"""
    pointless_reindexToMatch: CCP4 GUI Project
    Copyright (C) 2014 Newcastle University
    
    This library is free software: you can redistribute it and/or
    modify it under the terms of the GNU Lesser General Public License
    version 3, modified in accordance with the provisions of the
    license to address the requirements of UK law.
    
    You should have received a copy of the modified GNU Lesser General
    Public License along with this library.  If not, copies may be
    downloaded from http://www.ccp4.ac.uk/ccp4license.php
    
    This program is distributed in the hope that it will be useful,S
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU Lesser General Public License for more details.
    """

from CCP4PluginScript import CPluginScript
import CCP4ErrorHandling
from lxml import etree
import sys, os


class pointless_reindexToMatch(CPluginScript):
    TASKNAME = 'pointless_reindexToMatch'
    TASKCOMMAND = 'pointless'
    TASKVERSION= 0.0
    ASYNCHRONOUS = False
    
    ERROR_CODES = { 201 : {'description' : 'Failed to make input files' }, 202 : {'description' : 'Failed to make output files' }, 203 : {'description' : 'Failed to identify a best reindexing' }}
    
    
    def formatCellLength(self, p):
        return "%7.1f" % float(p)

    def formatCellAngle(self, p):
        return "%7.1f" % (float(p) * 57.29577951308233)

    def shortformatCell(self, cell):
        s = ""
        s += self.formatCellLength(cell.a).strip()+','
        s += self.formatCellLength(cell.b).strip()+','
        s += self.formatCellLength(cell.c).strip()+','
        s += self.formatCellAngle(cell.alpha).strip()+','
        s += self.formatCellAngle(cell.beta).strip()+','
        s += self.formatCellAngle(cell.gamma).strip()
        return s

    def makeCommandAndScript(self):
        par = self.container.controlParameters
        self.mergedFilename = os.path.join(self.workDirectory,'MergedToReindex.mtz')
        self.appendCommandScript("XMLOUT %s" % str( self.makeFileName( 'PROGRAMXML' )))
        if str(self.container.controlParameters.REFERENCE) == 'HKLIN_FOBS_REF':
            self.appendCommandLine(['HKLREF',str(self.container.inputData.HKLIN_FOBS_REF.fullPath)])
        elif str(self.container.controlParameters.REFERENCE) == 'HKLIN_FC_REF':
            self.appendCommandLine(['HKLREF',str(self.container.inputData.HKLIN_FC_REF.fullPath)])
        elif str(self.container.controlParameters.REFERENCE) == 'HKLIN_FMAP_REF':
            self.appendCommandLine(['HKLREF',str(self.container.inputData.HKLIN_FMAP_REF.fullPath)])
        elif str(self.container.controlParameters.REFERENCE) == 'XYZIN_REF':
            self.appendCommandLine(['XYZIN',str(self.container.inputData.XYZIN_REF.fullPath)])
        elif str(self.container.controlParameters.REFERENCE) == 'SPECIFY':
            if self.container.controlParameters.CHOOSE_SPACEGROUP.isSet():
                self.appendCommandScript('spacegroup '+str(self.container.controlParameters.CHOOSE_SPACEGROUP))
                # always put in reindex operator if space group is set                 
                # if self.container.controlParameters.REINDEX_OPERATOR.isSet():
                self.appendCommandScript("reindex %s, %s, %s" % (par.REINDEX_OPERATOR.h,par.REINDEX_OPERATOR.k,par.REINDEX_OPERATOR.l))
        mergedFilename = os.path.join(self.workDirectory,'MergedToReindex.mtz')
        self.appendCommandLine(['HKLIN',mergedFilename])
        reindexedFilename = os.path.join(self.workDirectory,'Reindexed.mtz')
        self.appendCommandLine(['HKLOUT',reindexedFilename])
        return CPluginScript.SUCCEEDED

    def processInputFiles(self):
        try:
            self.container.inputData.F_SIGF.loadFile()
            colList = self.container.inputData.F_SIGF.fileContent.getListOfColumns()
            print '\n\n\n\n F_SIGF',self.container.inputData.F_SIGF
            print '\n\n\n\n fileContent',self.container.inputData.F_SIGF.fileContent
            print '\n\n\n\n colList',colList
            fSigFLabelList = [str(column.get('columnLabel')) for column in colList]
            self.fSigFLabelsString = ','.join(fSigFLabelList)
            fileList = []
            fileList += [(str(self.container.inputData.F_SIGF.fullPath), self.fSigFLabelsString, self.fSigFLabelsString)]
            if self.container.inputData.FREERFLAG.isSet():
                colList = self.container.inputData.FREERFLAG.fileContent.getListOfColumns()
                freeRFlagLabelList = [str(column.columnLabel) for column in colList]
                self.freeRFlagLabelsString = ','.join(freeRFlagLabelList)
                fileList += [(str(self.container.inputData.FREERFLAG.fullPath), self.freeRFlagLabelsString, self.freeRFlagLabelsString)]
            mergedFilename = os.path.join(self.workDirectory,'MergedToReindex.mtz')
            rv = self.joinMtz(mergedFilename, fileList)
            return rv
        except:
            self.appendErrorReport(201,'Pointless_reindexToMatch: processInputFiles: exception in process')
            return CPluginScript.FAILED

    def processOutputFiles(self):
        try:
            outputFilesList = ['F_SIGF_OUT']
            outputColumnsList  = [self.fSigFLabelsString]
            outputContentsList = [1]
            if self.container.inputData.FREERFLAG.isSet():
                outputFilesList += ['FREERFLAG_OUT']
                outputColumnsList  += [self.freeRFlagLabelsString]
                outputContentsList += [1]
            reindexedFilename = os.path.join(self.workDirectory,'Reindexed.mtz')
            #set contentFlag here so that splitmtz (as called from splitHklout) will know what columns to expect
            self.container.outputData.F_SIGF_OUT.contentFlag = self.container.inputData.F_SIGF.contentFlag
            error = self.splitHklout(outputFilesList,outputColumnsList,infile = reindexedFilename)
            if error.maxSeverity()>CCP4ErrorHandling.SEVERITY_WARNING:
                self.appendErrorReport(202,'Pointless_reindexToMatch: error in splitting file')
                return CPluginScript.FAILED
            else:
                # update the annotations
                self.container.outputData.F_SIGF_OUT.contentFlag = self.container.inputData.F_SIGF.contentFlag
                #print "FSF", self.container.outputData.F_SIGF_OUT.fileContent
                
                #MN Did filecontent change frmo having spaceGroupName attribute to spaceGroup ????
                try: sgname = self.container.outputData.F_SIGF_OUT.fileContent.spaceGroupName
                except: sgname = str(self.container.outputData.F_SIGF_OUT.fileContent.spaceGroup)
                
                highres = "%7.2f" % self.container.outputData.F_SIGF_OUT.fileContent.resolutionRange.high
                title ='SG:'+str(sgname).strip()+';Resolution:'+highres.strip()+\
                        ";Cell:"+self.shortformatCell(self.container.outputData.F_SIGF_OUT.fileContent.cell)
                print '#1'
                if self.container.controlParameters.REINDEX_OPERATOR.isSet():
                    par = self.container.controlParameters
                    reindexop = "Reindexed:"+("[%s, %s, %s]" % (par.REINDEX_OPERATOR.h,par.REINDEX_OPERATOR.k,par.REINDEX_OPERATOR.l)).strip()
                    title = reindexop + ";" + title
                else:
                    title = "New" + title
                print '#2'

                self.container.outputData.F_SIGF_OUT.annotation = \
                     str(self.container.inputData.F_SIGF.annotation) + " " + title
                print '#3'

                self.container.outputData.F_SIGF_OUT.subType = self.container.inputData.F_SIGF.subType
                if self.container.inputData.FREERFLAG.isSet():
                    self.container.outputData.FREERFLAG_OUT.annotation = title
                print '#4'

            try:
                import CCP4Utils
                
                with open(self.makeFileName('PROGRAMXML'),'r') as unfixedXMLFile:
                    text = unfixedXMLFile.read()
                try:
                    rootNode = etree.fromstring(text)
                except:
                    #MN Pointless's XML can be corrupt...I've spotted this in instances where the XYZIN_REF has been set, and
                    #the corresponding XML closing tag is split across two lines.
                    #Also, the attributes listed within markup may not be space delimited
                    #Here is a kludged fix
                    fixedText = ''
                    inMarkup = False
                    inQuote = False
                    for iChar in range(len(text)-1):
                        character = text[iChar:iChar+1]
                        if character == '<': inMarkup = True
                        elif character == '>': inMarkup = False
                        if inMarkup and character == '"':
                            if inQuote: character += ' '
                            inQuote = not inQuote
                        if (inMarkup and character != '\n') or not inMarkup: fixedText += character
                    with open(self.makeFileName('PROGRAMXML'),'w') as fixedXMLFile:
                        fixedXMLFile.write(fixedText)
                    rootNode = etree.fromstring(fixedText)
                #print '\n\n rootNode',rootNode
                bestReindexNodes = rootNode.xpath('//BestReindex')
                scoreCountNodes = rootNode.xpath('//ScoreCount')
                copyMessageNodes = rootNode.xpath('//CopyMessage')
                if len(bestReindexNodes) == 0 and len(scoreCountNodes) == 0 and len(copyMessageNodes) == 0:
                    self.container.outputData.BestReindexIdentified = False
                    self.appendErrorReport(203, 'No reindex found')
                    return CPluginScript.FAILED
                else:
                    self.container.outputData.BestReindexIdentified = True
            except:
                self.appendErrorReport(203, 'Unable to complete check for best reindex found')
                return CPluginScript.FAILED
                    
        except:
            self.appendErrorReport(202,'Pointless_reindexToMatch: processOutputFiles exception in process')
            return CPluginScript.FAILED

        return CPluginScript.SUCCEEDED