Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/schema_salad/python_codegen.py @ 0:26e78fe6e8c4 draft

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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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0
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1 """Python code generator for a given schema salad definition."""
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2 from typing import IO, Any, Dict, List, MutableMapping, MutableSequence, Union
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3
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4 from pkg_resources import resource_stream
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5 from six import iteritems, itervalues, text_type
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6 from io import StringIO
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7 from typing_extensions import Text # pylint: disable=unused-import
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8
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9 from . import schema
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10 from .exceptions import SchemaException
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11 from .codegen_base import CodeGenBase, TypeDef
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12 from .schema import shortname
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13
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14 # move to a regular typing import when Python 3.3-3.6 is no longer supported
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15
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16
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17 class PythonCodeGen(CodeGenBase):
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18 """Generation of Python code for a given Schema Salad definition."""
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19
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20 def __init__(self, out):
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21 # type: (IO[Text]) -> None
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22 super(PythonCodeGen, self).__init__()
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23 self.out = out
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24 self.current_class_is_abstract = False
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25 self.serializer = StringIO()
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26 self.idfield = u""
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27
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28 @staticmethod
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29 def safe_name(name): # type: (Text) -> Text
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30 avn = schema.avro_name(name)
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31 if avn in ("class", "in"):
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32 # reserved words
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33 avn = avn + "_"
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34 return avn
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35
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36 def prologue(self):
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37 # type: () -> None
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38
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39 self.out.write(
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40 u"""#
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41 # This file was autogenerated using schema-salad-tool --codegen=python
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42 # The code itself is released under the Apache 2.0 license and the help text is
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43 # subject to the license of the original schema.
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44 #
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45 """
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46 )
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47
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48 stream = resource_stream(__name__, "python_codegen_support.py")
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49 self.out.write(stream.read().decode("UTF-8"))
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50 stream.close()
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51 self.out.write(u"\n\n")
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52
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53 for primative in itervalues(self.prims):
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54 self.declare_type(primative)
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55
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56 def begin_class(
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57 self, # pylint: disable=too-many-arguments
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58 classname, # type: Text
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59 extends, # type: MutableSequence[Text]
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60 doc, # type: Text
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61 abstract, # type: bool
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62 field_names, # type: MutableSequence[Text]
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63 idfield, # type: Text
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64 ): # type: (...) -> None
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65 classname = self.safe_name(classname)
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66
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67 if extends:
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68 ext = ", ".join(self.safe_name(e) for e in extends)
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69 else:
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70 ext = "Savable"
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71
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72 self.out.write(u"class {}({}):\n".format(classname, ext))
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73
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74 if doc:
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75 self.out.write(u' """\n')
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76 self.out.write(text_type(doc))
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77 self.out.write(u'\n """\n')
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78
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79 self.serializer = StringIO()
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80
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81 self.current_class_is_abstract = abstract
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82 if self.current_class_is_abstract:
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83 self.out.write(u" pass\n\n\n")
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84 return
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85
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86 safe_inits = [" self,"] # type: List[Text]
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87 safe_inits.extend(
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88 [
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89 " {}, # type: Any".format(self.safe_name(f))
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90 for f in field_names
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91 if f != "class"
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92 ]
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93 )
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94 self.out.write(
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95 u" def __init__(\n"
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96 + u"\n".join(safe_inits)
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97 + u"\n extension_fields=None, "
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98 + u"# type: Optional[Dict[Text, Any]]"
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99 + u"\n loadingOptions=None # type: Optional[LoadingOptions]"
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100 + u"\n ): # type: (...) -> None\n"
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101 + u"""
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102 if extension_fields:
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103 self.extension_fields = extension_fields
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104 else:
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105 self.extension_fields = yaml.comments.CommentedMap()
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106 if loadingOptions:
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107 self.loadingOptions = loadingOptions
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108 else:
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109 self.loadingOptions = LoadingOptions()
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110 """
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111 )
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112 field_inits = u""
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113 for name in field_names:
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114 if name == "class":
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115 field_inits += u""" self.class_ = "{}"
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116 """.format(
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117 classname
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118 )
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119 else:
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120 field_inits += u""" self.{0} = {0}
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121 """.format(
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122 self.safe_name(name)
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123 )
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124 self.out.write(
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125 field_inits
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126 + u"""
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127 @classmethod
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128 def fromDoc(cls, doc, baseuri, loadingOptions, docRoot=None):
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129 # type: (Any, Text, LoadingOptions, Optional[Text]) -> {}
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130
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131 _doc = copy.copy(doc)
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132 if hasattr(doc, 'lc'):
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133 _doc.lc.data = doc.lc.data
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134 _doc.lc.filename = doc.lc.filename
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135 _errors__ = []
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136 """.format(
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137 classname
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138 )
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139 )
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140
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141 self.idfield = idfield
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142
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143 self.serializer.write(
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144 u"""
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145 def save(self, top=False, base_url="", relative_uris=True):
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146 # type: (bool, Text, bool) -> Dict[Text, Any]
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147 r = yaml.comments.CommentedMap() # type: Dict[Text, Any]
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148 for ef in self.extension_fields:
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149 r[prefix_url(ef, self.loadingOptions.vocab)] = self.extension_fields[ef]
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150 """
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151 )
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152
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153 if "class" in field_names:
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154 self.out.write(
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155 u"""
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156 if _doc.get('class') != '{class_}':
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157 raise ValidationException("Not a {class_}")
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158
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159 """.format(
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160 class_=classname
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161 )
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162 )
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163
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164 self.serializer.write(
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165 u"""
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166 r['class'] = '{class_}'
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167 """.format(
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168 class_=classname
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169 )
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170 )
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171
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172 def end_class(self, classname, field_names):
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173 # type: (Text, List[Text]) -> None
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174
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175 if self.current_class_is_abstract:
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176 return
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177
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178 self.out.write(
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179 u"""
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180 extension_fields = yaml.comments.CommentedMap()
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181 for k in _doc.keys():
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182 if k not in cls.attrs:
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183 if ":" in k:
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184 ex = expand_url(k,
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185 u"",
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186 loadingOptions,
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187 scoped_id=False,
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188 vocab_term=False)
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189 extension_fields[ex] = _doc[k]
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190 else:
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191 _errors__.append(
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192 ValidationException(
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193 "invalid field `%s`, expected one of: {attrstr}" % (k),
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194 SourceLine(_doc, k, str)
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195 )
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196 )
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197 break
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198
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199 if _errors__:
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200 raise ValidationException(\"Trying '{class_}'\", None, _errors__)
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201 """.format(
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202 attrstr=", ".join(["`{}`".format(f) for f in field_names]),
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203 class_=self.safe_name(classname),
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204 )
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205 )
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206
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207 self.serializer.write(
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208 u"""
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209 if top and self.loadingOptions.namespaces:
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210 r["$namespaces"] = self.loadingOptions.namespaces
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211
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212 """
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213 )
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214
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215 self.serializer.write(u" return r\n\n")
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216
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217 self.serializer.write(
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218 u" attrs = frozenset({attrs})\n".format(attrs=field_names)
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219 )
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220
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221 safe_inits = [
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222 self.safe_name(f) for f in field_names if f != "class"
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223 ] # type: List[Text]
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224
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225 safe_inits.extend(
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226 ["extension_fields=extension_fields", "loadingOptions=loadingOptions"]
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227 )
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228
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229 self.out.write(
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230 u""" loadingOptions = copy.deepcopy(loadingOptions)
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231 loadingOptions.original_doc = _doc
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232 """
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233 )
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234 self.out.write(u" return cls(" + ", ".join(safe_inits) + ")\n")
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235
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236 self.out.write(text_type(self.serializer.getvalue()))
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237
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238 self.out.write(u"\n\n")
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239
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240 prims = {
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241 u"http://www.w3.org/2001/XMLSchema#string": TypeDef(
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242 "strtype", "_PrimitiveLoader((str, text_type))"
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243 ),
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244 u"http://www.w3.org/2001/XMLSchema#int": TypeDef(
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245 "inttype", "_PrimitiveLoader(int)"
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246 ),
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247 u"http://www.w3.org/2001/XMLSchema#long": TypeDef(
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248 "inttype", "_PrimitiveLoader(int)"
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249 ),
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250 u"http://www.w3.org/2001/XMLSchema#float": TypeDef(
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251 "floattype", "_PrimitiveLoader(float)"
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252 ),
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253 u"http://www.w3.org/2001/XMLSchema#double": TypeDef(
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254 "floattype", "_PrimitiveLoader(float)"
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255 ),
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256 u"http://www.w3.org/2001/XMLSchema#boolean": TypeDef(
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257 "booltype", "_PrimitiveLoader(bool)"
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258 ),
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259 u"https://w3id.org/cwl/salad#null": TypeDef(
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260 "None_type", "_PrimitiveLoader(type(None))"
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261 ),
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262 u"https://w3id.org/cwl/salad#Any": TypeDef("Any_type", "_AnyLoader()"),
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263 }
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264
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265 def type_loader(self, type_declaration):
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266 # type: (Union[List[Any], Dict[Text, Any], Text]) -> TypeDef
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267
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268 if isinstance(type_declaration, MutableSequence):
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269 sub = [self.type_loader(i) for i in type_declaration]
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parents:
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270 return self.declare_type(
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271 TypeDef(
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parents:
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272 "union_of_{}".format("_or_".join(s.name for s in sub)),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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273 "_UnionLoader(({},))".format(", ".join(s.name for s in sub)),
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274 )
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275 )
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276 if isinstance(type_declaration, MutableMapping):
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277 if type_declaration["type"] in (
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278 "array",
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279 "https://w3id.org/cwl/salad#array",
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280 ):
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281 i = self.type_loader(type_declaration["items"])
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282 return self.declare_type(
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283 TypeDef(
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284 "array_of_{}".format(i.name), "_ArrayLoader({})".format(i.name)
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285 )
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286 )
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287 if type_declaration["type"] in ("enum", "https://w3id.org/cwl/salad#enum"):
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288 for sym in type_declaration["symbols"]:
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289 self.add_vocab(shortname(sym), sym)
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290 return self.declare_type(
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291 TypeDef(
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292 self.safe_name(type_declaration["name"]) + "Loader",
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parents:
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293 '_EnumLoader(("{}",))'.format(
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parents:
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294 '", "'.join(
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295 self.safe_name(sym)
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296 for sym in type_declaration["symbols"]
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297 )
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parents:
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298 ),
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parents:
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299 )
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parents:
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300 )
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parents:
diff changeset
301 if type_declaration["type"] in (
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302 "record",
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303 "https://w3id.org/cwl/salad#record",
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parents:
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304 ):
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parents:
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305 return self.declare_type(
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parents:
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306 TypeDef(
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parents:
diff changeset
307 self.safe_name(type_declaration["name"]) + "Loader",
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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308 "_RecordLoader({})".format(
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parents:
diff changeset
309 self.safe_name(type_declaration["name"])
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310 ),
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311 )
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parents:
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312 )
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parents:
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313 raise SchemaException("wft {}".format(type_declaration["type"]))
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parents:
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314 if type_declaration in self.prims:
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parents:
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315 return self.prims[type_declaration]
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parents:
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316 return self.collected_types[self.safe_name(type_declaration) + "Loader"]
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317
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parents:
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318 def declare_id_field(self, name, fieldtype, doc, optional):
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parents:
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319 # type: (Text, TypeDef, Text, bool) -> None
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parents:
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320
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parents:
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321 if self.current_class_is_abstract:
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parents:
diff changeset
322 return
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parents:
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323
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parents:
diff changeset
324 self.declare_field(name, fieldtype, doc, True)
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parents:
diff changeset
325
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parents:
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326 if optional:
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parents:
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327 opt = """{safename} = "_:" + str(_uuid__.uuid4())""".format(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
328 safename=self.safe_name(name)
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parents:
diff changeset
329 )
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parents:
diff changeset
330 else:
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parents:
diff changeset
331 opt = """raise ValidationException("Missing {fieldname}")""".format(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
332 fieldname=shortname(name)
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parents:
diff changeset
333 )
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parents:
diff changeset
334
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parents:
diff changeset
335 self.out.write(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
336 u"""
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
337 if {safename} is None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
338 if docRoot is not None:
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parents:
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339 {safename} = docRoot
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parents:
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340 else:
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parents:
diff changeset
341 {opt}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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342 baseuri = {safename}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
343 """.format(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
344 safename=self.safe_name(name), fieldname=shortname(name), opt=opt
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parents:
diff changeset
345 )
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parents:
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346 )
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parents:
diff changeset
347
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parents:
diff changeset
348 def declare_field(self, name, fieldtype, doc, optional):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
349 # type: (Text, TypeDef, Text, bool) -> None
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parents:
diff changeset
350
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parents:
diff changeset
351 if self.current_class_is_abstract:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
352 return
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
353
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
354 if shortname(name) == "class":
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
355 return
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
356
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
357 if optional:
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parents:
diff changeset
358 self.out.write(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
359 u" if '{fieldname}' in _doc:\n".format(fieldname=shortname(name))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
360 )
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
361 spc = " "
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
362 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
363 spc = ""
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
364 self.out.write(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
365 u"""{spc} try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
366 {spc} {safename} = load_field(_doc.get(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
367 {spc} '{fieldname}'), {fieldtype}, baseuri, loadingOptions)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
368 {spc} except ValidationException as e:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
369 {spc} _errors__.append(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
370 {spc} ValidationException(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
371 {spc} \"the `{fieldname}` field is not valid because:\",
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
372 {spc} SourceLine(_doc, '{fieldname}', str),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
373 {spc} [e]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
374 {spc} )
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
375 {spc} )
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
376 """.format(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
377 safename=self.safe_name(name),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
378 fieldname=shortname(name),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
379 fieldtype=fieldtype.name,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
380 spc=spc,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
381 )
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
382 )
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
383 if optional:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
384 self.out.write(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
385 u""" else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
386 {safename} = None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
387 """.format(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
388 safename=self.safe_name(name)
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389 )
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390 )
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391
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392 if name == self.idfield or not self.idfield:
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393 baseurl = "base_url"
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394 else:
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395 baseurl = "self.{}".format(self.safe_name(self.idfield))
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396
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397 if fieldtype.is_uri:
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398 self.serializer.write(
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diff changeset
399 u"""
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400 if self.{safename} is not None:
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parents:
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401 u = save_relative_uri(
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parents:
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402 self.{safename},
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parents:
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403 {baseurl},
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404 {scoped_id},
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405 {ref_scope},
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406 relative_uris)
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407 if u:
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408 r['{fieldname}'] = u
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409 """.format(
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410 safename=self.safe_name(name),
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411 fieldname=shortname(name).strip(),
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412 baseurl=baseurl,
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413 scoped_id=fieldtype.scoped_id,
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414 ref_scope=fieldtype.ref_scope,
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415 )
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416 )
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417 else:
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418 self.serializer.write(
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419 u"""
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420 if self.{safename} is not None:
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421 r['{fieldname}'] = save(
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422 self.{safename},
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423 top=False,
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424 base_url={baseurl},
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425 relative_uris=relative_uris)
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426 """.format(
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427 safename=self.safe_name(name),
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428 fieldname=shortname(name),
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429 baseurl=baseurl,
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430 )
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431 )
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432
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433 def uri_loader(self, inner, scoped_id, vocab_term, ref_scope):
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434 # type: (TypeDef, bool, bool, Union[int, None]) -> TypeDef
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435 return self.declare_type(
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436 TypeDef(
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437 "uri_{}_{}_{}_{}".format(inner.name, scoped_id, vocab_term, ref_scope),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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438 "_URILoader({}, {}, {}, {})".format(
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439 inner.name, scoped_id, vocab_term, ref_scope
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440 ),
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441 is_uri=True,
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442 scoped_id=scoped_id,
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443 ref_scope=ref_scope,
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444 )
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445 )
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446
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447 def idmap_loader(self, field, inner, map_subject, map_predicate):
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448 # type: (Text, TypeDef, Text, Union[Text, None]) -> TypeDef
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449 return self.declare_type(
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450 TypeDef(
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451 "idmap_{}_{}".format(self.safe_name(field), inner.name),
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452 "_IdMapLoader({}, '{}', '{}')".format(
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453 inner.name, map_subject, map_predicate
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diff changeset
454 ),
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455 )
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456 )
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457
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458 def typedsl_loader(self, inner, ref_scope):
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459 # type: (TypeDef, Union[int, None]) -> TypeDef
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460 return self.declare_type(
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461 TypeDef(
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462 "typedsl_{}_{}".format(inner.name, ref_scope),
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463 "_TypeDSLLoader({}, {})".format(inner.name, ref_scope),
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464 )
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465 )
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466
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467 def epilogue(self, root_loader):
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diff changeset
468 # type: (TypeDef) -> None
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469 self.out.write(u"_vocab = {\n")
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470 for k in sorted(self.vocab.keys()):
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diff changeset
471 self.out.write(u' "{}": "{}",\n'.format(k, self.vocab[k]))
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472 self.out.write(u"}\n")
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diff changeset
473
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diff changeset
474 self.out.write(u"_rvocab = {\n")
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parents:
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475 for k in sorted(self.vocab.keys()):
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diff changeset
476 self.out.write(u' "{}": "{}",\n'.format(self.vocab[k], k))
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parents:
diff changeset
477 self.out.write(u"}\n\n")
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diff changeset
478
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479 for _, collected_type in iteritems(self.collected_types):
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parents:
diff changeset
480 self.out.write(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
481 u"{} = {}\n".format(collected_type.name, collected_type.init)
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482 )
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483 self.out.write(u"\n")
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diff changeset
484
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485 self.out.write(
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486 u"""
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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487 def load_document(doc, baseuri=None, loadingOptions=None):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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488 # type: (Any, Optional[Text], Optional[LoadingOptions]) -> Any
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489 if baseuri is None:
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parents:
diff changeset
490 baseuri = file_uri(os.getcwd()) + "/"
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parents:
diff changeset
491 if loadingOptions is None:
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492 loadingOptions = LoadingOptions()
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493 return _document_load(%(name)s, doc, baseuri, loadingOptions)
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494
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495
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496 def load_document_by_string(string, uri, loadingOptions=None):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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497 # type: (Any, Text, Optional[LoadingOptions]) -> Any
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498 result = yaml.round_trip_load(string, preserve_quotes=True)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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499 add_lc_filename(result, uri)
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500
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501 if loadingOptions is None:
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502 loadingOptions = LoadingOptions(fileuri=uri)
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503 loadingOptions.idx[uri] = result
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504
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505 return _document_load(%(name)s, result, uri, loadingOptions)
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parents:
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506 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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507 % dict(name=root_loader.name)
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parents:
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508 )