from CCP4PluginScript import CPluginScript from PyQt4 import QtCore import os,re,time,sys from lxml import etree import CCP4Utils class ccp4mg_edit_model(CPluginScript): TASKMODULE = 'bioinformatics' # Where this plugin will appear on the gui TASKTITLE = 'Interactive model preparation - CCP4mg and MrBUMP' # A short title for gui menu TASKNAME = 'ccp4mg_edit_model' # Task name - should be same as class name TASKCOMMAND = 'ccp4mg' # The command to run the executable TASKVERSION= 0.1 # Version of this plugin ASYNCHRONOUS = True TIMEOUT_PERIOD = 9999999.9 MAINTAINER = 'stuart.mcnicholas@york.ac.uk' ERROR_CODES = { 200 : { 'description' : 'CCP4MG exited with error status' }, 201 : { 'description' : 'Failed in harvest operation' },202 : { 'description' : 'Failed in processOutputFiles' }} def makeCommandAndScript(self): import CCP4Utils self.dropDir = os.path.join(self.workDirectory,'CCP4MG_FILE_DROP') if not os.path.exists(self.dropDir): try: os.mkdir(self.dropDir) except: self.dropDir = self.workDirectory print 'Could not make dropDir reset to',self.dropDir # Make a script file with additional menu options to save to i2 self.mgStatusPath = os.path.normpath(os.path.join(self.workDirectory,'script.mgpic.xml')) if sys.platform == 'win32': self.mgStatusPath = re.sub(r'\\\\',r'\\',self.mgStatusPath) # Declare script text then re.sub in the variables if sys.platform == "win32": i2dir = CCP4Utils.getCCP4I2Dir().replace('\\','/') else: i2dir = CCP4Utils.getCCP4I2Dir() status_xml = "" NSMAP = {'xsi':"http://www.w3.org/2001/XMLSchema-instance"} NS = NSMAP['xsi'] location_attribute = '{%s}noNamespaceSchemaLocation' % NS tree = etree.Element("CCP4MG_Status",nsmap = NSMAP,attrib={location_attribute: 'http://www.ysbl.york.ac.uk/~mcnicholas/schema/CCP4MGApplicationOutput.xsd'}) status_xml += etree.tostring(tree,encoding='utf-8', pretty_print=True) print "Writing",self.mgStatusPath print status_xml CCP4Utils.saveFile(self.mgStatusPath,status_xml) clArgs = [ '-norestore',self.mgStatusPath ] origInterface_fname = os.path.join(CCP4Utils.getCCP4I2Dir(),"wrappers","ccp4mg_edit_model","script","ccp4i2CCP4MGInterface.py") print origInterface_fname origInterface = open(origInterface_fname) origInterface_s = origInterface.read() origInterface.close() interface_s = origInterface_s interface_fname = os.path.join(self.workDirectory,"ccp4i2CCP4MGInterface.py") interface = open(interface_fname,"w+") interface.write(interface_s) interface.close() clArgs.extend(['-scr',interface_fname]) if self.container.inputData.SEQUENCE_LIST.isSet(): for sequenceFile in self.container.inputData.SEQUENCE_LIST: clArgs.append(sequenceFile) if self.container.inputData.REDUNDANCYLEVEL: if str(self.container.inputData.REDUNDANCYLEVEL) == '100': clArgs.extend(["-scriptArg","mrBumpSim=100"]) elif str(self.container.inputData.REDUNDANCYLEVEL) == '95': clArgs.extend(["-scriptArg","mrBumpSim=95"]) elif str(self.container.inputData.REDUNDANCYLEVEL) == '90': clArgs.extend(["-scriptArg","mrBumpSim=90"]) elif str(self.container.inputData.REDUNDANCYLEVEL) == '70': clArgs.extend(["-scriptArg","mrBumpSim=70"]) elif str(self.container.inputData.REDUNDANCYLEVEL) == '50': clArgs.extend(["-scriptArg","mrBumpSim=50"]) self.appendCommandLine(clArgs) # Use Qt class to watch the drop directory self.fileSystemWatcher = QtCore.QFileSystemWatcher(parent=self) self.fileSystemWatcher.addPath(self.dropDir) self.connect(self.fileSystemWatcher,QtCore.SIGNAL('directoryChanged(const QString &)'),self.handleFileDrop) return CPluginScript.SUCCEEDED def numberOfOutputFiles(self): import glob outList = glob.glob(os.path.normpath(os.path.join(self.dropDir,'output*.pdb'))) #print 'numberOfOutputFiles outList',os.path.join(self.dropDir,'output*.pdb'),outList #print 'numberOfOutputFiles xmlList',glob.glob(os.path.normpath(os.path.join(self.workDirectory,'*.xml'))) maxIndx = 0 for f in outList: fpath,fname = os.path.split(f) #print 'numberOfOutputFiles fpath,fname', fpath,fname maxIndx = max(maxIndx,int(fname[6:-4])) return maxIndx def handleFileDrop(self,directory): import time,glob print 'ccp4mg_edit_model',time.time() print 'ccp4mg_edit_model',glob.glob(os.path.join(self.workDirectory,'*.*')) #print 'handleFileDrop',directory #Note that I don't copy the file to the appropriate xyzout filename here, since the file may not yet #be closed and/or flushed def processOutputFiles(self): import shutil from stat import S_ISREG, ST_CTIME, ST_MODE try: # First up import PDB files that have been output import os, glob, shutil globPath = os.path.normpath(os.path.join(self.dropDir,'output*.pdb')) outList = glob.glob(globPath) xyzoutList = self.container.outputData.XYZOUT for outputPDB in outList: fpath,fname = os.path.split(outputPDB) iFile = int(fname[6:-4]) xyzoutList.append(xyzoutList.makeItem()) outputFilePath = os.path.normpath(os.path.join(self.workDirectory,'XYZOUT_'+str(iFile)+'-coordinates.pdb')) shutil.copyfile(outputPDB, outputFilePath) xyzoutList[-1].setFullPath(outputFilePath) xyzoutList[-1].annotation = "CCP4MG output file number"+str(iFile) xyzoutList[-1].subType = 1 # Create an xml output file and harvest the MrBUMP log files. from lxml import etree self.xmlroot = etree.Element('ccp4mg_edit_model') e = etree.Element('number_output_files') e.text = str(self.numberOfOutputFiles()) self.xmlroot.append(e) logFName = os.path.join(self.workDirectory,"log.txt") if os.path.exists(logFName): with open(logFName) as f: logLines = f.readlines() try: mrBumpDir = None for logL in logLines: if logL.startswith("MRBUMP_DIRECTORY"): mrBumpDir = logL.split()[1].strip() if mrBumpDir is not None: edir = etree.Element('MGMRBUMPDIR') edir.text = str(mrBumpDir) self.xmlroot.append(edir) logs = glob.glob(os.path.normpath(os.path.join(mrBumpDir,'logs','*.log'))) logs.extend(glob.glob(os.path.normpath(os.path.join(mrBumpDir,'logs','*.txt')))) # Sort the logs by creation date. I guess XML keeps order? Is this guaranteed? logs = ((os.stat(path), path) for path in logs) logs = ((stat[ST_CTIME], path) for stat, path in logs if S_ISREG(stat[ST_MODE])) for cdate, log in sorted(logs): elog = etree.Element(os.path.basename(log)) elog.text = str(log) self.xmlroot.append(elog) shutil.copyfile(log, os.path.join(self.workDirectory,"mrbump_"+os.path.basename(log))) except: print "No MrBump directory reported in log file." except: exc_type, exc_value,exc_tb = sys.exc_info()[:3] sys.stderr.write(str(exc_type)+'\n') sys.stderr.write(str(exc_value)+'\n') self.appendErrorReport(202,'Data harvesting failed') CCP4Utils.saveEtreeToFile(self.xmlroot,self.makeFileName('PROGRAMXML')) """ if ( len(outList) ) > 0: return CPluginScript.SUCCEEDED else: return CPluginScript.MARK_TO_DELETE """ return CPluginScript.SUCCEEDED def addReportWarning(self, text): from lxml import etree warningsNode = None warningsNodes = self.xmlroot.xpath('//Warnings') if len(warningsNodes) == 0: warningsNode = etree.SubElement(self.xmlroot, 'Warnings') else: warningsNode = warningsNodes[0] warningNode = etree.SubElement(warningsNode,'Warning') warningNode.text = text