Mercurial > repos > shellac > sam_consensus_v3

annotate env/lib/python3.9/site-packages/cwltool/expression.py @ 0:4f3585e2f14b draft default tip

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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author shellac
date Mon, 22 Mar 2021 18:12:50 +0000
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0
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1 """Parse CWL expressions."""
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2
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3 import copy
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4 import json
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5 import re
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6 from typing import (
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7 Any,
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8 Dict,
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9 List,
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10 Mapping,
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11 MutableMapping,
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12 MutableSequence,
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13 Optional,
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14 Tuple,
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15 Union,
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16 cast,
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17 )
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18
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19 from schema_salad.utils import json_dumps
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20
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21 from .errors import WorkflowException
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22 from .loghandler import _logger
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23 from .sandboxjs import JavascriptException, default_timeout, execjs
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24 from .utils import (
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25 CWLObjectType,
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26 CWLOutputType,
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27 bytes2str_in_dicts,
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28 docker_windows_path_adjust,
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29 )
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30
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31
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32 def jshead(engine_config: List[str], rootvars: CWLObjectType) -> str:
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33 # make sure all the byte strings are converted
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34 # to str in `rootvars` dict.
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35
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36 return "\n".join(
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37 engine_config
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38 + [
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39 "var {} = {};".format(k, json_dumps(v, indent=4))
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40 for k, v in rootvars.items()
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41 ]
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42 )
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43
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44
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45 # decode all raw strings to unicode
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46 seg_symbol = r"""\w+"""
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47 seg_single = r"""\['([^']|\\')+'\]"""
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48 seg_double = r"""\["([^"]|\\")+"\]"""
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49 seg_index = r"""\[[0-9]+\]"""
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50 segments = fr"(\.{seg_symbol}|{seg_single}|{seg_double}|{seg_index})"
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51 segment_re = re.compile(segments, flags=re.UNICODE)
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52 param_str = fr"\(({seg_symbol}){segments}*\)$"
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53 param_re = re.compile(param_str, flags=re.UNICODE)
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54
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55
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56 class SubstitutionError(Exception):
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57 pass
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58
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59
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60 def scanner(scan: str) -> Optional[Tuple[int, int]]:
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61 DEFAULT = 0
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62 DOLLAR = 1
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63 PAREN = 2
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64 BRACE = 3
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65 SINGLE_QUOTE = 4
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66 DOUBLE_QUOTE = 5
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67 BACKSLASH = 6
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68
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69 i = 0
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70 stack = [DEFAULT]
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71 start = 0
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72 while i < len(scan):
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73 state = stack[-1]
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74 c = scan[i]
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75
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76 if state == DEFAULT:
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77 if c == "$":
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78 stack.append(DOLLAR)
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79 elif c == "\\":
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80 stack.append(BACKSLASH)
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81 elif state == BACKSLASH:
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82 stack.pop()
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83 if stack[-1] == DEFAULT:
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84 return (i - 1, i + 1)
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85 elif state == DOLLAR:
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86 if c == "(":
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87 start = i - 1
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88 stack.append(PAREN)
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89 elif c == "{":
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90 start = i - 1
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91 stack.append(BRACE)
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92 else:
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93 stack.pop()
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94 i -= 1
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95 elif state == PAREN:
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96 if c == "(":
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97 stack.append(PAREN)
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98 elif c == ")":
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99 stack.pop()
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100 if stack[-1] == DOLLAR:
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101 return (start, i + 1)
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102 elif c == "'":
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103 stack.append(SINGLE_QUOTE)
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104 elif c == '"':
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105 stack.append(DOUBLE_QUOTE)
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106 elif state == BRACE:
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107 if c == "{":
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108 stack.append(BRACE)
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109 elif c == "}":
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110 stack.pop()
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111 if stack[-1] == DOLLAR:
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112 return (start, i + 1)
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113 elif c == "'":
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114 stack.append(SINGLE_QUOTE)
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115 elif c == '"':
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116 stack.append(DOUBLE_QUOTE)
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117 elif state == SINGLE_QUOTE:
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118 if c == "'":
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119 stack.pop()
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120 elif c == "\\":
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121 stack.append(BACKSLASH)
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122 elif state == DOUBLE_QUOTE:
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123 if c == '"':
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124 stack.pop()
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125 elif c == "\\":
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126 stack.append(BACKSLASH)
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127 i += 1
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128
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129 if len(stack) > 1 and not (len(stack) == 2 and stack[1] in (BACKSLASH, DOLLAR)):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
130 raise SubstitutionError(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
131 "Substitution error, unfinished block starting at position {}: '{}' stack was {}".format(
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parents:
diff changeset
132 start, scan[start:], stack
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parents:
diff changeset
133 )
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shellac
parents:
diff changeset
134 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
135 return None
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shellac
parents:
diff changeset
136
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shellac
parents:
diff changeset
137
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parents:
diff changeset
138 def next_seg(
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parents:
diff changeset
139 parsed_string: str, remaining_string: str, current_value: CWLOutputType
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
140 ) -> CWLOutputType:
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shellac
parents:
diff changeset
141 if remaining_string:
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parents:
diff changeset
142 m = segment_re.match(remaining_string)
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parents:
diff changeset
143 if not m:
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parents:
diff changeset
144 return current_value
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parents:
diff changeset
145 next_segment_str = m.group(0)
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parents:
diff changeset
146
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diff changeset
147 key = None # type: Optional[Union[str, int]]
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parents:
diff changeset
148 if next_segment_str[0] == ".":
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parents:
diff changeset
149 key = next_segment_str[1:]
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parents:
diff changeset
150 elif next_segment_str[1] in ("'", '"'):
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parents:
diff changeset
151 key = next_segment_str[2:-2].replace("\\'", "'").replace('\\"', '"')
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parents:
diff changeset
152
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parents:
diff changeset
153 if key is not None:
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shellac
parents:
diff changeset
154 if (
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
155 isinstance(current_value, MutableSequence)
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shellac
parents:
diff changeset
156 and key == "length"
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parents:
diff changeset
157 and not remaining_string[m.end(0) :]
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parents:
diff changeset
158 ):
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parents:
diff changeset
159 return len(current_value)
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parents:
diff changeset
160 if not isinstance(current_value, MutableMapping):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
161 raise WorkflowException(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
162 "%s is a %s, cannot index on string '%s'"
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parents:
diff changeset
163 % (parsed_string, type(current_value).__name__, key)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
164 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
165 if key not in current_value:
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parents:
diff changeset
166 raise WorkflowException(f"{parsed_string} does not contain key '{key}'")
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shellac
parents:
diff changeset
167 else:
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shellac
parents:
diff changeset
168 try:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
169 key = int(next_segment_str[1:-1])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
170 except ValueError as v:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
171 raise WorkflowException(str(v)) from v
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
172 if not isinstance(current_value, MutableSequence):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
173 raise WorkflowException(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
174 "%s is a %s, cannot index on int '%s'"
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shellac
parents:
diff changeset
175 % (parsed_string, type(current_value).__name__, key)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
176 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
177 if key and key >= len(current_value):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
178 raise WorkflowException(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
179 "%s list index %i out of range" % (parsed_string, key)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
180 )
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shellac
parents:
diff changeset
181
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parents:
diff changeset
182 if isinstance(current_value, Mapping):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
183 try:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
184 return next_seg(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
185 parsed_string + remaining_string,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
186 remaining_string[m.end(0) :],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
187 cast(CWLOutputType, current_value[cast(str, key)]),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
188 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
189 except KeyError:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
190 raise WorkflowException(f"{parsed_string} doesn't have property {key}")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
191 elif isinstance(current_value, list) and isinstance(key, int):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
192 try:
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shellac
parents:
diff changeset
193 return next_seg(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
194 parsed_string + remaining_string,
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parents:
diff changeset
195 remaining_string[m.end(0) :],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
196 current_value[key],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
197 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
198 except KeyError:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
199 raise WorkflowException(f"{parsed_string} doesn't have property {key}")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
200 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
201 raise WorkflowException(f"{parsed_string} doesn't have property {key}")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
202 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
203 return current_value
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
204
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
205
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
206 def evaluator(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
207 ex: str,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
208 jslib: str,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
209 obj: CWLObjectType,
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shellac
parents:
diff changeset
210 timeout: float,
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shellac
parents:
diff changeset
211 fullJS: bool = False,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
212 force_docker_pull: bool = False,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
213 debug: bool = False,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
214 js_console: bool = False,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
215 ) -> Optional[CWLOutputType]:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
216 match = param_re.match(ex)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
217
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shellac
parents:
diff changeset
218 expression_parse_exception = None
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
219 expression_parse_succeeded = False
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
220
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
221 if match is not None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
222 first_symbol = match.group(1)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
223 first_symbol_end = match.end(1)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
224
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
225 if first_symbol_end + 1 == len(ex) and first_symbol == "null":
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
226 return None
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
227 try:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
228 if obj.get(first_symbol) is None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
229 raise WorkflowException("%s is not defined" % first_symbol)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
230
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
231 return next_seg(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
232 first_symbol,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
233 ex[first_symbol_end:-1],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
234 cast(CWLOutputType, obj[first_symbol]),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
235 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
236 except WorkflowException as werr:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
237 expression_parse_exception = werr
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
238 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
239 expression_parse_succeeded = True
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
240
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
241 if fullJS and not expression_parse_succeeded:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
242 return execjs(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
243 ex,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
244 jslib,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
245 timeout,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
246 force_docker_pull=force_docker_pull,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
247 debug=debug,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
248 js_console=js_console,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
249 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
250 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
251 if expression_parse_exception is not None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
252 raise JavascriptException(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
253 "Syntax error in parameter reference '%s': %s. This could be "
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
254 "due to using Javascript code without specifying "
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
255 "InlineJavascriptRequirement." % (ex[1:-1], expression_parse_exception)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
256 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
257 else:
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258 raise JavascriptException(
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259 "Syntax error in parameter reference '%s'. This could be due "
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260 "to using Javascript code without specifying "
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261 "InlineJavascriptRequirement." % ex
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262 )
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263
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264
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265 def _convert_dumper(string: str) -> str:
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266 return "{} + ".format(json.dumps(string))
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267
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268
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269 def interpolate(
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270 scan: str,
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271 rootvars: CWLObjectType,
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272 timeout: float = default_timeout,
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273 fullJS: bool = False,
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274 jslib: str = "",
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275 force_docker_pull: bool = False,
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276 debug: bool = False,
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277 js_console: bool = False,
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278 strip_whitespace: bool = True,
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279 escaping_behavior: int = 2,
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280 convert_to_expression: bool = False,
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281 ) -> Optional[CWLOutputType]:
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282 """
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283 Interpolate and evaluate.
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284
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285 Note: only call with convert_to_expression=True on CWL Expressions in $()
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286 form that need interpolation.
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287 """
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288 if strip_whitespace:
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289 scan = scan.strip()
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290 parts = []
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291 if convert_to_expression:
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292 dump = _convert_dumper
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293 parts.append("${return ")
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294 else:
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295 dump = lambda x: x
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296 w = scanner(scan)
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297 while w:
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298 if convert_to_expression:
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299 parts.append('"{}" + '.format(scan[0 : w[0]]))
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300 else:
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301 parts.append(scan[0 : w[0]])
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302
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303 if scan[w[0]] == "$":
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304 if not convert_to_expression:
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305 e = evaluator(
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306 scan[w[0] + 1 : w[1]],
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307 jslib,
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308 rootvars,
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309 timeout,
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310 fullJS=fullJS,
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311 force_docker_pull=force_docker_pull,
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312 debug=debug,
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313 js_console=js_console,
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314 )
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315 if w[0] == 0 and w[1] == len(scan) and len(parts) <= 1:
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316 return e
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317
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318 leaf = json_dumps(e, sort_keys=True)
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319 if leaf[0] == '"':
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320 leaf = json.loads(leaf)
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321 parts.append(leaf)
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322 else:
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323 parts.append(
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324 "function(){var item ="
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325 + scan[w[0] : w[1]][2:-1]
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326 + '; if (typeof(item) === "string"){ return item; } else { return JSON.stringify(item); }}() + '
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327 )
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328 elif scan[w[0]] == "\\":
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329 if escaping_behavior == 1:
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330 # Old behavior. Just skip the next character.
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331 e = scan[w[1] - 1]
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332 parts.append(dump(e))
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333 elif escaping_behavior == 2:
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334 # Backslash quoting requires a three character lookahead.
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335 e = scan[w[0] : w[1] + 1]
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336 if e in ("\\$(", "\\${"):
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337 # Suppress start of a parameter reference, drop the
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338 # backslash.
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339 parts.append(dump(e[1:]))
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340 w = (w[0], w[1] + 1)
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341 elif e[1] == "\\":
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342 # Double backslash, becomes a single backslash
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343 parts.append(dump("\\"))
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344 else:
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345 # Some other text, add it as-is (including the
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346 # backslash) and resume scanning.
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347 parts.append(dump(e[:2]))
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348 else:
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349 raise Exception("Unknown escaping behavior %s" % escaping_behavior)
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350 scan = scan[w[1] :]
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351 w = scanner(scan)
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352 if convert_to_expression:
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353 parts.append(f'"{scan}"')
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354 parts.append(";}")
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355 else:
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356 parts.append(scan)
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357 return "".join(parts)
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358
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359
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360 def needs_parsing(snippet: Any) -> bool:
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361 return isinstance(snippet, str) and ("$(" in snippet or "${" in snippet)
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362
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363
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364 def do_eval(
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365 ex: Optional[CWLOutputType],
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366 jobinput: CWLObjectType,
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367 requirements: List[CWLObjectType],
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368 outdir: Optional[str],
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369 tmpdir: Optional[str],
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370 resources: Dict[str, Union[float, int, str]],
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371 context: Optional[CWLOutputType] = None,
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372 timeout: float = default_timeout,
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373 force_docker_pull: bool = False,
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374 debug: bool = False,
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375 js_console: bool = False,
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376 strip_whitespace: bool = True,
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377 cwlVersion: str = "",
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378 ) -> Optional[CWLOutputType]:
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379
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380 runtime = cast(MutableMapping[str, Union[int, str, None]], copy.deepcopy(resources))
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381 runtime["tmpdir"] = docker_windows_path_adjust(tmpdir) if tmpdir else None
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382 runtime["outdir"] = docker_windows_path_adjust(outdir) if outdir else None
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383
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384 rootvars = cast(
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385 CWLObjectType,
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386 bytes2str_in_dicts({"inputs": jobinput, "self": context, "runtime": runtime}),
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387 )
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388
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389 if isinstance(ex, str) and needs_parsing(ex):
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390 fullJS = False
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391 jslib = ""
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392 for r in reversed(requirements):
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393 if r["class"] == "InlineJavascriptRequirement":
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394 fullJS = True
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395 jslib = jshead(cast(List[str], r.get("expressionLib", [])), rootvars)
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396 break
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397
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398 try:
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399 return interpolate(
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400 ex,
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401 rootvars,
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402 timeout=timeout,
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403 fullJS=fullJS,
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404 jslib=jslib,
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405 force_docker_pull=force_docker_pull,
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406 debug=debug,
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407 js_console=js_console,
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408 strip_whitespace=strip_whitespace,
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409 escaping_behavior=1
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410 if cwlVersion
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411 in (
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412 "v1.0",
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413 "v1.1.0-dev1",
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414 "v1.1",
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415 "v1.2.0-dev1",
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416 "v1.2.0-dev2",
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417 "v1.2.0-dev3",
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418 )
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419 else 2,
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420 )
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421
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422 except Exception as e:
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423 _logger.exception(e)
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424 raise WorkflowException("Expression evaluation error:\n%s" % str(e)) from e
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425 else:
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426 return ex