Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/cwltool/validate_js.py @ 4:79f47841a781 draft

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"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:47:39 -0400
parents 26e78fe6e8c4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 import copy
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2 import itertools
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3 import json
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4 import logging
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5 from collections import namedtuple
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6 from typing import (cast, Any, Dict, List, MutableMapping, MutableSequence,
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7 Optional, Tuple, Union)
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8
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9 from pkg_resources import resource_stream
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10 from ruamel.yaml.comments import CommentedMap # pylint: disable=unused-import
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11 from six import string_types
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12 from typing_extensions import Text # pylint: disable=unused-import
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13 from schema_salad import avro
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14 from schema_salad.sourceline import SourceLine
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15 from schema_salad.validate import Schema # pylint: disable=unused-import
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16 from schema_salad.validate import validate_ex
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17
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18 from .errors import WorkflowException
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19 from .expression import scanner as scan_expression
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20 from .expression import SubstitutionError
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21 from .loghandler import _logger
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22 from .sandboxjs import code_fragment_to_js, exec_js_process
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23 from .utils import json_dumps
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24
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25
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26 def is_expression(tool, schema):
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27 # type: (Any, Optional[Schema]) -> bool
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28 return isinstance(schema, avro.schema.EnumSchema) \
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29 and schema.name == "Expression" and isinstance(tool, string_types)
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30
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31 class SuppressLog(logging.Filter):
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32 def __init__(self, name): # type: (Text) -> None
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33 """Initialize this log suppressor."""
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34 name = str(name)
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35 super(SuppressLog, self).__init__(name)
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36
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37 def filter(self, record): # type: (logging.LogRecord) -> bool
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38 return False
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39
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40
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41 _logger_validation_warnings = logging.getLogger("cwltool.validation_warnings")
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42 _logger_validation_warnings.addFilter(SuppressLog("cwltool.validation_warnings"))
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43
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44 def get_expressions(tool, # type: Union[CommentedMap, Text]
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45 schema, # type: Optional[avro.schema.Schema]
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46 source_line=None # type: Optional[SourceLine]
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47 ): # type: (...) -> List[Tuple[Text, Optional[SourceLine]]]
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48 if is_expression(tool, schema):
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49 return [(cast(Text, tool), source_line)]
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50 elif isinstance(schema, avro.schema.UnionSchema):
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51 valid_schema = None
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52
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53 for possible_schema in schema.schemas:
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54 if is_expression(tool, possible_schema):
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55 return [(cast(Text, tool), source_line)]
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56 elif validate_ex(possible_schema, tool, raise_ex=False,
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57 logger=_logger_validation_warnings):
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58 valid_schema = possible_schema
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59
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60 return get_expressions(tool, valid_schema, source_line)
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61 elif isinstance(schema, avro.schema.ArraySchema):
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62 if not isinstance(tool, MutableSequence):
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63 return []
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64
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65 return list(itertools.chain(
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66 *map(lambda x: get_expressions(x[1], schema.items, SourceLine(tool, x[0])), enumerate(tool))
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67 ))
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68
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69 elif isinstance(schema, avro.schema.RecordSchema):
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70 if not isinstance(tool, MutableMapping):
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71 return []
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72
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73 expression_nodes = []
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74
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75 for schema_field in schema.fields:
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76 if schema_field.name in tool:
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77 expression_nodes.extend(get_expressions(
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78 tool[schema_field.name],
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79 schema_field.type,
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80 SourceLine(tool, schema_field.name)
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81 ))
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82
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83 return expression_nodes
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84 else:
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85 return []
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86
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87
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88 JSHintJSReturn = namedtuple("jshint_return", ["errors", "globals"])
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89
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90 def jshint_js(js_text, # type: Text
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91 globals=None, # type: Optional[List[Text]]
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92 options=None # type: Optional[Dict[Text, Union[List[Text], Text, int]]]
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93 ): # type: (...) -> Tuple[List[Text], List[Text]]
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94 if globals is None:
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95 globals = []
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96 if options is None:
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97 options = {
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98 "includewarnings": [
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99 "W117", # <VARIABLE> not defined
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100 "W104", "W119" # using ES6 features
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101 ],
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102 "strict": "implied",
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103 "esversion": 5
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104 }
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105
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106 with resource_stream(__name__, "jshint/jshint.js") as file:
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107 # NOTE: we need a global variable for lodash (which jshint depends on)
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108 jshint_functions_text = "var global = this;" + file.read().decode('utf-8')
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109
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110 with resource_stream(__name__, "jshint/jshint_wrapper.js") as file:
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111 # NOTE: we need to assign to ob, as the expression {validateJS: validateJS} as an expression
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112 # is interpreted as a block with a label `validateJS`
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113 jshint_functions_text += "\n" + file.read().decode('utf-8') + "\nvar ob = {validateJS: validateJS}; ob"
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114
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115 returncode, stdout, stderr = exec_js_process(
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116 "validateJS(%s)" % json_dumps({
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117 "code": js_text,
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118 "options": options,
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119 "globals": globals
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120 }),
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121 timeout=30,
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122 context=jshint_functions_text
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123 )
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124
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125 def dump_jshint_error():
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126 # type: () -> None
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127 raise RuntimeError("jshint failed to run succesfully\nreturncode: %d\nstdout: \"%s\"\nstderr: \"%s\"" % (
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128 returncode,
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129 stdout,
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130 stderr
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131 ))
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132
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133 if returncode == -1:
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134 _logger.warning("jshint process timed out")
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135
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136 if returncode != 0:
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137 dump_jshint_error()
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138
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139 try:
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140 jshint_json = json.loads(stdout)
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141 except ValueError:
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142 dump_jshint_error()
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143
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144 jshint_errors = [] # type: List[Text]
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145
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146 js_text_lines = js_text.split("\n")
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147
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148 for jshint_error_obj in jshint_json.get("errors", []):
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149 text = u"JSHINT: " + js_text_lines[jshint_error_obj["line"] - 1] + "\n"
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150 text += u"JSHINT: " + " " * (jshint_error_obj["character"] - 1) + "^\n"
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151 text += u"JSHINT: %s: %s" % (jshint_error_obj["code"], jshint_error_obj["reason"])
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152 jshint_errors.append(text)
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153
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154 return JSHintJSReturn(jshint_errors, jshint_json.get("globals", []))
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155
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156
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157 def print_js_hint_messages(js_hint_messages, source_line):
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158 # type: (List[Text], Optional[SourceLine]) -> None
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159 if source_line is not None:
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160 for js_hint_message in js_hint_messages:
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161 _logger.warning(source_line.makeError(js_hint_message))
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162
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163 def validate_js_expressions(tool, # type: CommentedMap
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164 schema, # type: Schema
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165 jshint_options=None # type: Optional[Dict[Text, Union[List[Text], Text, int]]]
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166 ): # type: (...) -> None
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167
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168 if tool.get("requirements") is None:
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169 return
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170
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171 requirements = tool["requirements"]
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172
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173 default_globals = [u"self", u"inputs", u"runtime", u"console"]
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174
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175 for prop in reversed(requirements):
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176 if prop["class"] == "InlineJavascriptRequirement":
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177 expression_lib = prop.get("expressionLib", [])
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178 break
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179 else:
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180 return
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181
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182 js_globals = copy.deepcopy(default_globals)
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183
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184 for i, expression_lib_line in enumerate(expression_lib):
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185 expression_lib_line_errors, expression_lib_line_globals = jshint_js(expression_lib_line, js_globals, jshint_options)
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186 js_globals.extend(expression_lib_line_globals)
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187 print_js_hint_messages(expression_lib_line_errors, SourceLine(expression_lib, i))
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188
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189 expressions = get_expressions(tool, schema)
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190
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191 for expression, source_line in expressions:
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192 unscanned_str = expression.strip()
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193 try:
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194 scan_slice = scan_expression(unscanned_str)
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195 except SubstitutionError as se:
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196 if source_line:
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197 source_line.raise_type = WorkflowException
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198 raise source_line.makeError(str(se))
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199 else:
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200 raise se
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201
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202 while scan_slice:
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203 if unscanned_str[scan_slice[0]] == '$':
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204 code_fragment = unscanned_str[scan_slice[0] + 1:scan_slice[1]]
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205 code_fragment_js = code_fragment_to_js(code_fragment, "")
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206 expression_errors, _ = jshint_js(code_fragment_js, js_globals, jshint_options)
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207 print_js_hint_messages(expression_errors, source_line)
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208
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209 unscanned_str = unscanned_str[scan_slice[1]:]
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210 scan_slice = scan_expression(unscanned_str)