def run(self):
try:
if not os.path.exists(self.outputFile):
Configs.log("Running a task, output file: {}".format(
self.outputFile))
mod = importlib.import_module(
Task.functionModuleMap[self.taskType])
func = getattr(mod, self.taskType)
func(**self.taskArgs)
Configs.log("Completed a task, output file: {}".format(
self.outputFile))
else:
Configs.log("File already exists: {}".format(self.outputFile))
except Exception as exc:
Configs.error("Task for {} threw an exception:\n{}".format(
self.outputFile, exc))
Configs.error(traceback.format_exc())
raise
finally:
self.isFinished = True
def main():
'''
Resolve the args/configs, spin up the task manager (which deals with worker threads and handles parallelism),
and get started on the main alignment task.
'''
startTime = time.time()
args = parseArgs()
buildConfigs(args)
Configs.log("MAGUS was run with: {}".format(" ".join(sys.argv)))
try:
manager.startTaskManager()
mainAlignmentTask()
except:
Configs.error("MAGUS aborted with an exception..")
Configs.error(traceback.format_exc())
finally:
manager.stopTaskManager()
endTime = time.time()
Configs.log("MAGUS finished in {} seconds..".format(endTime - startTime))
def runCommand(**kwargs):
command = kwargs["command"]
Configs.log("Running an external tool, command: {}".format(command))
runner = subprocess.run(command, shell = True, cwd = kwargs["workingDir"], universal_newlines = True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
try:
runner.check_returncode()
except:
Configs.error("Command encountered error: {}".format(command))
Configs.error("Exit code: {}".format(runner.returncode))
Configs.error("Output: {}".format(runner.stdout))
raise
for srcPath, destPath in kwargs.get("fileCopyMap", {}).items():
shutil.move(srcPath, destPath)
def checkTaskManager():
if not TaskManager.managerFuture.running():
Configs.error("Task manager is dead for some reason..")
TaskManager.managerFuture.result()
raise Exception("Task manager is dead for some reason..")
