--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.7/site-packages/cwltool/sandboxjs.py	Sat May 02 07:14:21 2020 -0400
@@ -0,0 +1,382 @@
+"""Evaluate CWL Javascript Expressions in a sandbox."""
+from __future__ import absolute_import
+
+import errno
+import json
+import os
+import re
+import select
+import sys
+import threading
+from io import BytesIO
+from typing import cast, Any, Dict, List, Optional, Tuple, Union
+
+import six
+from future.utils import raise_from
+from pkg_resources import resource_stream
+from typing_extensions import Text  # pylint: disable=unused-import
+# move to a regular typing import when Python 3.3-3.6 is no longer supported
+
+from schema_salad.utils import json_dumps
+
+from .loghandler import _logger
+from .utils import onWindows, processes_to_kill, subprocess
+try:
+    import queue  # type: ignore
+except ImportError:
+    import Queue as queue  # type: ignore
+
+
+class JavascriptException(Exception):
+    pass
+
+
+JSON = Union[Dict[Text, Any], List[Any], Text, int, float, bool, None]
+
+localdata = threading.local()
+
+default_timeout = 20
+have_node_slim = False
+# minimum acceptable version of nodejs engine
+minimum_node_version_str = '0.10.26'
+
+def check_js_threshold_version(working_alias):
+    # type: (str) -> bool
+    """
+    Check if the nodeJS engine version on the system with the allowed minimum version.
+
+    https://github.com/nodejs/node/blob/master/CHANGELOG.md#nodejs-changelog
+    """
+    # parse nodejs version into int Tuple: 'v4.2.6\n' -> [4, 2, 6]
+    current_version_str = subprocess.check_output(
+        [working_alias, "-v"]).decode('utf-8')
+
+    current_version = [int(v) for v in current_version_str.strip().strip('v').split('.')]
+    minimum_node_version = [int(v) for v in minimum_node_version_str.split('.')]
+
+    return current_version >= minimum_node_version
+
+
+def new_js_proc(js_text, force_docker_pull=False):
+    # type: (Text, bool) -> subprocess.Popen
+
+    required_node_version, docker = (False,)*2
+    nodejs = None
+    trynodes = ("nodejs", "node")
+    for n in trynodes:
+        try:
+            if subprocess.check_output([n, "--eval", "process.stdout.write('t')"]).decode('utf-8') != "t":
+                continue
+            else:
+                nodejs = subprocess.Popen([n, "--eval", js_text],
+                                          stdin=subprocess.PIPE,
+                                          stdout=subprocess.PIPE,
+                                          stderr=subprocess.PIPE)
+                processes_to_kill.append(nodejs)
+                required_node_version = check_js_threshold_version(n)
+                break
+        except (subprocess.CalledProcessError, OSError):
+            pass
+
+    if nodejs is None or nodejs is not None and required_node_version is False:
+        try:
+            nodeimg = "node:slim"
+            global have_node_slim
+
+            if not have_node_slim:
+                dockerimgs = subprocess.check_output(["docker", "images", "-q", nodeimg]).decode('utf-8')
+                # if output is an empty string
+                if (len(dockerimgs.split("\n")) <= 1) or force_docker_pull:
+                    # pull node:slim docker container
+                    nodejsimg = subprocess.check_output(["docker", "pull", nodeimg]).decode('utf-8')
+                    _logger.info("Pulled Docker image %s %s", nodeimg, nodejsimg)
+                have_node_slim = True
+            nodejs = subprocess.Popen(["docker", "run",
+                                       "--attach=STDIN", "--attach=STDOUT", "--attach=STDERR",
+                                       "--sig-proxy=true", "--interactive",
+                                       "--rm", nodeimg, "node", "--eval", js_text],
+                                      stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+            processes_to_kill.append(nodejs)
+            docker = True
+        except OSError as e:
+            if e.errno == errno.ENOENT:
+                pass
+            else:
+                raise
+        except subprocess.CalledProcessError:
+            pass
+
+    # docker failed and nodejs not on system
+    if nodejs is None:
+        raise JavascriptException(
+            u"cwltool requires Node.js engine to evaluate and validate "
+            u"Javascript expressions, but couldn't find it.  Tried {}, "
+            u"docker run node:slim".format(u", ".join(trynodes)))
+
+    # docker failed, but nodejs is installed on system but the version is below the required version
+    if docker is False and required_node_version is False:
+        raise JavascriptException(
+            u'cwltool requires minimum v{} version of Node.js engine.'.format(
+                minimum_node_version_str),
+            u'Try updating: https://docs.npmjs.com/getting-started/installing-node')
+
+    return nodejs
+
+PROCESS_FINISHED_STR = "r1cepzbhUTxtykz5XTC4\n"
+
+def exec_js_process(js_text,                  # type: Text
+                    timeout=default_timeout,  # type: float
+                    js_console=False,         # type: bool
+                    context=None,             # type: Optional[Text]
+                    force_docker_pull=False,  # type: bool
+                   ):
+    # type: (...) -> Tuple[int, Text, Text]
+
+    if not hasattr(localdata, "procs"):
+        localdata.procs = {}
+
+    if js_console and context is not None:
+        raise NotImplementedError("js_console=True and context not implemented")
+
+    if js_console:
+        js_engine = 'cwlNodeEngineJSConsole.js'
+        _logger.warning(
+            "Running with support for javascript console in expressions (DO NOT USE IN PRODUCTION)")
+    elif context is not None:
+        js_engine = "cwlNodeEngineWithContext.js"
+    else:
+        js_engine = 'cwlNodeEngine.js'
+
+    created_new_process = False
+
+    if context is not None:
+        nodejs = localdata.procs.get((js_engine, context))
+    else:
+        nodejs = localdata.procs.get(js_engine)
+
+    if nodejs is None \
+            or nodejs.poll() is not None \
+            or onWindows():
+        res = resource_stream(__name__, js_engine)
+        js_engine_code = res.read().decode('utf-8')
+
+        created_new_process = True
+
+        new_proc = new_js_proc(js_engine_code, force_docker_pull=force_docker_pull)
+
+        if context is None:
+            localdata.procs[js_engine] = new_proc
+            nodejs = new_proc
+        else:
+            localdata.procs[(js_engine, context)] = new_proc
+            nodejs = new_proc
+
+    killed = []
+
+    def terminate():  # type: () -> None
+        """Kill the node process if it exceeds timeout limit."""
+        try:
+            killed.append(True)
+            nodejs.kill()
+        except OSError:
+            pass
+
+    timer = threading.Timer(timeout, terminate)
+    timer.daemon = True
+    timer.start()
+
+    stdin_text = u""
+    if created_new_process and context is not None:
+        stdin_text = json_dumps(context) + "\n"
+    stdin_text += json_dumps(js_text) + "\n"
+
+    stdin_buf = BytesIO(stdin_text.encode('utf-8'))
+    stdout_buf = BytesIO()
+    stderr_buf = BytesIO()
+
+    rselect = [nodejs.stdout, nodejs.stderr]  # type: List[BytesIO]
+    wselect = [nodejs.stdin]  # type: List[BytesIO]
+
+
+    def process_finished():  # type: () -> bool
+        return stdout_buf.getvalue().decode('utf-8').endswith(PROCESS_FINISHED_STR) and \
+            stderr_buf.getvalue().decode('utf-8').endswith(PROCESS_FINISHED_STR)
+
+    # On windows system standard input/output are not handled properly by select module
+    # (modules like  pywin32, msvcrt, gevent don't work either)
+    if sys.platform == 'win32':
+        READ_BYTES_SIZE = 512
+
+        # creating queue for reading from a thread to queue
+        input_queue = queue.Queue()
+        output_queue = queue.Queue()
+        error_queue = queue.Queue()
+
+        # To tell threads that output has ended and threads can safely exit
+        no_more_output = threading.Lock()
+        no_more_output.acquire()
+        no_more_error = threading.Lock()
+        no_more_error.acquire()
+
+        # put constructed command to input queue which then will be passed to nodejs's stdin
+        def put_input(input_queue):
+            while True:
+                buf = stdin_buf.read(READ_BYTES_SIZE)
+                if buf:
+                    input_queue.put(buf)
+                else:
+                    break
+
+        # get the output from nodejs's stdout and continue till output ends
+        def get_output(output_queue):
+            while not no_more_output.acquire(False):
+                buf = os.read(nodejs.stdout.fileno(), READ_BYTES_SIZE)
+                if buf:
+                    output_queue.put(buf)
+
+        # get the output from nodejs's stderr and continue till error output ends
+        def get_error(error_queue):
+            while not no_more_error.acquire(False):
+                buf = os.read(nodejs.stderr.fileno(), READ_BYTES_SIZE)
+                if buf:
+                    error_queue.put(buf)
+
+        # Threads managing nodejs.stdin, nodejs.stdout and nodejs.stderr respectively
+        input_thread = threading.Thread(target=put_input, args=(input_queue,))
+        input_thread.daemon = True
+        input_thread.start()
+        output_thread = threading.Thread(target=get_output, args=(output_queue,))
+        output_thread.daemon = True
+        output_thread.start()
+        error_thread = threading.Thread(target=get_error, args=(error_queue,))
+        error_thread.daemon = True
+        error_thread.start()
+
+        finished = False
+
+        while not finished and timer.is_alive():
+            try:
+                if nodejs.stdin in wselect:
+                    if not input_queue.empty():
+                        os.write(nodejs.stdin.fileno(), input_queue.get())
+                    elif not input_thread.is_alive():
+                        wselect = []
+                if nodejs.stdout in rselect:
+                    if not output_queue.empty():
+                        stdout_buf.write(output_queue.get())
+
+                if nodejs.stderr in rselect:
+                    if not error_queue.empty():
+                        stderr_buf.write(error_queue.get())
+
+                if process_finished() and error_queue.empty() and output_queue.empty():
+                    finished = True
+                    no_more_output.release()
+                    no_more_error.release()
+            except OSError:
+                break
+
+    else:
+        while not process_finished() and timer.is_alive():
+            rready, wready, _ = select.select(rselect, wselect, [])
+            try:
+                if nodejs.stdin in wready:
+                    buf = stdin_buf.read(select.PIPE_BUF)
+                    if buf:
+                        os.write(nodejs.stdin.fileno(), buf)
+                for pipes in ((nodejs.stdout, stdout_buf), (nodejs.stderr, stderr_buf)):
+                    if pipes[0] in rready:
+                        buf = os.read(pipes[0].fileno(), select.PIPE_BUF)
+                        if buf:
+                            pipes[1].write(buf)
+            except OSError:
+                break
+    timer.cancel()
+
+    stdin_buf.close()
+    stdoutdata = stdout_buf.getvalue()[:-len(PROCESS_FINISHED_STR) - 1]
+    stderrdata = stderr_buf.getvalue()[:-len(PROCESS_FINISHED_STR) - 1]
+
+    nodejs.poll()
+
+    if nodejs.poll() not in (None, 0):
+        if killed:
+            returncode = -1
+        else:
+            returncode = nodejs.returncode
+    else:
+        returncode = 0
+        # On windows currently a new instance of nodejs process is used due to
+        # problem with blocking on read operation on windows
+        if onWindows():
+            nodejs.kill()
+
+    return returncode, stdoutdata.decode('utf-8'), stderrdata.decode('utf-8')
+
+def code_fragment_to_js(jscript, jslib=""):
+    # type: (Text, Text) -> Text
+    if isinstance(jscript, six.string_types) \
+            and len(jscript) > 1 and jscript[0] == '{':
+        inner_js = jscript
+    else:
+        inner_js = "{return (%s);}" % jscript
+
+    return u"\"use strict\";\n{}\n(function(){})()".format(jslib, inner_js)
+
+def execjs(js,                       # type: Text
+           jslib,                    # type: Text
+           timeout,                  # type: float
+           force_docker_pull=False,  # type: bool
+           debug=False,              # type: bool
+           js_console=False          # type: bool
+          ):  # type: (...) -> JSON
+
+    fn = code_fragment_to_js(js, jslib)
+
+    returncode, stdout, stderr = exec_js_process(
+        fn, timeout, js_console=js_console,
+        force_docker_pull=force_docker_pull)
+
+    if js_console:
+        if stderr is not None:
+            _logger.info("Javascript console output:")
+            _logger.info("----------------------------------------")
+            _logger.info('\n'.join(re.findall(
+                r'^[[](?:log|err)[]].*$', stderr, flags=re.MULTILINE)))
+            _logger.info("----------------------------------------")
+
+    def stdfmt(data):  # type: (Text) -> Text
+        if "\n" in data:
+            return "\n" + data.strip()
+        return data
+
+    def fn_linenum():  # type: () -> Text
+        lines = fn.splitlines()
+        ofs = 0
+        maxlines = 99
+        if len(lines) > maxlines:
+            ofs = len(lines) - maxlines
+            lines = lines[-maxlines:]
+        return u"\n".join(u"%02i %s" % (i + ofs + 1, b) for i, b in enumerate(lines))
+
+    if returncode != 0:
+        if debug:
+            info = u"returncode was: %s\nscript was:\n%s\nstdout was: %s\nstderr was: %s\n" %\
+                (returncode, fn_linenum(), stdfmt(stdout), stdfmt(stderr))
+        else:
+            info = u"Javascript expression was: %s\nstdout was: %s\nstderr was: %s" %\
+                (js, stdfmt(stdout), stdfmt(stderr))
+
+        if returncode == -1:
+            raise JavascriptException(
+                u"Long-running script killed after {} seconds: {}".format(
+                    timeout, info))
+        else:
+            raise JavascriptException(info)
+
+    try:
+        return cast(JSON, json.loads(stdout))
+    except ValueError as err:
+        raise_from(JavascriptException(
+            u"{}\nscript was:\n{}\nstdout was: '{}'\nstderr was: '{}'\n".format(
+                err, fn_linenum(), stdout, stderr)), err)