def run(self, fileStore):
self.configNode = ET.parse(fileStore.readGlobalFile(self.project.getConfigID())).getroot()
self.configWrapper = ConfigWrapper(self.configNode)
self.configWrapper.substituteAllPredefinedConstantsWithLiterals()
# Log the stats for the un-preprocessed assemblies
for name, sequence in self.project.getInputSequenceIDMap().items():
self.addChildJobFn(logAssemblyStats, "Before preprocessing", name, sequence)
# Create jobs to create the output sequences
logger.info("Reading config file from: %s" % self.project.getConfigID())
configFile = fileStore.readGlobalFile(self.project.getConfigID())
configNode = ET.parse(configFile).getroot()
ConfigWrapper(configNode).substituteAllPredefinedConstantsWithLiterals() #This is necessary..
#Add the preprocessor child job. The output is a job promise value that will be
#converted into a list of the IDs of the preprocessed sequences in the follow on job.
preprocessorJob = self.addChild(CactusPreprocessor(self.project.getInputSequenceIDs(), configNode))
self.project.setOutputSequenceIDs([preprocessorJob.rv(i) for i in range(len(self.project.getInputSequenceIDs()))])
#Now build the progressive-down job
schedule = Schedule()
schedule.loadProject(self.project, fileStore=fileStore)
schedule.compute()
self.options.event = self.project.mcTree.getRootName()
leafNames = [ self.project.mcTree.getName(i) for i in self.project.mcTree.getLeaves() ]
fileStore.logToMaster("Leaf names = %s" % leafNames)
self.options.globalLeafEventSet = set(leafNames)
return self.addFollowOn(RunCactusPreprocessorThenProgressiveDown2(options=self.options, project=self.project, event=self.options.event, schedule=schedule, memory=self.configWrapper.getDefaultMemory())).rv()
