#!/usr/bin/python
from PIPRes.util.io import getCipresTestFileDir, expandPath, getCipresTmpDir
from PIPRes.util.cipres import getCipresProperty
from PIPRes.testing import *
_LOG = cipresGetLogger('test_cipres.test_read_nexus')

parDir = getCipresTmpDir()

test_install_dir = os.path.dirname(__file__)
pipres_root = os.path.dirname(test_install_dir)
testFilesDir = os.path.join(pipres_root, 'test', 'files')
installTestFileDir = os.path.join(test_install_dir, 'files')


            
class TestReadNexus(CipresTestingClient):
    serviceRegistryEntry = composeRegistryQuery(interface='ReadNexus')
    serviceType = CipresIDL_api1.ReadNexus
    def implPathMatrixTest(self, fileMatrixPairs):
        for path, expectedTaxa, expectedMatrix in fileMatrixPairs:
            dataFile = expandPath(path)
            if os.path.exists(dataFile):
                content = getContentFromNexus(dataFile, treatStringAsPath = True)
                triple = content[0]
                matrix = triple.matrixList[0]
                self.assertEqual(triple.taxa, expectedTaxa)
                self.assertEqual(matrix, expectedMatrix)
            else:
                _LOG.warn('%s not found!, test skipped.' % dataFile)
    def implTestFile(self, fileName):
        _LOG.debug('testing NEXUS reader on %s' % fileName)
        triple = getContentFromNexus(fileName, treatStringAsPath = True)[0]
        if len(triple.matrixList) == 0:
            _LOG.debug('No matrix found in %s' % fileName)
            return
        matrix = triple.matrixList[0]
        tmpFD, fn = tempfile.mkstemp(suffix = '.nex', dir=parDir)
        try:
            try:
                tempFile = os.fdopen(tmpFD, 'w')
            except:
                os.close(tmpFD)
                raise
            try:
                tempFile.write('#NEXUS\n')
                #_LOG.warn(str(matrix.symbolLookup))
                writeNexusDataMatrix(tempFile, matrix, triple.taxa)
                if triple.treeList:
                    triple.treeList = [CipresTree(i) for i in triple.treeList]
                    writeTreesBlock(tempFile, triple.treeList, triple.taxa)
                tempFile.flush()
                sec = getContentFromNexus(fn, treatStringAsPath = True)[0]
                self.assertEqual(sec.matrixList[0], matrix)
                for i, t in enumerate(triple.treeList):
                    self.assertEquals(t, CipresTree(sec.treeList[i]))
                self.assertEquals(sec.taxa, triple.taxa)
            finally:
                tempFile.close()
            
        finally:
            os.remove(fn)
            
    def implEnvFileListTests(self, parPath, fileList):
        if not os.path.exists(parPath):
            _LOG.warn('some tests were skipped because the directory %s does not exist' % parPath)
            return
        for file in fileList:
            dataFile = os.path.join(parPath, file)
            _LOG.debug('testing %s' % dataFile)
            if os.path.exists(dataFile):
                self.implTestFile(dataFile)
            else:
                _LOG.warn('%s not found!, test skipped.' % dataFile)

    def testSimple(self):
        '''This just reads a file with the NEXUS reader, writes it out (using python), reads it again, and verifies that the CipresIDL_api1.DataMatrix from both parsings are identical.'''
        filesToTest = [
            'from_hell.nex',
            'taylor.nex'
            ]
        self.implEnvFileListTests(test_install_dir, filesToTest)

    def testInternalPoundNEXUS(self):
        self.implEnvFileListTests(test_install_dir, ['internalPoundNexus.nex'])

    def testMatrix(self):
        fileTaxaMatrixTuples = [ 
            (   os.path.join(testFilesDir, 'from_hell.nex'),
                ['a b', 'c d', "e' 'f", 'g h'],
                CipresIDL_api1.DataMatrix('ACGT?N', 4L, 10L, [[0], [1], [2], [3], [-1, 0, 1, 2, 3], [0, 1, 2, 3]], 
                    [
                        [ 4,  5, -1, -1, -1, 1, 1, 0, 0, 0],
                        [-1, -1, -1, -1, -1, 1, 1, 0, 0, 0],
                        [ 4,  4,  4,  4,  4, 0, 3, 1, 2, 2],
                        [ 5,  5,  5,  5,  5, 0, 3, 1, 2, 2],
                    ], CipresIDL_api1.DNA_DATATYPE)
            ),
            ]
        self.implPathMatrixTest(fileTaxaMatrixTuples)

    def testPipres(self):
        '''This just reads a file with the NEXUS reader, writes it out (using python), reads it again, and verifies that the CipresIDL_api1.DataMatrix from both parsings are identical.'''
        filesToTest = [
            '12Tx432C.nex',
            ]
        self.implEnvFileListTests(testFilesDir, filesToTest)

    def testFiles(self):
        someFiles = [ 'rbcl500TPaupTree.nex', 'mrB_9Tx720C.nex', 'rbcl500T.nex', 'TestNexusFile.nex',]
        someMoreFiles = 'SLOW_CIPRES_TESTS' in os.environ and  ['11361Tx1360C.nex', '12Tx432C.nex', '49Tx2543C.nex', '500Tx759C.nex', '567Tx2153C.nex', '7180Tx1359C.nex'] or []
        self.implEnvFileListTests(testFilesDir, someFiles + someMoreFiles)
        
    def _testMBFiles(self):
        self.implEnvFileListTests(None, [os.path.abspath('/Applications'), 'PhylogenetiX','MrBayes_V3.0_mac'], ['adh.nex', 'anolis.nex', 'avian_ovomucoids.nex', 'bglobin.nex', 'replicase.nex'])

if __name__ == '__main__':
    if '-f' in sys.argv:
        def fast(self):
            print 'test skipped - fast mode'
        TestReadNexus.testFiles = fast
        sys.argv.remove('-f')
    try:
        nexusReader = TestReadNexus.getTestingRegistry().getServiceOrThrow(CipresIDL_api1.ReadNexus)
        nexusReader.remove()
    except:
        logException(_LOG)
        _LOG.warn('Tests skipped: Registry error')
        sys.exit(0)
    main()