def conformance_test(context, app, job_dict, basedir):
job_dict['@type'] = 'Job'
job_dict['@id'] = basedir
job_dict['app'] = app
if not app.outputs:
app.outputs = rabix.schema.JsonSchema(context, {
'type': 'object',
'properties': {}
})
inputs = rebase_paths(app, job_dict['inputs'], basedir)
inputs = get_inputs(app, inputs)
dot_update_dict(job_dict['inputs'], inputs)
job = context.from_dict(job_dict)
adapter = CLIJob(job)
print(json.dumps({
'args': adapter.make_arg_list(),
'stdin': adapter.stdin,
'stdout': adapter.stdout,
}))
def conformance_test(context, app, job_dict, basedir):
job_dict['class'] = 'Job'
job_dict['id'] = basedir
job_dict['app'] = app
if not app.outputs:
app.outputs = []
job_dict['inputs'] = get_inputs(job_dict, app.inputs, basedir)
job = Job.from_dict(context, job_dict)
adapter = CLIJob(job)
result = {
'args': adapter.make_arg_list(),
'stdin': adapter.stdin,
'stdout': adapter.stdout,
}
cfr = app.get_requirement(CreateFileRequirement)
e = ValueResolver(job)
if cfr:
result['createfiles'] = {
name: content
for name, content in cfr.resolve_file_defs(e)
}
print(json.dumps(result))
def conformance_test(context, app, job_dict, basedir):
job_dict['class'] = 'Job'
job_dict['id'] = basedir
job_dict['app'] = app
if not app.outputs:
app.outputs = []
job_dict['inputs'] = get_inputs(job_dict, app.inputs, basedir)
job = Job.from_dict(context, job_dict)
adapter = CLIJob(job)
print(json.dumps({
'args': adapter.make_arg_list(),
'stdin': adapter.stdin,
'stdout': adapter.stdout,
}))
def conformance_test(context, app, job_dict, basedir):
job_dict['class'] = 'Job'
job_dict['id'] = basedir
job_dict['app'] = app
if not app.outputs:
app.outputs = []
job_dict['inputs'] = get_inputs(job_dict, app.inputs, basedir)
job = Job.from_dict(context, job_dict)
adapter = CLIJob(job)
print(
json.dumps({
'args': adapter.make_arg_list(),
'stdin': adapter.stdin,
'stdout': adapter.stdout,
}))
def conformance_test(context, app, job_dict, basedir):
job_dict['@type'] = 'Job'
job_dict['@id'] = basedir
job_dict['app'] = app
if not app.outputs:
app.outputs = rabix.schema.JsonSchema(context, {
'type': 'object',
'properties': {}
})
job_dict['inputs'] = get_inputs(app, job_dict['inputs'], basedir)
job = context.from_dict(job_dict)
adapter = CLIJob(job)
print(json.dumps({
'args': adapter.make_arg_list(),
'stdin': adapter.stdin,
'stdout': adapter.stdout,
}))
def main():
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:
print("Couldn't find tool.")
return
fix_types(tool, dry_run_args.get('--type', 'CommandLine'))
context = init_context()
app = context.from_dict(tool)
job = None
if isinstance(app, Job):
job = app
app = job.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 = TEMPLATE_JOB
logging.root.setLevel(log_level(dry_run_args['--verbose']))
if args['--inp-file']:
basedir = os.path.dirname(args.get('--inp-file'))
input_file = from_url(args.get('--inp-file'))
rebased = rebase_paths(app, input_file, basedir)
dot_update_dict(
job_dict['inputs'],
get_inputs(app, rebased)
)
input_usage = job_dict['inputs']
if job:
basedir = os.path.dirname(args.get('<tool>'))
rebased = rebase_paths(app, job.inputs, basedir)
dot_update_dict(job.inputs, rebased)
job.inputs.update(get_inputs(app, job.inputs))
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
inp = get_inputs(app, app_inputs)
if not job:
job_dict['inputs'].update(inp)
job_dict['@id'] = args.get('--dir')
job_dict['app'] = app
job = Job.from_dict(context, job_dict)
else:
job.inputs.update(inp)
if args['--print-cli']:
if not isinstance(app, CliApp):
print(dry_run_args['<tool>'] + " is not a command line app")
return
print(CLIJob(job).cmd_line())
return
if not job.inputs and not args['--']:
print(app_usage)
return
try:
context.executor.execute(job, lambda _, result: print(result))
except RabixError as err:
print(err.message)
sys.exit(1)
except docopt.DocoptExit:
print(app_usage)
sys.exit(1)
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)