#!/usr/bin/python
'''Utility classes with implementation details that are common to wrapping NEXUS-based programs'''
import os
from PIPRes.basic import writeTreesBlock, writeNexusDataMatrix
from PIPRes.wrap.external_program import *
import threading
_LOG = cipresGetLogger('pipres.wrap.nexus_program_server.py')

class WrapNexusProgram(WrapExternalProgram):
    '''This class implements the intersection of functionality between the mb and paup wrappers.'''
    def _createTempDataFile(self, **kwargs):
        '''returns (tempDirectory, fileName, openFileStream, toExternalTranslation, treeTaxLabels) with the matrix and tree already written to the fileStream.
kwargs can contain:
    tree
    matrix
    writeMatrix (boolean def = True)
    writeTree (boolean def = True)
    supportsTaxaSubsets  (boolean def = False)
    dirPref
    filename (default = data.nex)
    writePoundNexus (boolean def = True)
    
The field self.mappedTree will be overwritten.
    '''
        tree = kwargs.get('tree')
        matrix = kwargs.get('matrix')
        dirPref = kwargs.get('dirPref', 'wrap')
        supportsTaxaSubsets = kwargs.get('supportsTaxaSubsets', False)
        
        if tree is not None and not supportsTaxaSubsets:
           self.mappedTree, treeTaxLabels, rows, fromExternalTranslation = mapTreeToLeafSubset(tree)
        else:
            self.mappedTree, treeTaxLabels, rows, fromExternalTranslation = None, [], None, None
        tempDirectory = makeCipresTempDir(prefix=dirPref)
        _LOG.debug('created directory %s' % tempDirectory)
        filename = kwargs.get('filename', 'data' + os.path.extsep + 'nex')
        filePath = os.path.join(tempDirectory, filename)
        f = open(filePath, 'w')
        if kwargs.get('writePoundNexus', True):
            f.write('#NEXUS\n')
        if matrix is not None and kwargs.get('writeData', True):
            _LOG.debug('writing matrix to ' + filename)
            writeNexusDataMatrix(matrix, f, rowSlice = rows)
        if tree is not None and kwargs.get('writeTree', True):
            treeToWrite = supportsTaxaSubsets and tree or self.mappedTree
            writeTreesBlock(f, [treeToWrite], treeTaxLabels)
        return ExternalInvocationContext(   
                tempDir=tempDirectory, 
                filename=filename, 
                fileObj=f, 
                fromExternalTranslation=fromExternalTranslation,
                treeTaxLabels=treeTaxLabels)

class SimpleNexusWrapperServer(SimpleServer, WrapNexusProgram):
    def __init__(self, registry):
        SimpleServer.__init__(self, registry)
        self.nexusReader = None
        self.runningProcesses = [] #children to be killed on exit
        self.exiting = False
        self.nexusReaderLock = threading.Lock()
    def getUIXml(self):
        return ''
    def __del__(self):
        try:
            self.nexusReaderLock.acquire()
        except:
            sys.exit('YIKES')
        try:
            self.exiting = True
            _LOG.debug('__del__() called')
            self.removeServants()
        finally:
            self.nexusReaderLock.release()
        
    def remove(self):
        try:
            self.nexusReaderLock.acquire()
        except:
            sys.exit('YIKES')
        try:
            self.exiting = True
            _LOG.debug('remove() called')
            self.removeServants()
        finally:
            self.nexusReaderLock.release()            
        SimpleServer.remove(self)

    def removeServants(self): 
        _LOG.debug('removeServants()')
        if self.nexusReader is not None:
            try:
                _LOG.debug('Releasing NexusReader')
                self.nexusReader.remove()
                self.nexusReader = None
            except:
                logException(_LOG)
        WrapExternalProgram.killChildProcesses(self.runningProcesses)
    def userCommands(self): 
        '''Returns a string that is a concatenation of all of the 
        commands sent using "execute()".
        This is simply self.userConfigCmdList joined with spaces.'''
        return ' '.join(self.userConfigCmdList)