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
