How to use the cwltool.pathmapper.visit_class function in cwltool

'{0}: Embedded tool outputs: \n {1}'.format(self.task_id, json.dumps(output, indent=4)))

        promises = {}


        for out in self.cwl_step.tool["outputs"]:

            out_id = shortname(out["id"])
            jobout_id = out_id.split("/")[-1]
            try:
                promises[out_id] = output[jobout_id]
            except:
                continue

        # Unsetting the Generation from final output object
        visit_class(promises, ("File",), MutationManager().unset_generation)

        data = {"promises": promises, "outdir": self.outdir}

        _logger.info(
            '{0}: Output: \n {1}'.format(self.task_id, json.dumps(data, indent=4)))

        return data

discover_secondary_files(
            obj["inputs"],
            {shortname(t["id"]): t["default"] for t in obj["inputs"]
             if "default" in t},
            discovered)

    visit_class(workflowobj, ("CommandLineTool", "Workflow"),
                discover_default_secondary_files)
    for entry in list(discovered.keys()):
        # Only interested in discovered secondaryFiles which are local
        # files that need to be uploaded.
        if not entry.startswith("file:"):
            del discovered[entry]
    visit_class(workflowobj, ("Directory"), functools.partial(
        ftp_upload, remote_storage_url, ftp_access))
    visit_class(workflowobj, ("File"), functools.partial(
        ftp_upload, remote_storage_url, ftp_access))
    visit_class(discovered, ("Directory"), functools.partial(
        ftp_upload, remote_storage_url, ftp_access))
    visit_class(discovered, ("File"), functools.partial(
        ftp_upload, remote_storage_url, ftp_access))

visit_class(obj["default"], ("File", "Directory"),
                    ensure_default_location)
        if remove[0]:
            del obj["default"]
    find_defaults(workflowobj, visit_default)

    discovered = {}

    def discover_default_secondary_files(obj):
        discover_secondary_files(
            obj["inputs"],
            {shortname(t["id"]): t["default"] for t in obj["inputs"]
             if "default" in t},
            discovered)

    visit_class(workflowobj, ("CommandLineTool", "Workflow"),
                discover_default_secondary_files)
    for entry in list(discovered.keys()):
        # Only interested in discovered secondaryFiles which are local
        # files that need to be uploaded.
        if not entry.startswith("file:"):
            del discovered[entry]
    visit_class(workflowobj, ("Directory"), functools.partial(
        ftp_upload, remote_storage_url, ftp_access))
    visit_class(workflowobj, ("File"), functools.partial(
        ftp_upload, remote_storage_url, ftp_access))
    visit_class(discovered, ("Directory"), functools.partial(
        ftp_upload, remote_storage_url, ftp_access))
    visit_class(discovered, ("File"), functools.partial(
        ftp_upload, remote_storage_url, ftp_access))

def import_files(tool):
                visit_class(tool, ("File", "Directory"), path_to_loc)
                visit_class(tool, ("File", ), functools.partial(
                    add_sizes, fs_access))
                normalizeFilesDirs(tool)
                adjustDirObjs(tool, functools.partial(
                    get_listing, fs_access, recursive=True))
                adjustFileObjs(tool, functools.partial(
                    uploadFile, toil.importFile, fileindex, existing,
                    skip_broken=True))

def discover_default_secondary_files(obj):
        discover_secondary_files(
            obj["inputs"],
            {shortname(t["id"]): t["default"] for t in obj["inputs"]
             if "default" in t},
            discovered)

    visit_class(workflowobj, ("CommandLineTool", "Workflow"),
                discover_default_secondary_files)
    for entry in list(discovered.keys()):
        # Only interested in discovered secondaryFiles which are local
        # files that need to be uploaded.
        if not entry.startswith("file:"):
            del discovered[entry]
    visit_class(workflowobj, ("Directory"), functools.partial(
        ftp_upload, remote_storage_url, ftp_access))
    visit_class(workflowobj, ("File"), functools.partial(
        ftp_upload, remote_storage_url, ftp_access))
    visit_class(discovered, ("Directory"), functools.partial(
        ftp_upload, remote_storage_url, ftp_access))
    visit_class(discovered, ("File"), functools.partial(
        ftp_upload, remote_storage_url, ftp_access))

{shortname(t["id"]): t["default"] for t in obj["inputs"]
             if "default" in t},
            discovered)

    visit_class(workflowobj, ("CommandLineTool", "Workflow"),
                discover_default_secondary_files)
    for entry in list(discovered.keys()):
        # Only interested in discovered secondaryFiles which are local
        # files that need to be uploaded.
        if not entry.startswith("file:"):
            del discovered[entry]
    visit_class(workflowobj, ("Directory"), functools.partial(
        ftp_upload, remote_storage_url, ftp_access))
    visit_class(workflowobj, ("File"), functools.partial(
        ftp_upload, remote_storage_url, ftp_access))
    visit_class(discovered, ("Directory"), functools.partial(
        ftp_upload, remote_storage_url, ftp_access))
    visit_class(discovered, ("File"), functools.partial(
        ftp_upload, remote_storage_url, ftp_access))

if p.type == "File":
            file_store.exportFile(FileID.unpack(p.resolved[7:]), "file://" + p.target)
        elif p.type == "Directory" and not os.path.exists(p.target):
            os.makedirs(p.target, 0o0755)
        elif p.type == "CreateFile":
            with open(p.target, "wb") as n:
                n.write(p.resolved.encode("utf-8"))

    def _check_adjust(f):
        f["location"] = schema_salad.ref_resolver.file_uri(
            pm.mapper(f["location"])[1])
        if "contents" in f:
            del f["contents"]
        return f

    visit_class(cwljob, ("File", "Directory"), _check_adjust)

def import_files(tool):
                visit_class(tool, ("File", "Directory"), path_to_loc)
                visit_class(tool, ("File", ), functools.partial(
                    add_sizes, fs_access))
                normalizeFilesDirs(tool)
                adjustDirObjs(tool, functools.partial(
                    get_listing, fs_access, recursive=True))
                adjustFileObjs(tool, functools.partial(
                    uploadFile, toil.importFile, fileindex, existing,
                    skip_broken=True))

def visit_default(obj):
        remove = [False]

        def ensure_default_location(fileobj):
            if "location" not in fileobj and "path" in fileobj:
                fileobj["location"] = fileobj["path"]
                del fileobj["path"]
            if "location" in fileobj \
                    and not ftp_access.exists(fileobj["location"]):
                # Delete "default" from workflowobj
                remove[0] = True
        visit_class(obj["default"], ("File", "Directory"),
                    ensure_default_location)
        if remove[0]:
            del obj["default"]
    find_defaults(workflowobj, visit_default)