""" xia2_run.py: CCP4 GUI Project Copyright (C) 2013 STFC """ import os,shutil,glob from lxml import etree import CCP4PluginScript RUN_TITLES = { '2d' : 'Mosflm-Scala integration and processing', '3d' : 'XDS-XSCALE integration and processing', '3dii' : 'XDS-XSCALE integration with image indexing and processing', '2da' : 'Mosflm-Aimless integration and processing', '3da' : 'XDS-XSCALE-Aimless integration and processing', '3daii' : 'XDS-Aimless integration with image indexing and processing' } class xia2_run(CCP4PluginScript.CPluginScript): TASKMODULE = None # Where this plugin will appear on the gui TASKTITLE = 'Import data processing results from XIA2' TASKNAME = 'xia2_run' # Task name - should be same as class name TASKVERSION= 0.0 # Version of this plugin ERROR_CODES = { 101 : {'description' : 'XIA2 run directory does not exist' }, 102 : {'description' : 'The XIA2 job failed with error file' }, 103 : {'description' : 'No XIA2 run report file found' }, 104 : {'description' : 'No XIA2 run output experimental data file found' }, 110 : {'description' : 'Unable to open ispyb.xml' }, 111 : {'description' : 'Unable to read performance data from ispyb.xml' } } WHATNEXT = ['aimless_pipe','molrep_mr','phaser_pipeline'] CLONEABLE = False PERFORMANCECLASS = 'CDataReductionPerformance' def runTitle(self,runMode): runModeList = self.container.controlParameters.RUN_MODE.qualifiers('enumerators') runTitleList = self.container.controlParameters.RUN_MODE.qualifiers('menuText') #print 'xia2_run.runTitle',runMode,runModeList,runMode in runModeList if runMode in runModeList: return 'XIA2: '+runTitleList[runModeList.index(runMode)] else: return None def process(self): #print 'xia2_run.process',self.container.inputData.XIA2_DIRECTORY runMode = str(self.container.controlParameters.RUN_MODE) xdir = os.path.join(self.container.inputData.XIA2_DIRECTORY.__str__(),runMode+'-run') if not os.path.exists(xdir): xdir = os.path.join(self.container.inputData.XIA2_DIRECTORY.__str__(),runMode) if not os.path.exists(xdir): self.appendErrorReport(cls=self.__class__,code=101,details=xdir) self.reportStatus(CCP4PluginScript.CPluginScript.FAILED) logfile = os.path.join(xdir,'xia2.html') if os.path.exists(logfile): shutil.copyfile(logfile,os.path.join(self.workDirectory,'xia2_log.html')) shutil.copytree(os.path.join(xdir,'xia2_html'),os.path.join(self.workDirectory,'xia2_html')) else: self.appendErrorReport(cls=self.__class__,code=103) ''' txtfile = os.path.join(xdir,'xia2.txt') if os.path.exists(txtfile): shutil.copyfile(txtfile,os.path.join(self.workDirectory,'report.txt')) ''' xmlfile = os.path.join(xdir,'ispyb.xml') #print 'xia2_run.process',xmlfile,os.path.exists(xmlfile) if os.path.exists(xmlfile): shutil.copyfile(xmlfile,os.path.join(self.workDirectory,'XMLOUT.xml')) mtzfiles = glob.glob(os.path.join(xdir,'DATAFILES','*.mtz')) self.container.outputData.HKLOUT.setFullPath(os.path.join(self.workDirectory,'hklout.mtz')) #print 'xia2_run mtzfiles',mtzfiles if len(mtzfiles) > 0: shutil.copyfile(mtzfiles[0],self.container.outputData.HKLOUT.__str__()) else: self.appendErrorReport(cls=self.__class__,code=104) self.splitHklout0() #error = self.splitHklout(['FPHIOUT','DIFFPHIOUT','ABCDOUT'],['FWT,PHWT','DELFWT,PHDELWT','HLACOMB,HLBCOMB,HLCCOMB,HLDCOMB']) pluginObj = self.makePluginObject('xia2_integration',pluginTitle=self.runTitle(runMode)) pluginObj.container.inputData.XIA2_DIRECTORY.setFullPath(xdir) pluginObj.process() #print 'xia2_run.process',pluginObj.container.outputData.HKLOUT if pluginObj.container.outputData.HKLOUT.isSet(): if len(self.container.outputData.UNMERGEDHKL)==0: self.container.outputData.UNMERGEDHKL.addItem() #self.container.outputData.UNMERGEDHKL[0].set(pluginObj.container.outputData.HKLOUT) self.container.outputData.UNMERGEDHKL[0].set(os.path.join(self.workDirectory,'UNMERGEDHKL'+ os.path.splitext(pluginObj.container.outputData.HKLOUT.baseName)[1])) shutil.copyfile(str( pluginObj.container.outputData.HKLOUT),self.container.outputData.UNMERGEDHKL[0].fullPath.__str__()) #print 'xia2_run.process UNMERGEDHKL',self.container.outputData.UNMERGEDHKL for subJob in ['pointless','aimless','ctruncate']: pluginObj = self.makePluginObject('xia2_'+subJob) pluginObj.container.inputData.XIA2_DIRECTORY.setFullPath(xdir) pluginObj.process() self.TASKTITLE = self.runTitle(runMode) self.setPerformance(runMode) self.makeXml(runMode) self.reportStatus(CCP4PluginScript.CPluginScript.SUCCEEDED) return CCP4PluginScript.CPluginScript.SUCCEEDED def splitHklout0(self): import re columnList = self.container.outputData.HKLOUT.fileContent.getListOfColumns() #print '\n\n** xia2_run columnNames',columnList fp = None ip = None for c in columnList: name= c.columnLabel.__str__() if fp is None and 'F(+)' in name: fp = name if ip is None and 'I(+)' in name: ip = name #print 'xia2_run fp,ip',fp,ip self.container.outputData.FREER.set(self.container.outputData.HKLOUT) self.container.outputData.FREER.baseName='FreeR.mtz' self.container.outputData.FREER.annotation='Free Rfactor' out = [[self.container.outputData.FREER.__str__(),'FreeR_flag','FREER']] # output as many data representations as are available outputDataObject = None relabelColumnFromList = '' relabelColumnToList = '' contentFlagList = [] outputFileBaseName = '' if ip is not None: #print '\n\n**ip not none' outputDataObject = self.container.outputData.IANOM outputDataObject.set(self.container.outputData.HKLOUT) outputFileBaseName = 'IANOM-' outputDataObject.annotation='Exptl data as anomalous intensities' self.container.outputData.IANOM.contentFlag = 1 self.container.outputData.IANOM.subType = 1 im = re.sub('\+','-',ip) #MN change: because internally, we assume labels of Iplus Iminus etc for this contentFlag and data type, and we have to notify system that this is what we have used relabelColumnFromList += (ip+','+'SIG'+ip+','+im+','+'SIG'+im) relabelColumnToList += 'Iplus,SIGIplus,Iminus,SIGIminus' contentFlagList += [1] elif fp is not None: #print '\n\n**fp not none' if outputDataObject is None: outputDataObject = self.container.outputData.FANOM outputDataObject.set(self.container.outputData.HKLOUT) outputFileBaseName = '' outputDataObject.annotation = '' else: relabelColumnFromList += ',' relabelColumnToList += ',' outputFileBaseName += 'FANOM-' outputDataObject.annotation = 'Exptl data as anomalous SFs' self.container.outputData.FANOM.contentFlag = 2 self.container.outputData.FANOM.subType = 1 fm = re.sub('\+','-',fp) #MN change: because internally, we assume labels of Fplus Fminus etc for this contentFlag and data type, and we have to notify system that this is what representation we have used relabelColumnFromList += (fp+','+'SIG'+fp+','+fm+','+'SIG'+fm+',') relabelColumnToList += 'Fplus,SIGFplus,Fminus,SIGFminus,' contentFlagList += [2] else: if outputDataObject is None: outputDataObject = self.container.outputData.FSIGF outputDataObject.set(self.container.outputData.HKLOUT) outputFileBaseName = '' outputDataObject.annotation = '' else: relabelColumnFromList += ',' relabelColumnToList += ',' outputFileBaseName += 'FSIGF-' outputDataObject.annotation += 'Exptl data as SFs' relabelColumnFromList += 'F,SIGF' relabelColumnToList += 'F,SIGF' contentFlagList += [4] outputFileBaseName += 'observed_data.mtz' outputDataObject.baseName = outputFileBaseName out.append([outputDataObject.__str__(), relabelColumnFromList, relabelColumnToList ] ) #MN change this...contentFlag needs to reflect possiblity of containing multiple data representations...should either be a list or a logically ORed set of flags outputDataObject.contentFlag = min(contentFlagList) err = self.splitMtz(self.container.outputData.HKLOUT.__str__(),out) print err def setPerformance(self,runMode): ispyb = os.path.join(self.container.inputData.XIA2_DIRECTORY.__str__(),runMode+'-run','ispyb.xml') #print 'xia2_run.setPerformance',ispyb try: import CCP4Utils xml = CCP4Utils.openFileToEtree(ispyb) except: self.appendErrorReport(110,ispyb,stack=False) else: try: self.container.outputData.PERFORMANCE.spaceGroup.set(xml.xpath('//spaceGroup')[0].text) self.container.outputData.PERFORMANCE.highResLimit.set(float(xml.xpath('//resolutionLimitHigh')[0].text)) self.container.outputData.PERFORMANCE.rMeas.set(float(xml.xpath('//rMeasAllIPlusIMinus')[0].text)) except: self.appendErrorReport(111,ispyb,stack=False) def makeXml(self,runMode): from lxml import etree import CCP4Utils self.xmlroot = etree.Element('XIA2Import') runXML = etree.SubElement(self.xmlroot,'XIA2Run',name=str(runMode)) ispyb = os.path.join(self.container.inputData.XIA2_DIRECTORY.__str__(),runMode+'-run','ispyb.xml') try: ispybxml = CCP4Utils.openFileToEtree(ispyb) except: self.appendErrorReport(110,ispyb,stack=False) else: runXML.append(ispybxml) for programName in ['pointless','aimless','truncate']: programEtree = self.harvestLogXML(runMode, programName) if programEtree is not None: runXML.append(programEtree) CCP4Utils.saveEtreeToFile(self.xmlroot,self.makeFileName('PROGRAMXML')) def harvestLogXML(self, runMode, programName): logFiles = glob.glob( os.path.join(self.container.inputData.XIA2_DIRECTORY.__str__(), runMode+'-run', 'LogFiles','') + "*" + programName + ".log" ) #print 'harvestLogXML',logFiles if len(logFiles)==0: return None root = etree.Element(programName.upper()) try: import smartie except: import CCP4Utils smartiePath = os.path.join(CCP4Utils.getCCP4I2Dir(),'smartie') import sys sys.path.append(smartiePath) import smartie import MGQTmatplotlib logfile = smartie.parselog(logFiles[0]) for smartieTable in logfile.tables(): if smartieTable.ngraphs() > 0: tableelement = MGQTmatplotlib.CCP4LogToEtree(smartieTable.rawtable() ) root.append(tableelement) summaryCount = logfile.nsummaries() for iSummary in range(summaryCount): summary = logfile.summary(iSummary) summaryTextLines = [] with open(logFiles[0]) as myLogFile: summaryTextLines = myLogFile.readlines()[summary.start():summary.end()-1] preElement = etree.SubElement(root,'CCP4Summary') preElementText = '' for summaryTextLine in summaryTextLines: preElementText += (summaryTextLine) preElement.text=etree.CDATA(preElementText) return root