Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/cwltool/sandboxjs.py @ 0:26e78fe6e8c4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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0
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1 """Evaluate CWL Javascript Expressions in a sandbox."""
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2 from __future__ import absolute_import
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3
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4 import errno
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5 import json
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6 import os
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7 import re
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8 import select
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9 import sys
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10 import threading
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11 from io import BytesIO
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12 from typing import cast, Any, Dict, List, Optional, Tuple, Union
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13
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14 import six
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15 from future.utils import raise_from
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16 from pkg_resources import resource_stream
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17 from typing_extensions import Text # pylint: disable=unused-import
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18 # move to a regular typing import when Python 3.3-3.6 is no longer supported
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19
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20 from schema_salad.utils import json_dumps
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21
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22 from .loghandler import _logger
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23 from .utils import onWindows, processes_to_kill, subprocess
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24 try:
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25 import queue # type: ignore
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26 except ImportError:
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27 import Queue as queue # type: ignore
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28
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29
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30 class JavascriptException(Exception):
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31 pass
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32
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33
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34 JSON = Union[Dict[Text, Any], List[Any], Text, int, float, bool, None]
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35
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36 localdata = threading.local()
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37
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38 default_timeout = 20
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39 have_node_slim = False
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40 # minimum acceptable version of nodejs engine
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41 minimum_node_version_str = '0.10.26'
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42
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43 def check_js_threshold_version(working_alias):
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44 # type: (str) -> bool
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45 """
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46 Check if the nodeJS engine version on the system with the allowed minimum version.
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47
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48 https://github.com/nodejs/node/blob/master/CHANGELOG.md#nodejs-changelog
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49 """
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50 # parse nodejs version into int Tuple: 'v4.2.6\n' -> [4, 2, 6]
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51 current_version_str = subprocess.check_output(
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52 [working_alias, "-v"]).decode('utf-8')
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53
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54 current_version = [int(v) for v in current_version_str.strip().strip('v').split('.')]
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55 minimum_node_version = [int(v) for v in minimum_node_version_str.split('.')]
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56
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57 return current_version >= minimum_node_version
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58
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59
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60 def new_js_proc(js_text, force_docker_pull=False):
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61 # type: (Text, bool) -> subprocess.Popen
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62
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63 required_node_version, docker = (False,)*2
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64 nodejs = None
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65 trynodes = ("nodejs", "node")
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66 for n in trynodes:
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67 try:
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68 if subprocess.check_output([n, "--eval", "process.stdout.write('t')"]).decode('utf-8') != "t":
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69 continue
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70 else:
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71 nodejs = subprocess.Popen([n, "--eval", js_text],
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72 stdin=subprocess.PIPE,
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73 stdout=subprocess.PIPE,
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74 stderr=subprocess.PIPE)
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75 processes_to_kill.append(nodejs)
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76 required_node_version = check_js_threshold_version(n)
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77 break
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78 except (subprocess.CalledProcessError, OSError):
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79 pass
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80
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81 if nodejs is None or nodejs is not None and required_node_version is False:
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82 try:
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83 nodeimg = "node:slim"
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84 global have_node_slim
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85
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86 if not have_node_slim:
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87 dockerimgs = subprocess.check_output(["docker", "images", "-q", nodeimg]).decode('utf-8')
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88 # if output is an empty string
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89 if (len(dockerimgs.split("\n")) <= 1) or force_docker_pull:
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90 # pull node:slim docker container
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91 nodejsimg = subprocess.check_output(["docker", "pull", nodeimg]).decode('utf-8')
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92 _logger.info("Pulled Docker image %s %s", nodeimg, nodejsimg)
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93 have_node_slim = True
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94 nodejs = subprocess.Popen(["docker", "run",
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95 "--attach=STDIN", "--attach=STDOUT", "--attach=STDERR",
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96 "--sig-proxy=true", "--interactive",
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97 "--rm", nodeimg, "node", "--eval", js_text],
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98 stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
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99 processes_to_kill.append(nodejs)
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100 docker = True
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101 except OSError as e:
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102 if e.errno == errno.ENOENT:
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103 pass
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104 else:
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105 raise
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106 except subprocess.CalledProcessError:
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107 pass
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108
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109 # docker failed and nodejs not on system
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110 if nodejs is None:
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111 raise JavascriptException(
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112 u"cwltool requires Node.js engine to evaluate and validate "
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113 u"Javascript expressions, but couldn't find it. Tried {}, "
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114 u"docker run node:slim".format(u", ".join(trynodes)))
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115
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116 # docker failed, but nodejs is installed on system but the version is below the required version
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117 if docker is False and required_node_version is False:
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118 raise JavascriptException(
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119 u'cwltool requires minimum v{} version of Node.js engine.'.format(
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120 minimum_node_version_str),
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121 u'Try updating: https://docs.npmjs.com/getting-started/installing-node')
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122
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123 return nodejs
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124
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125 PROCESS_FINISHED_STR = "r1cepzbhUTxtykz5XTC4\n"
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126
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127 def exec_js_process(js_text, # type: Text
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128 timeout=default_timeout, # type: float
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129 js_console=False, # type: bool
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130 context=None, # type: Optional[Text]
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131 force_docker_pull=False, # type: bool
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132 ):
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133 # type: (...) -> Tuple[int, Text, Text]
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134
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135 if not hasattr(localdata, "procs"):
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136 localdata.procs = {}
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137
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138 if js_console and context is not None:
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139 raise NotImplementedError("js_console=True and context not implemented")
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140
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141 if js_console:
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142 js_engine = 'cwlNodeEngineJSConsole.js'
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143 _logger.warning(
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144 "Running with support for javascript console in expressions (DO NOT USE IN PRODUCTION)")
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145 elif context is not None:
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146 js_engine = "cwlNodeEngineWithContext.js"
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147 else:
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148 js_engine = 'cwlNodeEngine.js'
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149
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150 created_new_process = False
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151
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152 if context is not None:
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153 nodejs = localdata.procs.get((js_engine, context))
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154 else:
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155 nodejs = localdata.procs.get(js_engine)
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156
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157 if nodejs is None \
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158 or nodejs.poll() is not None \
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159 or onWindows():
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160 res = resource_stream(__name__, js_engine)
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161 js_engine_code = res.read().decode('utf-8')
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162
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163 created_new_process = True
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164
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165 new_proc = new_js_proc(js_engine_code, force_docker_pull=force_docker_pull)
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166
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167 if context is None:
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168 localdata.procs[js_engine] = new_proc
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169 nodejs = new_proc
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170 else:
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171 localdata.procs[(js_engine, context)] = new_proc
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172 nodejs = new_proc
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173
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174 killed = []
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175
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176 def terminate(): # type: () -> None
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177 """Kill the node process if it exceeds timeout limit."""
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178 try:
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179 killed.append(True)
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180 nodejs.kill()
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181 except OSError:
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182 pass
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183
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184 timer = threading.Timer(timeout, terminate)
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185 timer.daemon = True
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186 timer.start()
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187
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188 stdin_text = u""
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189 if created_new_process and context is not None:
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190 stdin_text = json_dumps(context) + "\n"
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191 stdin_text += json_dumps(js_text) + "\n"
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192
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193 stdin_buf = BytesIO(stdin_text.encode('utf-8'))
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194 stdout_buf = BytesIO()
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195 stderr_buf = BytesIO()
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196
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197 rselect = [nodejs.stdout, nodejs.stderr] # type: List[BytesIO]
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198 wselect = [nodejs.stdin] # type: List[BytesIO]
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199
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200
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201 def process_finished(): # type: () -> bool
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202 return stdout_buf.getvalue().decode('utf-8').endswith(PROCESS_FINISHED_STR) and \
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203 stderr_buf.getvalue().decode('utf-8').endswith(PROCESS_FINISHED_STR)
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204
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205 # On windows system standard input/output are not handled properly by select module
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206 # (modules like pywin32, msvcrt, gevent don't work either)
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207 if sys.platform == 'win32':
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208 READ_BYTES_SIZE = 512
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209
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210 # creating queue for reading from a thread to queue
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211 input_queue = queue.Queue()
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212 output_queue = queue.Queue()
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213 error_queue = queue.Queue()
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214
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215 # To tell threads that output has ended and threads can safely exit
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216 no_more_output = threading.Lock()
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217 no_more_output.acquire()
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218 no_more_error = threading.Lock()
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219 no_more_error.acquire()
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220
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221 # put constructed command to input queue which then will be passed to nodejs's stdin
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222 def put_input(input_queue):
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223 while True:
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224 buf = stdin_buf.read(READ_BYTES_SIZE)
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225 if buf:
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226 input_queue.put(buf)
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227 else:
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228 break
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229
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230 # get the output from nodejs's stdout and continue till output ends
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231 def get_output(output_queue):
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232 while not no_more_output.acquire(False):
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233 buf = os.read(nodejs.stdout.fileno(), READ_BYTES_SIZE)
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234 if buf:
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235 output_queue.put(buf)
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236
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237 # get the output from nodejs's stderr and continue till error output ends
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238 def get_error(error_queue):
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239 while not no_more_error.acquire(False):
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240 buf = os.read(nodejs.stderr.fileno(), READ_BYTES_SIZE)
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241 if buf:
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242 error_queue.put(buf)
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243
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244 # Threads managing nodejs.stdin, nodejs.stdout and nodejs.stderr respectively
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245 input_thread = threading.Thread(target=put_input, args=(input_queue,))
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246 input_thread.daemon = True
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247 input_thread.start()
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248 output_thread = threading.Thread(target=get_output, args=(output_queue,))
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249 output_thread.daemon = True
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250 output_thread.start()
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251 error_thread = threading.Thread(target=get_error, args=(error_queue,))
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252 error_thread.daemon = True
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253 error_thread.start()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
254
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
255 finished = False
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
256
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
257 while not finished and timer.is_alive():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
258 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
259 if nodejs.stdin in wselect:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
260 if not input_queue.empty():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
261 os.write(nodejs.stdin.fileno(), input_queue.get())
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
262 elif not input_thread.is_alive():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
263 wselect = []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
264 if nodejs.stdout in rselect:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
265 if not output_queue.empty():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
266 stdout_buf.write(output_queue.get())
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
267
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
268 if nodejs.stderr in rselect:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
269 if not error_queue.empty():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
270 stderr_buf.write(error_queue.get())
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
271
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
272 if process_finished() and error_queue.empty() and output_queue.empty():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
273 finished = True
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
274 no_more_output.release()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
275 no_more_error.release()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
276 except OSError:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
277 break
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
278
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
279 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
280 while not process_finished() and timer.is_alive():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
281 rready, wready, _ = select.select(rselect, wselect, [])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
282 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
283 if nodejs.stdin in wready:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
284 buf = stdin_buf.read(select.PIPE_BUF)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
285 if buf:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
286 os.write(nodejs.stdin.fileno(), buf)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
287 for pipes in ((nodejs.stdout, stdout_buf), (nodejs.stderr, stderr_buf)):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
288 if pipes[0] in rready:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
289 buf = os.read(pipes[0].fileno(), select.PIPE_BUF)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
290 if buf:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
291 pipes[1].write(buf)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
292 except OSError:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
293 break
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
294 timer.cancel()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
295
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
296 stdin_buf.close()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
297 stdoutdata = stdout_buf.getvalue()[:-len(PROCESS_FINISHED_STR) - 1]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
298 stderrdata = stderr_buf.getvalue()[:-len(PROCESS_FINISHED_STR) - 1]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
299
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
300 nodejs.poll()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
301
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
302 if nodejs.poll() not in (None, 0):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
303 if killed:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
304 returncode = -1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
305 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
306 returncode = nodejs.returncode
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
307 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
308 returncode = 0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
309 # On windows currently a new instance of nodejs process is used due to
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
310 # problem with blocking on read operation on windows
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
311 if onWindows():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
312 nodejs.kill()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
313
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
314 return returncode, stdoutdata.decode('utf-8'), stderrdata.decode('utf-8')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
315
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
316 def code_fragment_to_js(jscript, jslib=""):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
317 # type: (Text, Text) -> Text
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
318 if isinstance(jscript, six.string_types) \
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
319 and len(jscript) > 1 and jscript[0] == '{':
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
320 inner_js = jscript
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
321 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
322 inner_js = "{return (%s);}" % jscript
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
323
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
324 return u"\"use strict\";\n{}\n(function(){})()".format(jslib, inner_js)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
325
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
326 def execjs(js, # type: Text
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
327 jslib, # type: Text
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
328 timeout, # type: float
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
329 force_docker_pull=False, # type: bool
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
330 debug=False, # type: bool
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
331 js_console=False # type: bool
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
332 ): # type: (...) -> JSON
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
333
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
334 fn = code_fragment_to_js(js, jslib)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
335
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
336 returncode, stdout, stderr = exec_js_process(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
337 fn, timeout, js_console=js_console,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
338 force_docker_pull=force_docker_pull)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
339
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
340 if js_console:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
341 if stderr is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
342 _logger.info("Javascript console output:")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
343 _logger.info("----------------------------------------")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
344 _logger.info('\n'.join(re.findall(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
345 r'^[[](?:log|err)[]].*$', stderr, flags=re.MULTILINE)))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
346 _logger.info("----------------------------------------")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
347
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
348 def stdfmt(data): # type: (Text) -> Text
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
349 if "\n" in data:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
350 return "\n" + data.strip()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
351 return data
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
352
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
353 def fn_linenum(): # type: () -> Text
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
354 lines = fn.splitlines()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
355 ofs = 0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
356 maxlines = 99
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
357 if len(lines) > maxlines:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
358 ofs = len(lines) - maxlines
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
359 lines = lines[-maxlines:]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
360 return u"\n".join(u"%02i %s" % (i + ofs + 1, b) for i, b in enumerate(lines))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
361
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
362 if returncode != 0:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
363 if debug:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
364 info = u"returncode was: %s\nscript was:\n%s\nstdout was: %s\nstderr was: %s\n" %\
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
365 (returncode, fn_linenum(), stdfmt(stdout), stdfmt(stderr))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
366 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
367 info = u"Javascript expression was: %s\nstdout was: %s\nstderr was: %s" %\
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
368 (js, stdfmt(stdout), stdfmt(stderr))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
369
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
370 if returncode == -1:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
371 raise JavascriptException(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
372 u"Long-running script killed after {} seconds: {}".format(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
373 timeout, info))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
374 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
375 raise JavascriptException(info)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
376
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
377 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
378 return cast(JSON, json.loads(stdout))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
379 except ValueError as err:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
380 raise_from(JavascriptException(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
381 u"{}\nscript was:\n{}\nstdout was: '{}'\nstderr was: '{}'\n".format(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
382 err, fn_linenum(), stdout, stderr)), err)