Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/cwltool/validate_js.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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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 ( |
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7 Any, |
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8 Dict, |
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9 List, |
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10 MutableMapping, |
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11 MutableSequence, |
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12 Optional, |
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13 Tuple, |
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14 Union, |
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15 cast, |
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16 ) |
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17 |
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18 from pkg_resources import resource_stream |
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19 from ruamel.yaml.comments import CommentedMap |
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20 from schema_salad.avro.schema import ( |
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21 ArraySchema, |
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22 EnumSchema, |
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23 RecordSchema, |
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24 Schema, |
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25 UnionSchema, |
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26 ) |
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27 from schema_salad.sourceline import SourceLine |
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28 from schema_salad.utils import json_dumps |
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29 from schema_salad.validate import validate_ex |
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30 |
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31 from .errors import WorkflowException |
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32 from .expression import SubstitutionError |
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33 from .expression import scanner as scan_expression |
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34 from .loghandler import _logger |
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35 from .sandboxjs import code_fragment_to_js, exec_js_process |
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36 |
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37 |
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38 def is_expression(tool, schema): |
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39 # type: (Any, Optional[Schema]) -> bool |
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40 return ( |
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41 isinstance(schema, EnumSchema) |
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42 and schema.name == "Expression" |
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43 and isinstance(tool, str) |
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44 ) |
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45 |
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46 |
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47 class SuppressLog(logging.Filter): |
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48 def __init__(self, name): # type: (str) -> None |
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49 """Initialize this log suppressor.""" |
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50 name = str(name) |
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51 super().__init__(name) |
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52 |
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53 def filter(self, record): # type: (logging.LogRecord) -> bool |
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54 return False |
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55 |
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56 |
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57 _logger_validation_warnings = logging.getLogger("cwltool.validation_warnings") |
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58 _logger_validation_warnings.addFilter(SuppressLog("cwltool.validation_warnings")) |
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59 |
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60 |
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61 def get_expressions( |
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62 tool: Union[CommentedMap, str], |
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63 schema: Optional[Union[Schema, ArraySchema]], |
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64 source_line: Optional[SourceLine] = None, |
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65 ) -> List[Tuple[str, Optional[SourceLine]]]: |
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66 if is_expression(tool, schema): |
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67 return [(cast(str, tool), source_line)] |
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68 elif isinstance(schema, UnionSchema): |
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69 valid_schema = None |
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70 |
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71 for possible_schema in schema.schemas: |
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72 if is_expression(tool, possible_schema): |
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73 return [(cast(str, tool), source_line)] |
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74 elif validate_ex( |
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75 possible_schema, |
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76 tool, |
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77 raise_ex=False, |
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78 logger=_logger_validation_warnings, |
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79 ): |
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80 valid_schema = possible_schema |
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81 |
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82 return get_expressions(tool, valid_schema, source_line) |
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83 elif isinstance(schema, ArraySchema): |
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84 if not isinstance(tool, MutableSequence): |
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85 return [] |
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86 |
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87 return list( |
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88 itertools.chain( |
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89 *map( |
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90 lambda x: get_expressions( |
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91 x[1], schema.items, SourceLine(tool, x[0]) # type: ignore |
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92 ), |
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93 enumerate(tool), |
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94 ) |
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95 ) |
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96 ) |
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97 |
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98 elif isinstance(schema, RecordSchema): |
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99 if not isinstance(tool, MutableMapping): |
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100 return [] |
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101 |
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102 expression_nodes = [] |
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103 |
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104 for schema_field in schema.fields: |
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105 if schema_field.name in tool: |
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106 expression_nodes.extend( |
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107 get_expressions( |
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108 tool[schema_field.name], |
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109 schema_field.type, |
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110 SourceLine(tool, schema_field.name), |
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111 ) |
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112 ) |
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113 |
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114 return expression_nodes |
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115 else: |
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116 return [] |
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117 |
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118 |
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119 JSHintJSReturn = namedtuple("JSHintJSReturn", ["errors", "globals"]) |
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120 |
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121 |
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122 def jshint_js( |
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123 js_text: str, |
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124 globals: Optional[List[str]] = None, |
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125 options: Optional[Dict[str, Union[List[str], str, int]]] = None, |
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126 ) -> JSHintJSReturn: |
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127 if globals is None: |
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128 globals = [] |
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129 if options is None: |
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130 options = { |
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131 "includewarnings": [ |
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132 "W117", # <VARIABLE> not defined |
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133 "W104", |
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134 "W119", # using ES6 features |
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135 ], |
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136 "strict": "implied", |
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137 "esversion": 5, |
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138 } |
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139 |
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140 with resource_stream(__name__, "jshint/jshint.js") as res: |
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141 # NOTE: we need a global variable for lodash (which jshint depends on) |
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142 jshint_functions_text = "var global = this;" + res.read().decode("utf-8") |
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143 |
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144 with resource_stream(__name__, "jshint/jshint_wrapper.js") as res2: |
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145 # NOTE: we need to assign to ob, as the expression {validateJS: validateJS} as an expression |
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146 # is interpreted as a block with a label `validateJS` |
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147 jshint_functions_text += ( |
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148 "\n" |
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149 + res2.read().decode("utf-8") |
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150 + "\nvar ob = {validateJS: validateJS}; ob" |
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151 ) |
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152 |
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153 returncode, stdout, stderr = exec_js_process( |
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154 "validateJS(%s)" |
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155 % json_dumps({"code": js_text, "options": options, "globals": globals}), |
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156 timeout=30, |
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157 context=jshint_functions_text, |
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158 ) |
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159 |
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160 def dump_jshint_error(): |
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161 # type: () -> None |
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162 raise RuntimeError( |
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163 'jshint failed to run succesfully\nreturncode: %d\nstdout: "%s"\nstderr: "%s"' |
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164 % (returncode, stdout, stderr) |
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165 ) |
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166 |
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167 if returncode == -1: |
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168 _logger.warning("jshint process timed out") |
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169 |
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170 if returncode != 0: |
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171 dump_jshint_error() |
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172 |
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173 try: |
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174 jshint_json = json.loads(stdout) |
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175 except ValueError: |
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176 dump_jshint_error() |
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177 |
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178 jshint_errors = [] # type: List[str] |
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179 |
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180 js_text_lines = js_text.split("\n") |
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181 |
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182 for jshint_error_obj in jshint_json.get("errors", []): |
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183 text = "JSHINT: " + js_text_lines[jshint_error_obj["line"] - 1] + "\n" |
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184 text += "JSHINT: " + " " * (jshint_error_obj["character"] - 1) + "^\n" |
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185 text += "JSHINT: {}: {}".format( |
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186 jshint_error_obj["code"], |
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187 jshint_error_obj["reason"], |
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188 ) |
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189 jshint_errors.append(text) |
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190 |
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191 return JSHintJSReturn(jshint_errors, jshint_json.get("globals", [])) |
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192 |
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193 |
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194 def print_js_hint_messages( |
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195 js_hint_messages: List[str], source_line: Optional[SourceLine] |
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196 ) -> None: |
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197 if source_line is not None: |
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198 for js_hint_message in js_hint_messages: |
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199 _logger.warning(source_line.makeError(js_hint_message)) |
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200 |
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201 |
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202 def validate_js_expressions( |
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203 tool: CommentedMap, |
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204 schema: Schema, |
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205 jshint_options: Optional[Dict[str, Union[List[str], str, int]]] = None, |
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206 ) -> None: |
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207 |
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208 if tool.get("requirements") is None: |
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209 return |
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210 |
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211 requirements = tool["requirements"] |
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212 |
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213 default_globals = ["self", "inputs", "runtime", "console"] |
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214 |
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215 for prop in reversed(requirements): |
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216 if prop["class"] == "InlineJavascriptRequirement": |
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217 expression_lib = prop.get("expressionLib", []) |
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218 break |
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219 else: |
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220 return |
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221 |
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222 js_globals = copy.deepcopy(default_globals) |
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223 |
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224 for i, expression_lib_line in enumerate(expression_lib): |
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225 expression_lib_line_errors, expression_lib_line_globals = jshint_js( |
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226 expression_lib_line, js_globals, jshint_options |
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227 ) |
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228 js_globals.extend(expression_lib_line_globals) |
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229 print_js_hint_messages( |
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230 expression_lib_line_errors, SourceLine(expression_lib, i) |
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231 ) |
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232 |
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233 expressions = get_expressions(tool, schema) |
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234 |
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235 for expression, source_line in expressions: |
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236 unscanned_str = expression.strip() |
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237 try: |
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238 scan_slice = scan_expression(unscanned_str) |
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239 except SubstitutionError as se: |
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240 if source_line: |
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241 source_line.raise_type = WorkflowException |
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242 raise source_line.makeError(str(se)) |
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243 else: |
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244 raise se |
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245 |
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246 while scan_slice: |
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247 if unscanned_str[scan_slice[0]] == "$": |
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248 code_fragment = unscanned_str[scan_slice[0] + 1 : scan_slice[1]] |
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249 code_fragment_js = code_fragment_to_js(code_fragment, "") |
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250 expression_errors, _ = jshint_js( |
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251 code_fragment_js, js_globals, jshint_options |
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252 ) |
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253 print_js_hint_messages(expression_errors, source_line) |
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254 |
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255 unscanned_str = unscanned_str[scan_slice[1] :] |
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256 scan_slice = scan_expression(unscanned_str) |