""" CCP4Launcher.py: CCP4 GUI Project Copyright (C) 2011 University of York 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, 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. """ """ Liz Potterton June 2011 - Class to launch other viewers """ from CCP4ErrorHandling import * from PyQt4 import QtCore import socket, sys, functools, os class NamedSocket(socket.socket): def __init__(self,domain,protocol): socket.socket.__init__(self,domain,protocol) self._myName = 'Unknown' self._isActive = True def setActive(self,Active): self._isActive = Active def getActive(self): return self._isActive def setName(self,name): self._myName = name def getName(self): return self._myName class CLauncher(QtCore.QObject): insts = None def __init__(self,parent=None): if parent is None: import CCP4Modules parent = CCP4Modules.QTAPPLICATION() QtCore.QObject.__init__(self,parent) if CLauncher.insts is None: CLauncher.insts = self self.hostPorts = { 'CCP4mg' : { 'hostname': 'localhost', 'port' : 9000 }} self.sockets = {} self.launchTries = {} self.blockExit = False def Exit(self): pass #sys.__stdout__.write('CLauncher.Exit blockExit '+str(self.blockExit)+'\n');sys.__stdout__.flush() def openSocket(self,hostname,port,name='Unknown',command=None): #print 'openSocket',self.launchTries,hostname,port,name,command self.blockExit = True csocket = NamedSocket(socket.AF_INET, socket.SOCK_STREAM) try: csocket.connect((hostname,port)) print "Successful connection to "+str(hostname)+':'+str(port) csocket.setName(name) self.sockets[name] = csocket if self.launchTries.has_key(name): del self.launchTries[name] except: print "Failed connection to "+str(hostname)+':'+str(port) if not self.launchTries.has_key(name): print 'openSocket launching:',name p = self.launch(name) if p is not None: self.launchTries[name] = 0 else: self.launchTries[name] = -1 print 'launchTries',self.launchTries if self.launchTries[name]>=0: self.launchTries[name] = self.launchTries[name] + 1 if self.launchTries[name]>10: print 'Failed to launch program',name self.launchTries[name] = -1 else: timer = QtCore.QTimer(self) timer.setSingleShot(True) self.connect(timer,QtCore.SIGNAL('timeout()'),functools.partial(self.openSocket,hostname,port,name,command)) timer.start(1000) if self.sockets.has_key(name) and command is not None: print 'openSocket trying send' self.sockets[name].send(command) self.blockExit = False def getExecutable(self,viewer,guiParent=None): import CCP4Modules,CCP4Utils viewer = viewer.lower() path = None if viewer == 'ccp4mg': path = str(CCP4Modules.PREFERENCES().CCP4MG_EXECUTABLE) if path is not None and os.path.isfile(path) and os.access(path, os.X_OK): return path if CCP4Utils.which(viewer) is not None: if sys.platform[0:3] == 'win': whichExe = CCP4Utils.which(viewer) if not viewer.lower().endswith(".bat") and whichExe.lower().endswith(".bat"): viewer = whichExe return viewer if sys.platform[0:3] == 'win': #path = os.path.join(os.environ['CCP4'],'bin','winccp4mg.exe') # FIXME : This is a temporary hack whilst MG's ccp4mg.bat is broken. path = os.path.join(CCP4Utils.getCCP4I2Dir(),'bin','ccp4mg.bat') else: path = os.path.join(os.environ['CCP4'],'bin','ccp4mg') if os.path.exists(path): return path if guiParent is not None: return self.queryExecutable(viewer=viewer,guiParent=guiParent) elif viewer == 'coot': path = str(CCP4Modules.PREFERENCES().COOT_EXECUTABLE) #print 'CLauncher.getExecutable prfrences coot',path if path is not None and os.path.isfile(path) and os.access(path, os.X_OK): if sys.platform == 'win32': altpath = self.modifyCootBat() if altpath is not None: return altpath return path if CCP4Utils.which(viewer) is not None: return viewer #import CCP4Config #path = CCP4Config.PATH(viewer) if guiParent is not None: return self.queryExecutable(viewer=viewer,guiParent=guiParent) elif viewer == 'lidia': path = str(CCP4Modules.PREFERENCES().COOT_EXECUTABLE) #print 'CLauncher.getExecutable prfrences coot',path if path is not None and os.path.isfile(path) and os.access(path, os.X_OK): if sys.platform == 'win32': altpath = self.modifyLidiaBat() if altpath is not None: return altpath return path if CCP4Utils.which(viewer) is not None: return viewer #import CCP4Config #path = CCP4Config.PATH(viewer) if guiParent is not None: return self.queryExecutable(viewer=viewer,guiParent=guiParent) return path def launch(self,viewer=None,argList=[],envEdit=[],projectId=None,logFile=None,callBack=None,guiParent=None): #Bother - launch() gets called directly from CCP4ReportWidgets # Beware multiple calls to launch (from coot_model_building) seems to retain previous envEdit editEnv = [] editEnv.extend(envEdit) pwdSet = False for item in editEnv: if item[0]=='PWD': pwdSet = True if viewer in ['ccp4mg','coot','moorhen']: if not pwdSet and projectId is not None: cootD = self.cootDir(projectId) if cootD is not None: editEnv.append( ['PWD',self.cootDir(projectId)] ) editEnv.append( ['PYTHONHOME'] ) """ if viewer == 'moorhen': import os,CCP4Utils argList.insert(0,os.path.normpath(os.path.join(CCP4Utils.getCCP4I2Dir(),'wrappers','coot_model_building','test_data','moorhen.py'))) exe = os.path.join(CCP4Utils.getCCP4I2Dir(),'bin','Python') """ if viewer == 'loggraph': import os,CCP4Utils argList.insert(0,os.path.normpath(os.path.join(CCP4Utils.getCCP4I2Dir(),'pimple','MGQTmatplotlib.py'))) if sys.platform == "win32" or sys.platform == "win64": exe = sys.executable else: exe = CCP4Utils.pythonExecutable() elif viewer == 'logview': import os,CCP4Utils exe = CCP4Utils.pythonExecutable() argList.insert(0,os.path.normpath(os.path.join(CCP4Utils.getCCP4I2Dir(),'smartie','qtrview.py'))) else: exe = self.getExecutable(viewer,guiParent=guiParent) if sys.platform[0:3] == "win" and viewer == "ccp4mg": import CCP4Utils whichExe = CCP4Utils.which(exe) if not exe.lower().endswith(".bat") and whichExe.lower().endswith(".bat"): exe = whichExe if exe is None: print 'Do not know executable path so calling as: ',viewer exe = viewer ''' import subprocess try: p = subprocess.Popen('-nore',executable=exe) #except: # print 'Error starting viewer',viewer,'with command',exe # return None ''' qArgList = QtCore.QStringList() for item in argList: if item is not None: qArgList.append(item) p = QtCore.QProcess(self) if len(editEnv)>0: #if len(editEnv)>1 or editEnv[0][0] not in ['pwd','PWD']: processEnvironment = QtCore.QProcessEnvironment.systemEnvironment() for editItem in editEnv: if len(editItem)==1: processEnvironment.remove(editItem[0]) else: if editItem[0] in ['pwd','PWD']: p.setWorkingDirectory(editItem[1]) print '1 Setting process working directory',editItem[1] #else: processEnvironment.insert(editItem[0],editItem[1]) p.setProcessEnvironment(processEnvironment) #else: # p.setWorkingDirectory(editEnv[0][1]) # print '2 Setting process working directory',editEnv[0][1] #print 'launch',viewer,type(viewer),exe,argList if logFile is not None: p.setStandardOutputFile(logFile) if callBack is not None: self.connect(p,QtCore.SIGNAL('finished(int,QProcess::ExitStatus)'),callBack) if exe is None: p.start(viewer,qArgList) else: #print '\n\nexe',exe,qArgList p.start(exe,qArgList) return p ''' # This version attempts to open viewer and then send commands through sockets # mg does not allow socket input def openInViewer(self,viewer=None,fileName=None,jobId=None): print 'CLauncher.openInViewer',viewer,fileName,jobId if fileName is not None: comLine = self.makeCommand(viewer=viewer,command='openFile',data=fileName) elif jobId is not None: # This will open just one file - need to talk to Stuart import CCP4Modules fileList = CCP4Modules.PROJECTSMANAGER().db().getJobFiles(jobId=jobId,mode='fullPath') if len(fileList)>0: comLine = self.makeCommand(viewer=viewer,command='openFile',data=fileList[0]) #print 'CLauncher.openInViewer command',str(comLine) if comLine is None: print 'Can not create launcher command for:',viewer,fileName,jobId return if self.sockets.has_key(viewer): try: self.sockets[viewer].sendall(comLine) except: # Send failed - assume the socket broken and try resetting self.sockets[viewer].close() del self.sockets[viewer] if not self.sockets.has_key(viewer): if not self.hostPorts.has_key(viewer): print 'Do not know hostname,port for viewer:',viewer return hostname= self.hostPorts[viewer]['hostname'] port = self.hostPorts[viewer]['port'] self.openSocket(hostname,port,viewer,comLine) ''' def modifyCootBat(self): import re import CCP4Modules,CCP4Utils cootBat = CCP4Modules.PREFERENCES().COOT_EXECUTABLE.__str__() if not os.path.splitext(cootBat)[1] == '.bat' or not os.path.exists(cootBat): return None text = CCP4Utils.readFile(cootBat) text0 = re.sub('start .* coot-real.exe','coot-real.exe',text) modFile = os.path.join(CCP4Utils.getDotDirectory(),'runwincoot.bat') CCP4Utils.saveFile(modFile,text0,overwrite=True) return modFile def modifyLidiaBat(self): import re import CCP4Modules,CCP4Utils cootBat = CCP4Modules.PREFERENCES().COOT_EXECUTABLE.__str__() if not os.path.splitext(cootBat)[1] == '.bat' or not os.path.exists(cootBat): return None text = CCP4Utils.readFile(cootBat) text0 = re.sub('start .* coot-bin.exe','lidia.exe',text) modFile = os.path.join(CCP4Utils.getDotDirectory(),'runlidia.bat') CCP4Utils.saveFile(modFile,text0,overwrite=True) return modFile def cootDir(self,projectId): import CCP4Modules #print ' cootDir',projectId,type(projectId),CCP4Modules.PROJECTSMANAGER().getProjectDirectory(projectId=projectId) if projectId is None: return None else: cootDir = os.path.join(CCP4Modules.PROJECTSMANAGER().getProjectDirectory(projectId=projectId),'CCP4_COOT') if not os.path.exists(cootDir): try: os.mkdir(cootDir) except: return None #print ' cootDir',projectId,cootDir return cootDir def openInViewer(self,viewer=None,fileName=None,jobId=None,projectId=None,style=None,guiParent=None,fileType='chemical/x-pdb'): if projectId is None and jobId is not None: try: from CCP4Modules import PROJECTSMANAGER projectId = PROJECTSMANAGER().db().getJobInfo(jobId,mode='projectid') except: pass #print 'LAUNCH.openInViewer viewer',viewer,jobId,projectId,fileName if viewer.lower() == 'ccp4mg': argList = self.mgComLine(fileName=fileName,jobId=jobId,style=style) self.launch(viewer='ccp4mg',argList=argList,projectId=projectId,guiParent=guiParent) elif viewer.lower() == 'coot0': argList = self.cootComLine(fileName=fileName,jobId=jobId) self.launch(viewer='coot',argList=argList,projectId=projectId,guiParent=guiParent) #else: # self.launch(viewer='moorhen',argList=argList) elif viewer.lower() == 'coot_job' or viewer.lower() == 'coot': self.runCootJob(contextJobId=jobId,projectId=projectId, fileName=fileName,fileType=fileType ) elif viewer.lower() == 'lidia': import CCP4Modules cootExeDir = None if hasattr(CCP4Modules.PREFERENCES(),'COOT_EXECUTABLE'): if os.path.isfile(str(CCP4Modules.PREFERENCES().COOT_EXECUTABLE)): cootExeDir = str(CCP4Modules.PREFERENCES().COOT_EXECUTABLE) if cootExeDir is None: import CCP4Utils cootExeDir = CCP4Utils.which('coot') cootDir = os.path.normpath(os.path.dirname(os.path.dirname(cootExeDir))) envEdit = [['COOT_PREFIX',cootDir]] COOT_DATA_DIR =os.path.normpath(os.path.join(cootDir,'share','coot')) envEdit.append(['COOT_DATA_DIR',COOT_DATA_DIR]) self.launch(viewer='lidia',argList=[fileName],envEdit=envEdit,projectId=projectId,guiParent=guiParent) elif viewer.lower() == 'viewhkl': if not isinstance(fileName,(tuple,list)): fileNameList = [fileName] else: fileNameList = fileName self.launch('viewhkl',fileNameList) elif viewer.lower() == 'loggraph': print 'openInViewer',fileName,jobId if fileName is not None: self.launch(viewer='loggraph',argList=[fileName]) elif jobId is not None: import CCP4Modules logfile = CCP4Modules.PROJECTSMANAGER().makeFileName(jobId=jobId,mode='REPORT') #print 'openInViewer loggraph',logfile self.launch(viewer='loggraph',argList=[logfile]) #self.launch(viewer='loggraph') def mgComLine(self,fileName=None,jobId=None,style='Bonds:All_atoms'): # common styles: 'bonds:all_atoms' 'ribbons:colour_chains' 'ribbons:colour_blend_thru_chain' 'ribbons:secondary_structure' #print 'LAUNCHER.mgComLine jobId',jobId if style is None: style = 'Bonds:All_atoms' line = ['-norestore','-drawing_style',style] if fileName is None: pass elif isinstance(fileName,(tuple,list)): line.extend(fileName) else: line.append(fileName) if jobId is not None: import CCP4Modules scenefileList =CCP4Modules.PROJECTSMANAGER().getSceneFiles(jobId=jobId) if len(scenefileList)>0: line.append(scenefileList[0]) else: fileList = self.getFilesToDisplay(jobId) line.extend(fileList) return line def runCootJob(self,projectId=None,contextJobId=None,fileName=None,fileType='chemical/x-pdb'): import traceback import CCP4DbUtils if projectId is None: import CCP4Modules projectId = CCP4Modules.PROJECTSMANAGER().db().getJobInfo(contextJobId,'projectid') openJob = CCP4DbUtils.COpenJob(projectId=projectId) openJob.createJob(taskName='coot_rebuild',contextJobId=contextJobId) if fileName is not None: #need to establish what sort of file we are trying to view...difficult from here since we have only a fileName #and a projectId from CCP4Modules import PROJECTSMANAGER db = PROJECTSMANAGER().db() #SELECT Files.JobId,Files.FileID,ImportFiles.ImportId,Files.FileTypeId,Files.Filename selectedInfos = [] fileInfos=db.getProjectFiles(projectId=projectId, topLevelOnly=False) selectedInfos = [anInfo for anInfo in fileInfos if db.getFullPath(anInfo[1]) == fileName] #print 'runCootJob selectedInfos',selectedInfos import CCP4DbApi if len(selectedInfos) > 0: partFileInfo = selectedInfos[0] fileInfo = db.getFileInfo(fileId=partFileInfo[1],mode=['jobid','filename','relpath','projectid','annotation','filecontent','filesubtype']) dobj = None if CCP4DbApi.FILETYPELIST[int(partFileInfo[3])][1] == 'chemical/x-pdb': dobj = openJob.container.inputData.XYZIN_LIST elif CCP4DbApi.FILETYPELIST[int(partFileInfo[3])][1] == 'application/CCP4-mtz-map' and fileInfo['filesubtype']== 1: dobj = openJob.container.inputData.FPHIIN_LIST elif CCP4DbApi.FILETYPELIST[int(partFileInfo[3])][1] == 'application/CCP4-mtz-map' and fileInfo['filesubtype']== 2: dobj = openJob.container.inputData.DELFPHIIN_LIST if dobj is not None: dobj.addItem() dobj[-1].set( { 'baseName' : fileInfo['filename'], 'relPath' : fileInfo['relpath'], 'project' : projectId, 'annotation' : fileInfo['annotation'], 'dbFileId' :selectedInfos[0][1], 'contentFlag' :fileInfo['filecontent'], 'subType' :fileInfo['filesubtype'] } ) else: dobj = openJob.container.inputData.XYZIN_LIST dobj.addItem() dobj[-1].setFullPath(fileName) openJob.runJob() def runLidiaJob(self,projectId=None,contextJobId=None,fileName=None): import CCP4DbUtils if projectId is None: import CCP4Modules projectId = CCP4Modules.PROJECTSMANAGER().db().getJobInfo(contextJobId,'projectid') openJob = CCP4DbUtils.COpenJob(projectId=projectId) openJob.createJob(taskName='Lidia',contextJobId=contextJobId) openJob.runJob() def cootComLine(self,fileName=None,jobId=None): line = ['--no-state-script'] if fileName is not None: fileNameList = [] if isinstance(fileName,(tuple,list)): fileNameList.extend(fileName) else: fileNameList.append(fileName) for f in fileNameList: ext = os.path.splitext(f)[1] if ext == '.pdb': line.extend(['--pdb',f]) elif ext == '.mtz': #line.extend(['--auto',f]) line.extend(['--data',f]) elif ext == '.map': line.extend(['--map',f]) return line elif jobId is not None: paramsFile,comLine = self.makeCootParamsFile(contextJobId=jobId) #line.extend(['--i2params',paramsFile]) line.extend(comLine) return line def makeCootParamsFile(self,contextJobId=None,projectId=None,taskName='coot_rebuild'): import CCP4Container,CCP4Modules,CCP4File,CCP4TaskManager import CCP4ModelData, CCP4XtalData comLine = [] # Make container defFile = CCP4TaskManager.TASKMANAGER().lookupDefFile(name=taskName) container = CCP4Container.CContainer() container.loadContentsFromXml(fileName=defFile) #Loop over inputData files to pull best file of type from database db = CCP4Modules.PROJECTSMANAGER().db() for key in container.inputData.dataOrder(): dobj = container.inputData.get(key) if isinstance(dobj,CCP4File.CDataFile): fileIdList = db.getFileByJobContext(contextJobId=contextJobId,fileType=dobj.qualifiers('mimeTypeName'), subType=dobj.qualifiers('requiredSubType'),contentFlag=dobj.qualifiers('requiredContentFlag'),projectId=projectId) #print 'makeCootParamsFile',contextJobId,key,dobj.qualifiers('mimeTypeName'),dobj.qualifiers('requiredSubType'),fileIdList if len(fileIdList)>0: fileInfo = db.getFileInfo(fileId=fileIdList[0],mode=['jobid','filename','relpath','projectid','annotation','filecontent','filesubtype']) if projectId is None: projectId = fileInfo['projectid'] dobj.set( { 'baseName' : fileInfo['filename'], 'relPath' : fileInfo['relpath'], 'project' : projectId, 'annotation' : fileInfo['annotation'], 'dbFileId' :fileIdList[0], 'contentFlag' :fileInfo['filecontent'], 'subType' :fileInfo['filesubtype'] } ) if isinstance(dobj,CCP4ModelData.CPdbDataFile): comLine.extend(['--pdb',dobj.__str__()]) elif isinstance(dobj,CCP4XtalData.CMapCoeffsDataFile): comLine.extend(['--data',dobj.__str__()]) paramsFileName = os.path.join(db.getProjectDirectory(jobId=contextJobId),'CCP4_COOT','params.xml') #print 'makeCootParamsFile paramsFileName',paramsFileName container.header.projectId = projectId container.saveDataToXml( fileName=paramsFileName ) return paramsFileName,comLine def getFilesToDisplay(self,jobId): import CCP4Modules,CCP4Data taskName = CCP4Modules.PROJECTSMANAGER().db().getJobInfo(jobId,'taskname') import CCP4TaskManager paramList = CCP4TaskManager.TASKMANAGER().getTaskAttribute(taskName,'MGDISPLAYFILES',None) # No DISPLAYFILES defined for task so Just give the output files if paramList is None: fileNameList = CCP4Modules.PROJECTSMANAGER().db().getJobFiles(jobId=jobId,mode='fullPath') else: import os container = CCP4Modules.PROJECTSMANAGER().db().getParamsContainer(jobId) fileNameList = [] for param in paramList: obj = container.find(param) #print 'LAUNCHER.getFilesToDisplay',param,repr(obj) if obj is not None: if isinstance(obj,(list,CCP4Data.CList)): for item in obj: fileName = str(item) if os.path.exists(fileName): fileNameList.append(fileName) else: fileName = str(obj) if os.path.exists(fileName): fileNameList.append(fileName) #print 'LAUNCHER.getFilesToDisplay',fileNameList return fileNameList def makeCommand(self,viewer='CCP4mg',command=None,data=None): #print 'makeCommand',viewer,command if viewer == 'CCP4mg': if command == 'openFile': if not isinstance(data,QtCore.QString): try: data = QtCore.QString(data) except: print 'Error converting data to QString: '+str(data) return None try: t = unicode(data.toUtf8()).encode('utf-8') except: print 'Error converting data to unicode: '+str(data) return None return "self.emit(QtCore.SIGNAL(\"postEvent\"),{"+ \ "\"type\":"+str(int(QtCore.QEvent.FileOpen))+ \ ",\"file\":"+'"'+t+'"'+ \ "})" return None def queryExecutable(self,viewer,guiParent): import functools from PyQt4 import QtGui import CCP4FileBrowser self.findViewerDialog = CCP4FileBrowser.CFileDialog(guiParent,'Find '+viewer,filters=[' (*)'],projectCombo=False) label = QtGui.QLabel("""Sorry - failed to find """+viewer+""". Please enter the program executable and then view again.\n The executable can also be set in Preferences.""",self.findViewerDialog) label.setStyleSheet( "QLabel { font-weight: bold; border: 2px solid} ") self.findViewerDialog.addWidget(label) self.connect(self.findViewerDialog,QtCore.SIGNAL('selectFile'),functools.partial(self.handleFindViewer,viewer)) self.findViewerDialog.show() self.findViewerDialog.raise_() def handleFindViewer(self,viewer,filePath): import CCP4Modules #print 'handleFindViewer',viewer,filePath if os.path.exists(filePath): if viewer in ['coot','coot_job']: CCP4Modules.PREFERENCES().COOT_EXECUTABLE.set(filePath) else: CCP4Modules.PREFERENCES().CCP4MG_EXECUTABLE.set(filePath) CCP4Modules.PREFERENCES().save() #=================================================================================================== import unittest def TESTSUITE(): suite = unittest.defaultTestLoader.loadTestsFromTestCase(testLaunch) return suite def testModule(): suite = TESTSUITE() unittest.TextTestRunner(verbosity=2).run(suite) class testLaunch(unittest.TestCase): def test1(self): l = CLauncher() com = l.makeCommand(viewer='CCP4mg',command='openFile',data='foo/bar') print 'testLaunch.test1',com self.assertEqual(com[0:7],'','makeCommand failed for openFile')