from CCP4PluginScript import CInternalPlugin,CPluginScript
from PyQt4 import QtCore
import os,glob,re,time,sys
import CCP4XtalData
from lxml import etree
import math
import CCP4Modules,CCP4Utils

class pdb_extract_wrapper(CPluginScript):
    TASKMODULE = 'wrappers'                               # Where this plugin will appear on the gui
    TASKTITLE = 'pdb_extract_wrapper'     # A short title for gui menu
    DESCRIPTION = 'Run pdb_extract'
    TASKNAME = 'pdb_extract_wrapper'                                  # Task name - should be same as class name
    TASKCOMMAND = 'pdb_extract'                                     # The command to run the executable
    TASKVERSION= 0.0                                     # Version of this plugin
    ASYNCHRONOUS = False
    TIMEOUT_PERIOD = 9999999.9
    #WHATNEXT = ['coot_rebuild','parrot','buccaneer_build_refine_mr']
    RUNEXTERNALPROCESS=False

    ERROR_CODES = {  200 : { 'description' : 'Failed to add item to mol list' },201 : { 'description' : 'Failed to setFullPath' },}
    
    def process(self):
        self.xmlroot = etree.Element('pdb_extract_wrapper')
        
        invalidFiles = self.checkInputData()
        if len(invalidFiles)>0:
            self.reportStatus(CPluginScript.FAILED)
        self.checkOutputData()
        
        PDB_EXTRACT_DIR = os.path.normpath(os.path.join(CCP4Utils.getCCP4I2Dir(),'pipelines','PrepareDeposit','wrappers','pdb_extract_wrapper'))
        envEdit = [['PDB_EXTRACT',PDB_EXTRACT_DIR]]
        envEdit.append(['PWD',os.path.normpath(self.getWorkDirectory())])
        
        if self.container.inputData.ENTRYDATAIN.isSet():
            argList = ['-r','refmac5','-ipdb',self.container.inputData.XYZIN.__str__(),'-iENT',self.container.inputData.ENTRYDATAIN.__str__()]
            print 'Arglist',argList
            print 'envEdit',envEdit
            p = CCP4Modules.LAUNCHER().launch(viewer='pdb_extract', argList = argList, callBack = self.handleFinished, envEdit=envEdit,logFile = self.makeFileName('LOG'))
            p.waitForFinished(-1)
        else:
            argList = ['-pdb',self.container.inputData.XYZIN.__str__()]
            print 'Arglist',argList
            print 'envEdit',envEdit
            p = CCP4Modules.LAUNCHER().launch(viewer='extract', argList = argList, callBack = self.handleFinished, envEdit=envEdit,logFile = self.makeFileName('LOG'))
            p.waitForFinished(-1)
        return CPluginScript.SUCCEEDED

    def handleFinished(self,exitCode,exitStatus):
        if not self.container.inputData.ENTRYDATAIN.isSet():
            entryPath = os.path.normpath(os.path.join(self.getWorkDirectory(),'data_template.text'))
            self.container.outputData.ENTRYDATA.setFullPath(entryPath)
        else:
            filePath = os.path.normpath(os.path.join(self.getWorkDirectory(),'pdb_extract.mmcif'))
            self.container.outputData.CIFFILE.setFullPath(filePath)
            print 'pdb_extract.mmcif',self.container.outputData.CIFFILE.__str__(), os.path.isfile(self.container.outputData.CIFFILE.__str__())
        with open(self.makeFileName('PROGRAMXML'),'w') as programXML:
            programXML.write(etree.tostring(self.xmlroot,pretty_print=True))
        
        self.reportStatus(CPluginScript.SUCCEEDED)