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)
