from CCP4PluginScript import CPluginScript import sys, os import CCP4ErrorHandling import CCP4Modules from lxml import etree import CCP4Utils class phaser_pipeline(CPluginScript): TASKNAME = 'phaser_pipeline' # Task name - should be same as class name TASKCOMMAND = '' # The command to run the executable TASKVERSION= 0.0 # Version of this plugin COMTEMPLATE = None # The program com file template COMTEMPLATEFILE = None # Name of file containing com file template ASYNCHRONOUS = False PERFORMANCECLASS = 'CRefinementPerformance' SEPARATEDATA=True INTERRUPTABLE=True ERROR_CODES = { 200 : { 'description' : 'Phaser exited with error statut' }, 202 : { 'description' : 'Failed in harvest operation' }, 203 : { 'description' : 'Columns not present' }, 204 : { 'description' : 'Failed in plugin:' },} WHATNEXT = ['prosmart_refmac','buccaneer_build_refine_mr','coot_rebuild'] ''' def __init__(self,parent=None,name=None,workDirectory=''): CPluginScript. __init__(self,parent=parent,name=name) ''' def process(self): invalidFiles = self.checkInputData() if len(invalidFiles)>0: self.reportStatus(CPluginScript.FAILED) self.checkOutputData() self.xmlroot = etree.Element('PhaserPipeline') self.phaserPlugin = self.makePluginObject('phaser_MR_AUTO') #This funky arrangement is the way to ensure that the plugin behaves the same #when it is a part of the ipeline as it does when it is run alone...something about defaults I guess for attrName in self.phaserPlugin.container.keywords.dataOrder(): if hasattr(self.container.keywords,attrName): attr = getattr(self.container.keywords,attrName) if hasattr(attr,'isSet') and attr.isSet(): setattr(self.phaserPlugin.container.keywords,attrName,attr) self.phaserPlugin.container.inputData=self.container.inputData self.phaserPlugin.container.inputData.KILLFILEPATH.set(os.path.join(self.getWorkDirectory(),'INTERRUPT')) self.phaserPlugin.async = False #self.phaserPlugin.waitForFinished = -1 #self.phaserPlugin.setFinishHandler(self.phaser_MR_AUTO_Finished) self.connectSignal(self.phaserPlugin,'finished', self.phaserFinished) self.oldXMLLength = 0 self.phaserPlugin.callbackObject.addResponder(self.phaserXMLUpdated) print 'Off to see the wizard' rv = self.phaserPlugin.process() print 'Rv', rv if rv == CPluginScript.FAILED: print 'Oh' with open(self.phaserPlugin.makeFileName('LOG'),"r") as logFile: wasInterrupted = 'KILL-FILE DETECTED ERROR' in logFile.read() print 'Was interrupted',wasInterrupted if wasInterrupted: self.reportStatus('CPluginScript.INTERRUPTED') return CPluginScript.INTERRUPTED else: self.reportStatus(rv) return CPluginScript.FAILED return CPluginScript.SUCCEEDED def phaserXMLUpdated(self, newXML): for oldNode in self.xmlroot.xpath('PhaserMrResults'): self.xmlroot.remove(oldNode) from copy import deepcopy self.xmlroot.append(deepcopy(newXML)) tmpFilename = self.makeFileName('PROGRAMXML')+'_tmp' with open(tmpFilename,'w') as xmlfile: xmlfile.write(etree.tostring(self.xmlroot,pretty_print=True)) import os self.renameFile(tmpFilename,self.makeFileName('PROGRAMXML')) def phaserFinished(self, statusDict = {}): import sys sys.stdout.flush() print 'StatusDict',statusDict sys.stdout.flush() if len(self.phaserPlugin.container.outputData.XYZOUT) > 0: self.checkFinishStatus(statusDict=statusDict,failedErrCode=200,outputFile = self.phaserPlugin.container.outputData.XYZOUT[0] ,noFileErrCode=207) else: self.appendErrorReport(207,'No output files in list') self.reportStatus(CPluginScript.FAILED) self.harvestPhaserPlugin() self.appendXML(self.phaserPlugin.makeFileName('PROGRAMXML'),'PhaserMrResults') F_SIGF_TOUSE = self.container.inputData.F_SIGF FREERFLAG_TOUSE = self.container.inputData.FREERFLAG XYZIN_TOUSE = self.container.outputData.XYZOUT[0] if self.phaserPlugin.container.outputData.dataReindexed: self.runPointless() F_SIGF_TOUSE = self.container.outputData.F_SIGF_OUT FREERFLAG_TOUSE = self.container.outputData.FREERFLAG_OUT if self.container.inputData.XYZIN_TARGET.isSet(): self.runCsymmatch() XYZIN_TOUSE = self.container.outputData.XYZOUT_CSYMMATCH if self.container.inputData.RUNCOOT: self.runCoot(MAPIN=self.container.outputData.MAPOUT[0], XYZIN=XYZIN_TOUSE) XYZIN_TOUSE = self.container.outputData.XYZOUT_COOT if self.container.inputData.RUNREFMAC: self.runRefmac(F_SIGF=F_SIGF_TOUSE, FREERFLAG=FREERFLAG_TOUSE, XYZIN=XYZIN_TOUSE) self.reportStatus(CPluginScript.SUCCEEDED) def harvestPhaserPlugin(self): pluginOutputs=self.phaserPlugin.container.outputData pipelineOutputs = self.container.outputData self.harvestFile(pluginOutputs.SOLOUT, pipelineOutputs.SOLOUT) for outputListType in ['XYZOUT', 'MAPOUT', 'DIFMAPOUT','PHASEOUT']: pluginOutputList = getattr(pluginOutputs, outputListType, None) pipelineOutputList = getattr(pipelineOutputs, outputListType, None) self.harvestList(pluginOutputList, pipelineOutputList) def runPointless(self): try: pointlessPlugin = self.makePluginObject('pointless_reindexToMatch') pointInp = pointlessPlugin.container.inputData pointlessPlugin.container.controlParameters.REFERENCE = 'HKLIN_FMAP_REF' pointInp.HKLIN_FMAP_REF = self.container.outputData.MAPOUT[0] pointInp.F_SIGF = self.container.inputData.F_SIGF if self.container.inputData.FREERFLAG.isSet(): pointInp.FREERFLAG = self.container.inputData.FREERFLAG rv = pointlessPlugin.process() if rv != CPluginScript.SUCCEEDED: self.reportStatus(rv) pluginOutputs = pointlessPlugin.container.outputData pipelineOutputs = self.container.outputData self.harvestFile(pluginOutputs.F_SIGF_OUT, pipelineOutputs.F_SIGF_OUT) if self.container.inputData.FREERFLAG.isSet(): self.harvestFile(pluginOutputs.FREERFLAG_OUT, pipelineOutputs.FREERFLAG_OUT) except: self.appendErrorReport(204,'pointless_reindexToMatch') self.reportStatus(CPluginScript.FAILED) return CPluginScript.SUCCEEDED def runCsymmatch(self): try: csymmatchPlugin = self.makePluginObject('csymmatch') csymmatchInp = csymmatchPlugin.container.inputData csymmatchInp.XYZIN_QUERY = self.container.outputData.XYZOUT[0] csymmatchInp.XYZIN_TARGET = self.container.inputData.XYZIN_TARGET rv = csymmatchPlugin.process() if rv != CPluginScript.SUCCEEDED: self.reportStatus(rv) pluginOutputs = csymmatchPlugin.container.outputData pipelineOutputs = self.container.outputData self.harvestFile(pluginOutputs.XYZOUT, pipelineOutputs.XYZOUT_CSYMMATCH) self.appendXML(csymmatchPlugin.makeFileName('PROGRAMXML'),'Csymmatch') pipelineOutputs.XYZOUT_CSYMMATCH.annotation='Coordinates moved to match reference structure' except: self.appendErrorReport(204,'csymmatch') self.reportStatus(CPluginScript.FAILED) return CPluginScript.SUCCEEDED def runCoot(self, MAPIN=None, XYZIN=None): try: try: cootPlugin = self.makePluginObject('coot_script_lines') xyzinList = cootPlugin.container.inputData.XYZIN xyzinList.append(xyzinList.makeItem()) xyzinList[-1].set(XYZIN) fphiinList = cootPlugin.container.inputData.FPHIIN fphiinList.append(fphiinList.makeItem()) fphiinList[-1].set(MAPIN) cootPlugin.container.controlParameters.SCRIPT = '''fill_partial_residues(MolHandle_1) fit_protein(MolHandle_1) write_pdb_file(MolHandle_1,os.path.join(dropDir,"output.pdb")) ''' except: self.appendErrorReport(204,'coot_script_lines -setup') self.reportStatus(CPluginScript.FAILED) try: cootPlugin.async=False rv = cootPlugin.process() if rv != CPluginScript.SUCCEEDED: self.reportStatus(rv) except: self.appendErrorReport(204,'coot_script_lines -execute') self.reportStatus(CPluginScript.FAILED) try: pluginOutputs = cootPlugin.container.outputData pipelineOutputs = self.container.outputData self.harvestFile(pluginOutputs.XYZOUT[0], pipelineOutputs.XYZOUT_COOT) self.appendXML(cootPlugin.makeFileName('PROGRAMXML'),'coot_script_lines') pipelineOutputs.XYZOUT_COOT.annotation='Coordinates filled and fitted by COOT' except: self.appendErrorReport(204,'coot_script_lines -postprocess') self.reportStatus(CPluginScript.FAILED) except: self.appendErrorReport(204,'coot_script_lines') self.reportStatus(CPluginScript.FAILED) return CPluginScript.SUCCEEDED def runRefmac(self,F_SIGF=None,FREERFLAG=None,XYZIN=None): try: # refmac wrapper run with 10 cycles self.refmacPlugin = self.makePluginObject('refmac') if XYZIN is not None: self.refmacPlugin.container.inputData.XYZIN.set( XYZIN) if F_SIGF is not None: self.refmacPlugin.container.inputData.F_SIGF.set(F_SIGF) if FREERFLAG is not None: self.refmacPlugin.container.inputData.FREERFLAG.set(FREERFLAG) self.refmacPlugin.container.controlParameters.HYDROGENS = 'NO' self.refmacPlugin.container.controlParameters.NCYCLES = 10 self.refmacPlugin.container.controlParameters.PHOUT = False self.refmacPlugin.container.controlParameters.USE_JELLY = True self.refmacPlugin.container.controlParameters.JELLY_SIGMA=0.05 self.refmacPlugin.container.controlParameters.MAKE_NEW_LIGAND_EXIT = False self.refmacPlugin.async=False rv = self.refmacPlugin.process() if rv == CPluginScript.FAILED: self.reportStatus(rv) pluginOutputs=self.refmacPlugin.container.outputData pipelineOutputs = self.container.outputData self.harvestFile(pluginOutputs.FPHIOUT, pipelineOutputs.MAPOUT_REFMAC) self.harvestFile(pluginOutputs.DIFFPHIOUT, pipelineOutputs.DIFMAPOUT_REFMAC) self.harvestFile(pluginOutputs.XYZOUT, pipelineOutputs.XYZOUT_REFMAC) self.appendXML(self.refmacPlugin.makeFileName('PROGRAMXML'),'REFMAC') except: self.appendErrorReport(204,'refmac Preamble') self.reportStatus(CPluginScript.FAILED) try: self.container.outputData.PERFORMANCEINDICATOR = self.refmacPlugin.container.outputData.PERFORMANCEINDICATOR except: self.appendErrorReport(204,'refmac PI') self.reportStatus(CPluginScript.FAILED) return CPluginScript.SUCCEEDED def harvestList(self, pluginOutputList, pipelineOutputList): for pluginOutputListItem in pluginOutputList: pipelineOutputList.append(pipelineOutputList.makeItem()) pipelineOutputListItem = pipelineOutputList[-1] pipelineOutputListItem.fullPath = os.path.join(self.workDirectory,os.path.basename(pluginOutputListItem.fullPath)) self.harvestFile(pluginOutputListItem, pipelineOutputListItem) def harvestFile(self, pluginOutputItem, pipelineOutputItem): import shutil try: shutil.copyfile(str(pluginOutputItem.fullPath), str(pipelineOutputItem.fullPath)) pipelineOutputItem.annotation = pluginOutputItem.annotation pipelineOutputItem.contentFlag = pluginOutputItem.contentFlag pipelineOutputItem.subType = pluginOutputItem.subType except: self.appendErrorReport(202,str(pluginOutputItem.fullPath)+' '+str(pipelineOutputItem.fullPath)) self.reportStatus(CPluginScript.FAILED) def appendXML(self, changedFile, replacingElementOfType=None): newXML = CCP4Utils.openFileToEtree(changedFile) destNode = self.xmlroot for oldNode in self.xmlroot.xpath(replacingElementOfType): self.xmlroot.remove(oldNode) destNode.append(newXML) with open(self.makeFileName('PROGRAMXML'),'w') as xmlfile: xmlfile.write(etree.tostring(self.xmlroot,pretty_print=True)) def checkFinishStatus( self, statusDict,failedErrCode,outputFile = None,noFileErrCode= None): import os if len(statusDict)>0 and statusDict['finishStatus'] == CPluginScript.FAILED: self.appendErrorReport(failedErrCode) self.reportStatus(statusDict['finishStatus']) try: assert outputFile.exists(),'Entity provided is not CDataFile or does not exist' except: self.appendErrorReport(noFileErrCode,'Expected file: '+str(outputFile)) self.reportStatus(CPluginScript.FAILED)