def updateProject(path): mcProj = MultiCactusProject() mcProj.readXML(path) basePath, name = os.path.split(path) for name,oldPath in mcProj.expMap.items(): fileName = os.path.basename(oldPath) dirName = os.path.dirname(oldPath).rpartition('/')[2] newPath = os.path.join(basePath, dirName, fileName) if not os.path.isfile(newPath): raise RuntimeError("Experiment file %s not found\n" % newPath) mcProj.expMap[name] = newPath exp = ExperimentWrapper(ET.parse(newPath).getroot()) oldDbDir = exp.getDbDir() if oldDbDir is not None: dbDirName = oldDbDir[oldDbDir.find(name):] newDbDir = os.path.join(basePath, dbDirName) exp.setDbDir(newDbDir) oldRefPath = exp.getReferencePath() if oldRefPath is not None: refName = oldRefPath[oldRefPath.find(name):] newRefPath = os.path.join(basePath, refName) exp.setReferencePath(newRefPath) oldHalPath = exp.getHALPath() if oldHalPath is not None: halName = oldHalPath[oldHalPath.find(name):] newHalPath = os.path.join(basePath, halName) exp.setHALPath(newHalPath) oldHalFastaPath = exp.getHALFastaPath() if oldHalFastaPath is not None: halFastaName = oldHalFastaPath[oldHalFastaPath.find(name):] newHalFastaPath = os.path.join(basePath, halFastaName) exp.setHALFastaPath(newHalFastaPath) # seems to have dissappeared from experiment? #oldMafPath = exp.getMAFPath() #if oldMafPath is not None: # mafName = oldMafPath[oldMafPath.find(name):] # newMafPath = os.path.join(basePath, mafName) # exp.setMAFPath(newMafPath) if exp.getDbType() == "kyoto_tycoon": oldHostName = exp.getDbHost() if oldHostName is not None: newHostName = socket.gethostname() exp.setDbHost(newHostName) system("cp %s %s.old" %(newPath, newPath)) exp.writeXML(newPath) mcProj.writeXML(path)