Mercurial > repos > shellac > guppy_basecaller
annotate env/lib/python3.7/site-packages/cwltool/expression.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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0
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1 """Parse CWL expressions.""" |
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2 from __future__ import absolute_import |
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3 |
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4 import copy |
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5 import re |
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6 from typing import (Any, Dict, List, Mapping, MutableMapping, MutableSequence, Optional, |
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7 Union) |
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8 |
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9 import six |
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10 from six import string_types, u |
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11 from future.utils import raise_from |
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12 from typing_extensions import Text # pylint: disable=unused-import |
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13 # move to a regular typing import when Python 3.3-3.6 is no longer supported |
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14 |
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15 from .sandboxjs import default_timeout, execjs, JavascriptException |
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16 from .errors import WorkflowException |
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17 from .utils import bytes2str_in_dicts, docker_windows_path_adjust, json_dumps |
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18 |
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19 |
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20 def jshead(engine_config, rootvars): |
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21 # type: (List[Text], Dict[Text, Any]) -> Text |
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22 |
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23 # make sure all the byte strings are converted |
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24 # to str in `rootvars` dict. |
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25 |
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26 return u"\n".join( |
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27 engine_config + [u"var {} = {};".format(k, json_dumps(v, indent=4)) |
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28 for k, v in rootvars.items()]) |
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29 |
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30 |
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31 # decode all raw strings to unicode |
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32 seg_symbol = r"""\w+""" |
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33 seg_single = r"""\['([^']|\\')+'\]""" |
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34 seg_double = r"""\["([^"]|\\")+"\]""" |
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35 seg_index = r"""\[[0-9]+\]""" |
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36 segments = r"(\.%s|%s|%s|%s)" % (seg_symbol, seg_single, seg_double, seg_index) |
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37 segment_re = re.compile(u(segments), flags=re.UNICODE) |
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38 param_str = r"\((%s)%s*\)$" % (seg_symbol, segments) |
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39 param_re = re.compile(u(param_str), flags=re.UNICODE) |
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40 |
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41 JSON = Union[Dict[Any, Any], List[Any], Text, int, float, bool, None] |
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42 |
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43 |
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44 class SubstitutionError(Exception): |
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45 pass |
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46 |
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47 |
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48 def scanner(scan): # type: (Text) -> List[int] |
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49 DEFAULT = 0 |
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50 DOLLAR = 1 |
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51 PAREN = 2 |
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52 BRACE = 3 |
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53 SINGLE_QUOTE = 4 |
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54 DOUBLE_QUOTE = 5 |
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55 BACKSLASH = 6 |
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56 |
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57 i = 0 |
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58 stack = [DEFAULT] |
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59 start = 0 |
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60 while i < len(scan): |
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61 state = stack[-1] |
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62 c = scan[i] |
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63 |
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64 if state == DEFAULT: |
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65 if c == '$': |
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66 stack.append(DOLLAR) |
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67 elif c == '\\': |
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68 stack.append(BACKSLASH) |
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69 elif state == BACKSLASH: |
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70 stack.pop() |
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71 if stack[-1] == DEFAULT: |
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72 return [i - 1, i + 1] |
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73 elif state == DOLLAR: |
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74 if c == '(': |
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75 start = i - 1 |
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76 stack.append(PAREN) |
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77 elif c == '{': |
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78 start = i - 1 |
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79 stack.append(BRACE) |
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80 else: |
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81 stack.pop() |
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82 elif state == PAREN: |
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83 if c == '(': |
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84 stack.append(PAREN) |
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85 elif c == ')': |
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86 stack.pop() |
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87 if stack[-1] == DOLLAR: |
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88 return [start, i + 1] |
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89 elif c == "'": |
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90 stack.append(SINGLE_QUOTE) |
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91 elif c == '"': |
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92 stack.append(DOUBLE_QUOTE) |
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93 elif state == BRACE: |
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94 if c == '{': |
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95 stack.append(BRACE) |
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96 elif c == '}': |
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97 stack.pop() |
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98 if stack[-1] == DOLLAR: |
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99 return [start, i + 1] |
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100 elif c == "'": |
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101 stack.append(SINGLE_QUOTE) |
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102 elif c == '"': |
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103 stack.append(DOUBLE_QUOTE) |
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104 elif state == SINGLE_QUOTE: |
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105 if c == "'": |
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106 stack.pop() |
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107 elif c == '\\': |
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108 stack.append(BACKSLASH) |
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109 elif state == DOUBLE_QUOTE: |
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110 if c == '"': |
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111 stack.pop() |
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112 elif c == '\\': |
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113 stack.append(BACKSLASH) |
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114 i += 1 |
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115 |
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116 if len(stack) > 1: |
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117 raise SubstitutionError( |
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118 "Substitution error, unfinished block starting at position {}: {}".format(start, scan[start:])) |
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119 else: |
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120 return [] |
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121 |
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122 |
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123 def next_seg(parsed_string, remaining_string, current_value): # type: (Text, Text, JSON) -> JSON |
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124 if remaining_string: |
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125 m = segment_re.match(remaining_string) |
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126 if not m: |
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127 return current_value |
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128 next_segment_str = m.group(0) |
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129 |
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130 key = None # type: Optional[Union[Text, int]] |
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131 if next_segment_str[0] == '.': |
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132 key = next_segment_str[1:] |
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133 elif next_segment_str[1] in ("'", '"'): |
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134 key = next_segment_str[2:-2].replace("\\'", "'").replace('\\"', '"') |
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135 |
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136 if key is not None: |
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137 if isinstance(current_value, MutableSequence) and key == "length" and not remaining_string[m.end(0):]: |
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138 return len(current_value) |
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139 if not isinstance(current_value, MutableMapping): |
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140 raise WorkflowException("%s is a %s, cannot index on string '%s'" % (parsed_string, type(current_value).__name__, key)) |
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141 if key not in current_value: |
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142 raise WorkflowException("%s does not contain key '%s'" % (parsed_string, key)) |
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143 else: |
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144 try: |
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145 key = int(next_segment_str[1:-1]) |
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146 except ValueError as v: |
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147 raise_from(WorkflowException(u(str(v))), v) |
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148 if not isinstance(current_value, MutableSequence): |
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149 raise WorkflowException("%s is a %s, cannot index on int '%s'" % (parsed_string, type(current_value).__name__, key)) |
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150 if key >= len(current_value): |
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151 raise WorkflowException("%s list index %i out of range" % (parsed_string, key)) |
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152 |
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153 if isinstance(current_value, Mapping): |
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154 try: |
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155 return next_seg(parsed_string + remaining_string, remaining_string[m.end(0):], current_value[key]) |
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156 except KeyError: |
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157 raise WorkflowException("%s doesn't have property %s" % (parsed_string, key)) |
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158 elif isinstance(current_value, list) and isinstance(key, int): |
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159 try: |
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160 return next_seg(parsed_string + remaining_string, remaining_string[m.end(0):], current_value[key]) |
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161 except KeyError: |
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162 raise WorkflowException("%s doesn't have property %s" % (parsed_string, key)) |
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163 else: |
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164 raise WorkflowException("%s doesn't have property %s" % (parsed_string, key)) |
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165 else: |
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166 return current_value |
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167 |
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168 |
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169 def evaluator(ex, # type: Text |
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170 jslib, # type: Text |
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171 obj, # type: Dict[Text, Any] |
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172 timeout, # type: float |
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173 fullJS=False, # type: bool |
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174 force_docker_pull=False, # type: bool |
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175 debug=False, # type: bool |
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176 js_console=False # type: bool |
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177 ): |
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178 # type: (...) -> JSON |
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179 match = param_re.match(ex) |
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180 |
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181 expression_parse_exception = None |
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182 expression_parse_succeeded = False |
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183 |
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184 if match is not None: |
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185 first_symbol = match.group(1) |
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186 first_symbol_end = match.end(1) |
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187 |
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188 if first_symbol_end + 1 == len(ex) and first_symbol == "null": |
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189 return None |
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190 try: |
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191 if obj.get(first_symbol) is None: |
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192 raise WorkflowException("%s is not defined" % first_symbol) |
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193 |
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194 return next_seg(first_symbol, ex[first_symbol_end:-1], obj[first_symbol]) |
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195 except WorkflowException as werr: |
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196 expression_parse_exception = werr |
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197 else: |
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198 expression_parse_succeeded = True |
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199 |
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200 if fullJS and not expression_parse_succeeded: |
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201 return execjs( |
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202 ex, jslib, timeout, force_docker_pull=force_docker_pull, |
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203 debug=debug, js_console=js_console) |
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204 else: |
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205 if expression_parse_exception is not None: |
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206 raise JavascriptException( |
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207 "Syntax error in parameter reference '%s': %s. This could be " |
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208 "due to using Javascript code without specifying " |
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209 "InlineJavascriptRequirement." % \ |
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210 (ex[1:-1], expression_parse_exception)) |
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211 else: |
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212 raise JavascriptException( |
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213 "Syntax error in parameter reference '%s'. This could be due " |
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214 "to using Javascript code without specifying " |
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215 "InlineJavascriptRequirement." % ex) |
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216 |
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217 |
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218 def interpolate(scan, # type: Text |
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219 rootvars, # type: Dict[Text, Any] |
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220 timeout=default_timeout, # type: float |
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221 fullJS=False, # type: bool |
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222 jslib="", # type: Text |
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223 force_docker_pull=False, # type: bool |
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224 debug=False, # type: bool |
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225 js_console=False, # type: bool |
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226 strip_whitespace=True # type: bool |
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227 ): # type: (...) -> JSON |
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228 if strip_whitespace: |
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229 scan = scan.strip() |
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230 parts = [] |
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231 w = scanner(scan) |
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232 while w: |
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233 parts.append(scan[0:w[0]]) |
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234 |
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235 if scan[w[0]] == '$': |
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236 e = evaluator(scan[w[0] + 1:w[1]], jslib, rootvars, timeout, |
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237 fullJS=fullJS, force_docker_pull=force_docker_pull, |
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238 debug=debug, js_console=js_console) |
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239 if w[0] == 0 and w[1] == len(scan) and len(parts) <= 1: |
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240 return e |
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241 leaf = json_dumps(e, sort_keys=True) |
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242 if leaf[0] == '"': |
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243 leaf = leaf[1:-1] |
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244 parts.append(leaf) |
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245 elif scan[w[0]] == '\\': |
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246 e = scan[w[1] - 1] |
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247 parts.append(e) |
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248 |
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249 scan = scan[w[1]:] |
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250 w = scanner(scan) |
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251 parts.append(scan) |
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252 return ''.join(parts) |
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253 |
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254 def needs_parsing(snippet): # type: (Any) -> bool |
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255 return isinstance(snippet, string_types) \ |
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256 and ("$(" in snippet or "${" in snippet) |
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257 |
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258 def do_eval(ex, # type: Union[Text, Dict[Text, Text]] |
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259 jobinput, # type: Dict[Text, JSON] |
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260 requirements, # type: List[Dict[Text, Any]] |
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261 outdir, # type: Optional[Text] |
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262 tmpdir, # type: Optional[Text] |
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263 resources, # type: Dict[str, int] |
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264 context=None, # type: Any |
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265 timeout=default_timeout, # type: float |
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266 force_docker_pull=False, # type: bool |
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267 debug=False, # type: bool |
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268 js_console=False, # type: bool |
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269 strip_whitespace=True # type: bool |
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270 ): # type: (...) -> Any |
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271 |
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272 runtime = copy.deepcopy(resources) # type: Dict[str, Any] |
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273 runtime["tmpdir"] = docker_windows_path_adjust(tmpdir) if tmpdir else None |
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274 runtime["outdir"] = docker_windows_path_adjust(outdir) if outdir else None |
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275 |
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276 rootvars = { |
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277 u"inputs": jobinput, |
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278 u"self": context, |
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279 u"runtime": runtime} |
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280 |
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281 # TODO: need to make sure the `rootvars dict` |
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282 # contains no bytes type in the first place. |
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283 if six.PY3: |
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284 rootvars = bytes2str_in_dicts(rootvars) # type: ignore |
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285 |
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286 if isinstance(ex, string_types) and needs_parsing(ex): |
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287 fullJS = False |
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288 jslib = u"" |
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289 for r in reversed(requirements): |
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290 if r["class"] == "InlineJavascriptRequirement": |
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291 fullJS = True |
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292 jslib = jshead(r.get("expressionLib", []), rootvars) |
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293 break |
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294 |
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295 try: |
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296 return interpolate(ex, |
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297 rootvars, |
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298 timeout=timeout, |
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299 fullJS=fullJS, |
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300 jslib=jslib, |
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301 force_docker_pull=force_docker_pull, |
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302 debug=debug, |
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303 js_console=js_console, |
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304 strip_whitespace=strip_whitespace) |
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305 |
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306 except Exception as e: |
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307 raise_from(WorkflowException("Expression evaluation error:\n%s" % Text(e)), e) |
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308 else: |
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309 return ex |