Generate an example input object for the given CWL process.
430684
def generate_input_template(tool):
    # type: (Process) -> Dict[Text, Any]
    """"""
    template = yaml.comments.CommentedMap()
    for inp in realize_input_schema(tool.tool["inputs"], tool.schemaDefs):
        name = shortname(inp["id"])
        value, comment = generate_example_input(
            inp['type'], inp.get('default', None))
        template.insert(0, name, value, comment)
    return template
729646
def _get_input_for_run(args, executable, preset_inputs=None, input_name_prefix=None):
    
    # The following may throw if the executable is a workflow with no
    # input spec available (because a stage is inaccessible)
    exec_inputs = try_call(ExecutableInputs,
                           executable,
                           input_name_prefix=input_name_prefix,
                           active_region=args.region)

    # Use input and system requirements from a cloned execution
    if args.input_json is None and args.filename is None:
        # --input-json and --input-json-file completely override input
        # from the cloned job
        exec_inputs.update(args.input_from_clone, strip_prefix=False)

    # Update with inputs passed to the this function
    if preset_inputs is not None:
        exec_inputs.update(preset_inputs, strip_prefix=False)

    # Update with inputs passed with -i, --input_json, --input_json_file, etc.
    # If batch_tsv is set, do not prompt for missing arguments
    require_all_inputs = (args.batch_tsv is None)
    try_call(exec_inputs.update_from_args, args, require_all_inputs)

    return exec_inputs.inputs
119476
def create(alphabet_size: int, output_dim: int, pretrained: bool=False, frozen: bool=False, source: TextData=None):
    
    def instantiate(**_):
        return EmbeddingInput(alphabet_size, output_dim, pretrained=pretrained, frozen=frozen, source=source)

    return ModelFactory.generic(instantiate)
548996
def _generate_examples(self, split_subsets, extraction_map):
    """"""
    source, _ = self.builder_config.language_pair

    def _get_local_paths(ds, extract_dirs):
      rel_paths = ds.get_path(source)
      if len(extract_dirs) == 1:
        extract_dirs = extract_dirs * len(rel_paths)
      return [os.path.join(ex_dir, rel_path) if rel_path else ex_dir
              for ex_dir, rel_path in zip(extract_dirs, rel_paths)]

    for ss_name in split_subsets:
      logging.info("Generating examples from: %s", ss_name)
      ds = DATASET_MAP[ss_name]
      extract_dirs = extraction_map[ss_name]
      files = _get_local_paths(ds, extract_dirs)
      if ss_name.startswith("czeng"):
        if ss_name.endswith("16pre"):
          sub_generator = functools.partial(
              _parse_tsv, language_pair=("en", "cs"))
        elif ss_name.endswith("17"):
          filter_path = _get_local_paths(
              _CZENG17_FILTER, extraction_map[_CZENG17_FILTER.name])[0]
          sub_generator = functools.partial(
              _parse_czeng, filter_path=filter_path)
        else:
          sub_generator = _parse_czeng
      elif len(files) == 2:
        if ss_name.endswith("_frde"):
          sub_generator = _parse_frde_bitext
        else:
          sub_generator = _parse_parallel_sentences
      elif len(files) == 1:
        fname = files[0]
         # Note: Due to formatting used by `download_manager`, the file
         # extension may not be at the end of the file path.
        if ".tsv" in fname:
          sub_generator = _parse_tsv
        elif ss_name.startswith("newscommentary_v14"):
          sub_generator = functools.partial(
              _parse_tsv, language_pair=self.builder_config.language_pair)
        elif "tmx" in fname:
          sub_generator = _parse_tmx
        elif ss_name.startswith("wikiheadlines"):
          sub_generator = _parse_wikiheadlines
        else:
          raise ValueError("Unsupported file format: %s" % fname)
      else:
        raise ValueError("Invalid number of files: %d" % len(files))

      for ex in sub_generator(*files):
        if not all(ex.values()):
          continue
        # TODO(adarob): Add subset feature.
        # ex["subset"] = subset
        yield ex
1033305
protected void _generate(SarlBehaviorUnit handler, PyAppendable it, IExtraLanguageGeneratorContext context) {
		final JvmTypeReference event = handler.getName();
		final String handleName = it.declareUniqueNameVariable(handler, "__on_" + event.getSimpleName() + "__"); //$NON-NLS-1$ //$NON-NLS-2$
		it.append("def ").append(handleName).append("(self, occurrence):"); //$NON-NLS-1$ //$NON-NLS-2$
		it.increaseIndentation().newLine();
		generateDocString(getTypeBuilder().getDocumentation(handler), it);
		if (handler.getExpression() != null) {
			generate(handler.getExpression(), null, it, context);
		} else {
			it.append("pass"); //$NON-NLS-1$
		}
		it.decreaseIndentation().newLine();
		final String key = this.qualifiedNameProvider.getFullyQualifiedName(handler.getDeclaringType()).toString();
		final Map<String, Map<String, List<Pair<XExpression, String>>>> map = context.getMapData(EVENT_GUARDS_MEMENTO);
		Map<String, List<Pair<XExpression, String>>> submap = map.get(key);
		if (submap == null) {
			submap = new HashMap<>();
			map.put(key, submap);
		}
		final String eventId = event.getIdentifier();
		List<Pair<XExpression, String>> guards = submap.get(eventId);
		if (guards == null) {
			guards = new ArrayList<>();
			submap.put(eventId, guards);
		}
		guards.add(new Pair<>(handler.getGuard(), handleName));
	}
789852
def main(argv=None):
    ''''''

    parser = argparse.ArgumentParser()
    parser.add_argument('-i','--input_file', required=True)
    parser.add_argument('--input_file_format', default='sequence')
    parser.add_argument('--input_data_type', default='json')
    parser.add_argument('--input_separator', default='\t')
    parser.add_argument('-o','--output_dir', required=True)
    parser.add_argument('--output_file_format', default='sequence')
    parser.add_argument('--output_data_type', default='json')
    parser.add_argument('--output_separator', default='\t')
    args=parser.parse_args()

    # can be inconvenient to specify tab on the command line
    args.input_separator = "\t" if args.input_separator=='tab' else args.input_separator
    args.output_separator = "\t" if args.output_separator=='tab' else args.output_separator

    sc = SparkContext(appName="fileUtil")
    fUtil = FileUtil(sc)

    ## CONFIG LOAD
    input_kwargs = {"file_format": args.input_file_format,
                   "data_type": args.input_data_type}
    parse_kwargs = {"separator": args.input_separator}
    load_kwargs = merge_dicts(input_kwargs, parse_kwargs)
    
    ## LOAD
    rdd = fUtil.load_file(args.input_file, **load_kwargs)

    ## CONFIG SAVE
    output_kwargs = {"file_format": args.output_file_format,
                     "data_type": args.output_data_type}
    emit_kwargs = {"separator": args.output_separator}
    save_kwargs = merge_dicts(output_kwargs, emit_kwargs)

    ## SAVE
    fUtil.save_file(rdd, args.output_dir, **save_kwargs)
893073
def _piped_input_cl(data, region, tmp_dir, out_base_file, prep_params):
    
    return data["work_bam"], _gatk_extract_reads_cl(data, region, prep_params, tmp_dir)
320945
def libvlc_vlm_set_input(p_instance, psz_name, psz_input):
    '''
    '''
    f = _Cfunctions.get('libvlc_vlm_set_input', None) or \
        _Cfunction('libvlc_vlm_set_input', ((1,), (1,), (1,),), None,
                    ctypes.c_int, Instance, ctypes.c_char_p, ctypes.c_char_p)
    return f(p_instance, psz_name, psz_input)
882990
def _create_examples(self, lines, set_type):
        """"""
        examples = []
        for (i, line) in enumerate(lines):
            if i == 0:
                continue
            guid = "%s-%s" % (set_type, i)
            text_a = line[3]
            text_b = line[4]
            label = line[0]
            examples.append(
                InputExample(guid=guid, text_a=text_a, text_b=text_b, label=label))
        return examples
1298433
def generate_instance_commands():
    ''' 

    '''
    from spython.instance import Instance

    from spython.main.base.logger import println
    from spython.main.instances import instances
    from spython.utils import run_command as run_cmd

    # run_command uses run_cmd, but wraps to catch error
    from spython.main.base.command import ( init_command, run_command )
    from spython.main.base.generate import RobotNamer
    from .start import start
    from .stop import stop

    Instance.RobotNamer = RobotNamer()
    Instance._init_command = init_command
    Instance.run_command = run_cmd
    Instance._run_command = run_command
    Instance._list = instances  # list command is used to get metadata
    Instance._println = println
    Instance.start = start     # intended to be called on init, not by user
    Instance.stop = stop

    # Give an instance the ability to breed :)
    Instance.instance = Instance
 
    return Instance
85900
def makeJob(tool, jobobj, step_inputs, runtime_context):
    

    if tool.tool["class"] == "Workflow":
        wfjob = CWLWorkflow(tool, jobobj, runtime_context)
        followOn = ResolveIndirect(wfjob.rv())
        wfjob.addFollowOn(followOn)
        return (wfjob, followOn)
    else:
        # get_requirement
        resourceReq, _ = tool.get_requirement("ResourceRequirement")
        if resourceReq:
            for req in ("coresMin", "coresMax", "ramMin", "ramMax",
                        "tmpdirMin", "tmpdirMax", "outdirMin", "outdirMax"):
                r = resourceReq.get(req)
                if isinstance(r, string_types) and ("$(" in r or "${" in r):
                    # Found a dynamic resource requirement so use a job wrapper
                    job = CWLJobWrapper(tool, jobobj, runtime_context)
                    return (job, job)
        job = CWLJob(tool, jobobj, runtime_context)
        return (job, job)
1008266
def _generate_examples(self, archive_paths, objects_getter, bboxes_getter,
                         prefixes=None):
    """"""
    trainable_classes = set(
        self.info.features['objects_trainable']['label'].names)
    for i, archive_path in enumerate(archive_paths):
      prefix = prefixes[i] if prefixes else None
      objects = objects_getter(prefix)
      bboxes = bboxes_getter(prefix)
      logging.info('Opening archive %s ...', archive_path)
      archive = tfds.download.iter_archive(
          archive_path, tfds.download.ExtractMethod.TAR_STREAM)
      for fpath, fobj in archive:
        fname = os.path.basename(fpath)
        image_id = int(os.path.splitext(fname)[0], 16)
        image_objects = [obj._asdict() for obj in objects.get(image_id, [])]
        image_bboxes = [bbox._asdict() for bbox in bboxes.get(image_id, [])]
        image_objects_trainable = [
            obj for obj in image_objects if obj['label'] in trainable_classes
        ]
        yield {
            'image': _resize_image_if_necessary(
                fobj, target_pixels=self.builder_config.target_pixels),
            'image/filename': fname,
            'objects': image_objects,
            'objects_trainable': image_objects_trainable,
            'bobjects': image_bboxes,
        }
1364958
def write_workflow(self, request, opts, cwd, wftype='cwl'):
        """"""

        workflow_url = request.get("workflow_url")

        # link the cwl and json into the cwd
        if workflow_url.startswith('file://'):
            os.link(workflow_url[7:], os.path.join(cwd, "wes_workflow." + wftype))
            workflow_url = os.path.join(cwd, "wes_workflow." + wftype)
        os.link(self.input_json, os.path.join(cwd, "wes_input.json"))
        self.input_json = os.path.join(cwd, "wes_input.json")

        extra_options = self.sort_toil_options(opts.getoptlist("extra"))
        if wftype == 'cwl':
            command_args = ['toil-cwl-runner'] + extra_options + [workflow_url, self.input_json]
        elif wftype == 'wdl':
            command_args = ['toil-wdl-runner'] + extra_options + [workflow_url, self.input_json]
        elif wftype == 'py':
            command_args = ['python'] + extra_options + [workflow_url]
        else:
            raise RuntimeError('workflow_type is not "cwl", "wdl", or "py": ' + str(wftype))

        return command_args
694466
def _nested_cwl_record(xs, want_attrs, input_files):
    
    if isinstance(xs, (list, tuple)):
        return [_nested_cwl_record(x, want_attrs, input_files) for x in xs]
    else:
        assert isinstance(xs, dict), pprint.pformat(xs)
        return _collapse_to_cwl_record_single(xs, want_attrs, input_files)
169808
def example(fn):
    ''''''

    @functools.wraps(fn)
    def wrapped():
        try:
            sys.stdout.write('Running: %s\n' % fn.__name__)
            fn()
            sys.stdout.write('\n')
        except KeyboardInterrupt:
            sys.stdout.write('\nSkipping example.\n\n')
            # Sleep a bit to make killing the script easier
            time.sleep(0.2)

    examples.append(wrapped)
    return wrapped
1064370
function(input) {
  var code = 'var $_parsers = {\n';
  var parsernames = Object.keys(parsers);
  for (var i = 0; i < parsernames.length; i++) {
    code += '  ' + JSON.stringify(parsernames[i]) + ': ' +
      parsers[parsernames[i]].toString() + ',\n';
  };
  code += '}\n';
  code += compile(input) + '\nif (typeof $_end === "function") {$_end();}';
  var script = new vm.Script(code, {timeout: 4 * 60 * 1000});
  var runner = function(scope) {
    var output = '';
    var pipeOpen = false;
    var ended = false;
    var stream = new Readable({
      encoding: 'utf8',
      read: function() {
        pipeOpen = true;
        if (ended && output === '') {
          pipeOpen = this.push(null);
        } else if (output !== '') {
          pipeOpen = this.push(output);
          output = '';
        }
      },
    });
    scope.$_scope = scope;
    scope.$_write = function(data) {
      output += '' + data;
      if (pipeOpen && output !== '') {
        pipeOpen = stream.push(output);
        output = '';
      }
    };
    scope.$_end = function() {
      ended = true;
      if (pipeOpen) { stream.push(null); }
    };
    script.runInNewContext(scope)
    return stream;
  };
  runner.code = code;
  return runner;
}
231380
def generate_command(self):
        
        example = []
        example.append(f"{sys.argv[0]}")
        for key in sorted(list(self.spec.keys())):
            if self.spec[key]['type'] == list:
                value = " ".join(self.spec[key].get('example', ''))
            elif self.spec[key]['type'] == dict:
                value = f"\'{json.dumps(self.spec[key].get('example', ''))}\'"
            else:
                value = self.spec[key].get('example', '')
            string = f"     --{key.lower()} {value}"
            example.append(string)
        print(" \\\n".join(example))