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annotate planemo/lib/python3.7/site-packages/cwltool/expression.py @ 0:d30785e31577 draft

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:18:57 -0400
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d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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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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guerler
parents:
diff changeset
131 if next_segment_str[0] == '.':
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guerler
parents:
diff changeset
132 key = next_segment_str[1:]
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
133 elif next_segment_str[1] in ("'", '"'):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
134 key = next_segment_str[2:-2].replace("\\'", "'").replace('\\"', '"')
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
135
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
136 if key is not None:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
137 if isinstance(current_value, MutableSequence) and key == "length" and not remaining_string[m.end(0):]:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
138 return len(current_value)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
139 if not isinstance(current_value, MutableMapping):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
140 raise WorkflowException("%s is a %s, cannot index on string '%s'" % (parsed_string, type(current_value).__name__, key))
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
141 if key not in current_value:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
142 raise WorkflowException("%s does not contain key '%s'" % (parsed_string, key))
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
143 else:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
144 try:
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parents:
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145 key = int(next_segment_str[1:-1])
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
146 except ValueError as v:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
147 raise_from(WorkflowException(u(str(v))), v)
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parents:
diff changeset
148 if not isinstance(current_value, MutableSequence):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
149 raise WorkflowException("%s is a %s, cannot index on int '%s'" % (parsed_string, type(current_value).__name__, key))
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
150 if key >= len(current_value):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
151 raise WorkflowException("%s list index %i out of range" % (parsed_string, key))
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diff changeset
152
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
153 if isinstance(current_value, Mapping):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
154 try:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
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155 return next_seg(parsed_string + remaining_string, remaining_string[m.end(0):], current_value[key])
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
156 except KeyError:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
157 raise WorkflowException("%s doesn't have property %s" % (parsed_string, key))
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
158 elif isinstance(current_value, list) and isinstance(key, int):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
159 try:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
160 return next_seg(parsed_string + remaining_string, remaining_string[m.end(0):], current_value[key])
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
161 except KeyError:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
162 raise WorkflowException("%s doesn't have property %s" % (parsed_string, key))
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
163 else:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
164 raise WorkflowException("%s doesn't have property %s" % (parsed_string, key))
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
165 else:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
166 return current_value
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
167
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
168
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
169 def evaluator(ex, # type: Text
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
170 jslib, # type: Text
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
171 obj, # type: Dict[Text, Any]
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parents:
diff changeset
172 timeout, # type: float
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
173 fullJS=False, # type: bool
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
174 force_docker_pull=False, # type: bool
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
175 debug=False, # type: bool
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
176 js_console=False # type: bool
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
177 ):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
178 # type: (...) -> JSON
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
179 match = param_re.match(ex)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
180
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
181 expression_parse_exception = None
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
182 expression_parse_succeeded = False
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
183
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
184 if match is not None:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
185 first_symbol = match.group(1)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
186 first_symbol_end = match.end(1)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
187
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
188 if first_symbol_end + 1 == len(ex) and first_symbol == "null":
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
189 return None
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
190 try:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
191 if obj.get(first_symbol) is None:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
192 raise WorkflowException("%s is not defined" % first_symbol)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
193
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
194 return next_seg(first_symbol, ex[first_symbol_end:-1], obj[first_symbol])
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
195 except WorkflowException as werr:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
196 expression_parse_exception = werr
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
197 else:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
198 expression_parse_succeeded = True
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
199
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
200 if fullJS and not expression_parse_succeeded:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
201 return execjs(
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
202 ex, jslib, timeout, force_docker_pull=force_docker_pull,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
203 debug=debug, js_console=js_console)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
204 else:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
205 if expression_parse_exception is not None:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
206 raise JavascriptException(
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
207 "Syntax error in parameter reference '%s': %s. This could be "
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
208 "due to using Javascript code without specifying "
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
209 "InlineJavascriptRequirement." % \
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
210 (ex[1:-1], expression_parse_exception))
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
211 else:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
212 raise JavascriptException(
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
213 "Syntax error in parameter reference '%s'. This could be due "
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
214 "to using Javascript code without specifying "
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
215 "InlineJavascriptRequirement." % ex)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
216
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
217
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
218 def interpolate(scan, # type: Text
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
219 rootvars, # type: Dict[Text, Any]
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
220 timeout=default_timeout, # type: float
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
221 fullJS=False, # type: bool
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
222 jslib="", # type: Text
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
223 force_docker_pull=False, # type: bool
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
224 debug=False, # type: bool
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
225 js_console=False, # type: bool
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
226 strip_whitespace=True # type: bool
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
227 ): # type: (...) -> JSON
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
228 if strip_whitespace:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
229 scan = scan.strip()
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
230 parts = []
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
231 w = scanner(scan)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
232 while w:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
233 parts.append(scan[0:w[0]])
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
234
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
235 if scan[w[0]] == '$':
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
236 e = evaluator(scan[w[0] + 1:w[1]], jslib, rootvars, timeout,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
237 fullJS=fullJS, force_docker_pull=force_docker_pull,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
238 debug=debug, js_console=js_console)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
239 if w[0] == 0 and w[1] == len(scan) and len(parts) <= 1:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
240 return e
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
241 leaf = json_dumps(e, sort_keys=True)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
242 if leaf[0] == '"':
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
243 leaf = leaf[1:-1]
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
244 parts.append(leaf)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
245 elif scan[w[0]] == '\\':
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
246 e = scan[w[1] - 1]
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
247 parts.append(e)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
248
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
249 scan = scan[w[1]:]
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
250 w = scanner(scan)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
251 parts.append(scan)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
252 return ''.join(parts)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
253
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
254 def needs_parsing(snippet): # type: (Any) -> bool
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
255 return isinstance(snippet, string_types) \
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
256 and ("$(" in snippet or "${" in snippet)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
257
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
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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