Mercurial > repos > shellac > guppy_basecaller
view env/lib/python3.7/site-packages/cwltool/sandboxjs.py @ 0:26e78fe6e8c4 draft
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author | shellac |
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date | Sat, 02 May 2020 07:14:21 -0400 |
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"""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)