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 from_dict(cls, context, d):
cls.infer_step_id(d)
converted = {
k: process_builder(context, v) if k == 'run' else context.from_dict(v)
for k, v in six.iteritems(d)
}
kwargs = Process.kwarg_dict(converted)
kwargs.update({
'app': converted['run'],
'inputs': [WorkflowStepInput.from_dict(context, inp)
for inp in converted.get('inputs', [])],
'outputs': [OutputParameter.from_dict(context, inp)
for inp in converted.get('outputs', [])],
'scatter': converted.get('scatter')
})
return cls(**kwargs)
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 get_outputs():
data = request.get_json(force=True)
tool = process_builder(ctx, data['tool_cfg'])
inputs = {strip_prefix(k): construct_files(v, tool._inputs[strip_prefix(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)
print data
# status = 'SUCCESS' if data['exit_code'] in data['tool_cfg'].get('successCodes', [0]) else 'FAILURE'
status = 'SUCCESS'
outputs = cli_job.get_outputs(data['job_dir'], job)
if inputs:
key = inputs.keys()[0]
prefix = key[0:key.rfind('.')+1]
outputs = {prefix + k: v for k, v in outputs.iteritems()}
return json.dumps({
'status': status,
'outputs': outputs,
})
def from_dict(cls, context, d):
cls.infer_step_id(d)
converted = {
k:
process_builder(context, v) if k == 'run' else context.from_dict(v)
for k, v in six.iteritems(d)
}
kwargs = Process.kwarg_dict(converted)
kwargs.update({
'app':
converted['run'],
'inputs': [
WorkflowStepInput.from_dict(context, inp)
for inp in converted.get('inputs', [])
],
'outputs': [
OutputParameter.from_dict(context, inp)
for inp in converted.get('outputs', [])
],
'scatter':
converted.get('scatter')
})
return cls(**kwargs)
def main():
disable_warnings()
logging.basicConfig(level=logging.WARN)
if len(sys.argv) == 1:
print(USAGE)
return
usage = USAGE.format(resources=make_resources_usage_string(),
inputs='<inputs>')
app_usage = usage
if len(sys.argv) == 2 and \
(sys.argv[1] == '--help' or sys.argv[1] == '-h'):
print(USAGE)
return
dry_run_args = dry_run_parse()
if not dry_run_args:
print(USAGE)
return
if not (dry_run_args['<tool>']):
print('You have to specify a tool, with --tool option')
print(usage)
return
tool = get_tool(dry_run_args)
if not tool:
fail("Couldn't find tool.")
if isinstance(tool, list):
tool = loader.index.get('#main')
if 'class' not in tool:
fail("Document must have a 'class' field")
if 'id' not in tool:
tool['id'] = dry_run_args['<tool>']
context = init_context(tool)
app = process_builder(context, tool)
job = None
if isinstance(app, Job):
job = app
app = job.app
rabix.expressions.update_engines(app)
if dry_run_args['--install']:
app.install()
print("Install successful.")
return
if dry_run_args['--conformance-test']:
job_dict = from_url(dry_run_args['<job>'])
conformance_test(context, app, job_dict, dry_run_args.get('--basedir'))
return
try:
args = docopt.docopt(usage, version=version, help=False)
job_dict = copy.deepcopy(TEMPLATE_JOB)
logging.root.setLevel(log_level(dry_run_args['--verbose']))
input_file_path = args.get('<inp>') or args.get('--inp-file')
if input_file_path:
basedir = os.path.dirname(os.path.abspath(input_file_path))
input_file = from_url(input_file_path)
inputs = get_inputs(input_file, app.inputs, basedir)
job_dict['inputs'].update(inputs)
input_usage = job_dict['inputs']
if job:
basedir = os.path.dirname(args.get('<tool>'))
job.inputs = get_inputs(job.inputs, app.inputs, basedir)
input_usage.update(job.inputs)
app_inputs_usage = make_app_usage_string(
app, template=TOOL_TEMPLATE, inp=input_usage)
app_usage = make_app_usage_string(app, USAGE, job_dict['inputs'])
try:
app_inputs = docopt.docopt(app_inputs_usage, args['<inputs>'])
except docopt.DocoptExit:
if not job:
raise
for inp in job.app.inputs:
if inp.required and inp.id not in job.inputs:
raise
app_inputs = {}
if args['--help']:
print(app_usage)
return
# trim leading --, and ignore empty arays
app_inputs = {
k[2:]: v
for k, v in six.iteritems(app_inputs)
if v != []
}
inp = get_inputs(app_inputs, app.inputs)
if not job:
job_dict['id'] = args.get('--outdir') or args.get('--dir')
job_dict['app'] = app
job = Job.from_dict(context, job_dict)
job.inputs.update(inp)
if args['--print-cli']:
if not isinstance(app, CommandLineTool):
fail(dry_run_args['<tool>'] + " is not a command line app")
print(CLIJob(job).cmd_line())
return
if args['--pretty-print']:
fmt = partial(result_str, job.id)
else:
fmt = lambda result: json.dumps(context.to_primitive(result))
if not job.inputs and not args['--'] and not args['--quiet']:
print(app_usage)
return
try:
context.executor.execute(job, lambda _, result: print(fmt(result)))
except RabixError as err:
fail(err.message)
except docopt.DocoptExit:
fail(app_usage)
def main():
disable_warnings()
logging.basicConfig(level=logging.WARN)
if len(sys.argv) == 1:
print(USAGE)
return
usage = USAGE.format(resources=make_resources_usage_string(),
inputs='<inputs>')
app_usage = usage
if len(sys.argv) == 2 and \
(sys.argv[1] == '--help' or sys.argv[1] == '-h'):
print(USAGE)
return
dry_run_args = dry_run_parse()
if not dry_run_args:
print(USAGE)
return
if not (dry_run_args['<tool>']):
print('You have to specify a tool, with --tool option')
print(usage)
return
tool = get_tool(dry_run_args)
if not tool:
fail("Couldn't find tool.")
if isinstance(tool, list):
tool = loader.index.get('#main')
if 'class' not in tool:
fail("Document must have a 'class' field")
if 'id' not in tool:
tool['id'] = dry_run_args['<tool>']
context = init_context(tool)
app = process_builder(context, tool)
job = None
if isinstance(app, Job):
job = app
app = job.app
rabix.expressions.update_engines(app)
if dry_run_args['--install']:
app.install()
print("Install successful.")
return
if dry_run_args['--conformance-test']:
job_dict = from_url(dry_run_args['<job>'])
conformance_test(context, app, job_dict, dry_run_args.get('--basedir'))
return
try:
args = docopt.docopt(usage, version=version, help=False)
job_dict = copy.deepcopy(TEMPLATE_JOB)
logging.root.setLevel(log_level(dry_run_args['--verbose']))
input_file_path = args.get('<inp>') or args.get('--inp-file')
if input_file_path:
basedir = os.path.dirname(os.path.abspath(input_file_path))
input_file = from_url(input_file_path)
inputs = get_inputs(input_file, app.inputs, basedir)
job_dict['inputs'].update(inputs)
input_usage = job_dict['inputs']
if job:
basedir = os.path.dirname(args.get('<tool>'))
job.inputs = get_inputs(job.inputs, app.inputs, basedir)
input_usage.update(job.inputs)
app_inputs_usage = make_app_usage_string(app,
template=TOOL_TEMPLATE,
inp=input_usage)
app_usage = make_app_usage_string(app, USAGE, job_dict['inputs'])
try:
app_inputs = docopt.docopt(app_inputs_usage, args['<inputs>'])
except docopt.DocoptExit:
if not job:
raise
for inp in job.app.inputs:
if inp.required and inp.id not in job.inputs:
raise
app_inputs = {}
if args['--help']:
print(app_usage)
return
# trim leading --, and ignore empty arays
app_inputs = {
k[2:]: v
for k, v in six.iteritems(app_inputs) if v != []
}
inp = get_inputs(app_inputs, app.inputs)
if not job:
job_dict['id'] = args.get('--outdir') or args.get('--dir')
job_dict['app'] = app
job = Job.from_dict(context, job_dict)
job.inputs.update(inp)
if args['--print-cli']:
if not isinstance(app, CommandLineTool):
fail(dry_run_args['<tool>'] + " is not a command line app")
print(CLIJob(job).cmd_line())
return
if args['--pretty-print']:
fmt = partial(result_str, job.id)
else:
fmt = lambda result: json.dumps(context.to_primitive(result))
if not job.inputs and not args['--'] and not args['--quiet']:
print(app_usage)
return
try:
context.executor.execute(job, lambda _, result: print(fmt(result)))
except RabixError as err:
fail(err.message)
except docopt.DocoptExit:
fail(app_usage)
