Beispiel #1
0
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))
Beispiel #2
0
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)
Beispiel #3
0
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)