hpcSPAdes rebase, cleanup & implementation #1380
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asl
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| if not options_storage.args.only_generate_config: | ||
| executor = executor_local.Executor(log) | ||
| executor.execute(commands) | ||
| executor = get_executor(log) |
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I don't like assigning a new functionality to the same variable, but overall fine I guess
| else: | ||
| jobs = executor.execute(commands) | ||
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| if jobs is not None and len(jobs): |
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I job is a list or None this will do as well
if jobs:
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| def get_executor(log): | ||
| import importlib | ||
| module_name = "executor_" + options_storage.args.grid_engine |
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would making grid_engine a function parameter make any sense?
| def generate_job_uuid(self): | ||
| return ('hpcSPAdes_' if self.mpi_support else 'SPAdes_') + \ | ||
| self.STAGE.replace(' ', '_') + "_" + \ | ||
| ''.join([random.choice(string.ascii_uppercase + string.digits) for k in range(32)]) |
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can also use
("%x" % random.randint(0, 1 << 128)).upper()
but doesn't matter really
| command = [commands_parser.Command( | ||
| STAGE="K%d" % self.K, | ||
| path=os.path.join(self.bin_home, "spades-core"), | ||
| path=os.path.join(self.bin_home, "{spades_core}"), |
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| class ExecutorCluster(ExecutorBase): | ||
| grid_engine = None |
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isn't it supposed to be inside __init__() ?
this defines static members, is it on purpose?
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| def get_MPI_command(self, command, prev_job_name=""): | ||
| cmd = self.grid_engine_submit_command + " " |
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does it makes sense to make a list of strings and then do command.join(' ')?
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| @abstractmethod | ||
| def touch_file(self, command): | ||
| def join(self, job_name): |
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you can also put raise NotImplementedError()
asl
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For now PR to run tests