
    logger.info("Ran cactus aligner")
    
    if getLogLevelString() == "DEBUG":
        system("cat %s" % tempAlignmentFile)
    
    #Cleanup
    experiment.cleanupDatabase()
    system("rm -rf %s" % tempDir)

def main():
    parseCactusSuiteTestOptions()
    sys.argv = sys.argv[:1]
    unittest.main()
        
if __name__ == '__main__':
    main()