def run(self, job, job_dir=None): job_dir = job_dir or job.id os.mkdir(job_dir) os.chmod(job_dir, os.stat(job_dir).st_mode | stat.S_IROTH | stat.S_IWOTH) self.cli_job = CLIJob(job) if self.requirements.container: self.ensure_files(job, job_dir) abspath_job = copy.deepcopy(job) self.install(job=job) cmd_line = self.command_line(job, job_dir) self.job_dump(job, job_dir) self.requirements.container.run(cmd_line) with open(os.path.abspath(job_dir) + '/result.cwl.json', 'w') as f: outputs = self.cli_job.get_outputs(os.path.abspath(job_dir), abspath_job) json.dump(outputs, f) for k, v in six.iteritems(outputs): if isinstance(v, list): for f in v: with open(f['path'] + '.rbx.json', 'w') as rx: json.dump(f, rx) elif isinstance(v, dict): with open(v['path'] + '.rbx.json', 'w') as rx: json.dump(v, rx) return outputs
def get_command_line(): data = request.get_json(force=True) tool = process_builder(ctx, data['tool_cfg']) inputs = { strip_prefix(k): construct_files(v, tool._inputs[k].validator) for k, v in data['input_map'].iteritems() } job = Job('Fake job ID', tool, inputs, {'cpu': 1, 'mem': 1024}, ctx) cli_job = CLIJob(job) return json.dumps( { 'arguments': cli_job.make_arg_list(), 'stdin': cli_job.stdin, 'stdout': cli_job.stdout, }, indent=2)
def get_outputs(): data = request.get_json(force=True) tool = process_builder(ctx, data['tool_cfg']) inputs = { strip_prefix(k): construct_files(v, tool._inputs[k].validator) for k, v in data['input_map'].iteritems() } job = Job('Fake job ID', tool, inputs, {'cpu': 1, 'mem': 1024}, ctx) cli_job = CLIJob(job) status = 'SUCCESS' if data['exit_code'] in data['tool_cfg'].get('successCodes', [0])\ else 'FAILURE' return json.dumps( { 'status': status, 'outputs': cli_job.get_outputs(data['job_dir'], job), }, indent=2)
def run(self, job, job_dir=None): job_dir = os.path.abspath(job_dir or job.id) if not job_dir.endswith('/'): job_dir += '/' os.mkdir(job_dir) os.chmod(job_dir, os.stat(job_dir).st_mode | stat.S_IROTH | stat.S_IWOTH) self.cli_job = CLIJob(job) if self.container: self.ensure_files(job, job_dir) abspath_job = Job(job.id, job.app, copy.deepcopy(job.inputs), job.allocated_resources, job.context) self.install(job=job) cmd_line = self.command_line(job, job_dir) self.job_dump(job, job_dir) self.container.run(cmd_line, job_dir) result_path = os.path.abspath(job_dir) + '/result.cwl.json' if os.path.exists(result_path): with open(result_path, 'r') as res: outputs = json.load(res) else: with open(result_path, 'w') as res: outputs = self.cli_job.get_outputs( os.path.abspath(job_dir), abspath_job) json.dump(outputs, res) outputs = { o.id: construct_files(outputs.get(o.id), o.validator) for o in job.app.outputs } self.unmap_paths(outputs) def write_rbx(f): if isinstance(f, File): with open(f.path + '.rbx.json', 'w') as rbx: json.dump(f.to_dict(), rbx) map_rec_collection(write_rbx, outputs) return outputs
def run(self, job, job_dir=None): self.load_input_content(job) job_dir = os.path.abspath(job_dir or job.id) if not job_dir.endswith('/'): job_dir += '/' if not os.path.exists(job_dir): os.mkdir(job_dir) os.chmod(job_dir, os.stat(job_dir).st_mode | stat.S_IROTH | stat.S_IWOTH) self.cli_job = CLIJob(job) eval = ValueResolver(job) cfr = self.get_requirement_or_hint(CreateFileRequirement) if cfr: cfr.create_files(job_dir, eval) env = None evr = self.get_requirement_or_hint(EnvVarRequirement) if evr: env = evr.var_map(eval) self.ensure_files(job, job_dir) self.install(job=job) abspath_job = Job(job.id, job.app, copy.deepcopy(job.inputs), job.allocated_resources, job.context) cmd_line = self.command_line(job, job_dir) log.info("Running: %s" % cmd_line) self.job_dump(job, job_dir) if self.container: self.container.run(cmd_line, job_dir, env) else: ret = subprocess.call(['bash', '-c', cmd_line], cwd=job_dir) if ret != 0: raise RabixError("Command failed with exit status %s" % ret) result_path = os.path.abspath(job_dir) + '/cwl.output.json' if os.path.exists(result_path): with open(result_path, 'r') as res: outputs = json.load(res) else: with open(result_path, 'w') as res: outputs = self.cli_job.get_outputs(os.path.abspath(job_dir), abspath_job) json.dump(job.context.to_primitive(outputs), res) self.unmap_paths(outputs) def write_rbx(f): if isinstance(f, File): with open(f.path + '.rbx.json', 'w') as rbx: json.dump(f.to_dict(), rbx) map_rec_collection(write_rbx, outputs) return outputs