Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/schema_salad/java_codegen.py @ 2:6af9afd405e9 draft

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"planemo upload commit 0a63dd5f4d38a1f6944587f52a8cd79874177fc1"
author shellac
date Thu, 14 May 2020 14:56:58 -0400
parents 26e78fe6e8c4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 """Work-in-progress Java code generator for a given schema salad definition."""
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2 import os
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3 import pkg_resources
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4 import string
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5 import shutil
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6 from io import open as io_open
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7 from typing import Any, Dict, List, MutableMapping, MutableSequence, Optional, Union
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8
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9 from six import iteritems, itervalues
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10 from six.moves import cStringIO, urllib
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11 from typing_extensions import Text # pylint: disable=unused-import
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12
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13 from . import schema
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14 from .codegen_base import CodeGenBase, TypeDef
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15 from .exceptions import SchemaException
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16 from .schema import shortname
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17
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18 # move to a regular typing import when Python 3.3-3.6 is no longer supported
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19
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20 # experiment at providing more typed objects building a optional type that allows
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21 # referencing one or a list of objects. It is useful for improving the RootLoader
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22 # for simple schema with a single root loader - but doesn't help with CWL at all and
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23 # may even confuse things a bit so turning these off be default.
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24 USE_ONE_OR_LIST_OF_TYPES = False
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25
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26
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27 def _ensure_directory_and_write(path, contents):
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28 # type: (Text, Text) -> None
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29 dirname = os.path.dirname(path)
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30 _safe_makedirs(dirname)
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31 with io_open(path, mode="w", encoding="utf-8") as f:
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32 f.write(contents)
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33
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34
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35 def doc_to_doc_string(doc, indent_level=0):
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36 # type: (Text, int) -> Text
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37 lead = " " + " " * indent_level + "* " * indent_level
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38 if doc:
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39 doc_str = "{}<BLOCKQUOTE>\n".format(lead)
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40 doc_str += "\n".join(["{}{}".format(lead, l) for l in doc.split("\n")])
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41 doc_str += "{}</BLOCKQUOTE>".format(lead)
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42 else:
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43 doc_str = ""
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44 return doc_str
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45
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46
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47 def _safe_makedirs(path):
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48 # type: (Text) -> None
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49 if not os.path.exists(path):
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50 os.makedirs(path)
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51
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52
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53 class JavaCodeGen(CodeGenBase):
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54 def __init__(self, base, target, examples):
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55 # type: (Text, Optional[str], Optional[str]) -> None
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56 super(JavaCodeGen, self).__init__()
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57 self.base_uri = base
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58 sp = urllib.parse.urlsplit(base)
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59 self.examples = examples
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60 self.package = ".".join(
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61 list(reversed(sp.netloc.split("."))) + sp.path.strip("/").split("/")
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62 )
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63 self.artifact = self.package.split(".")[-1]
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64 target = target or "."
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65 self.target_dir = target
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66 rel_package_dir = self.package.replace(".", "/")
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67 self.rel_package_dir = rel_package_dir
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68 self.main_src_dir = os.path.join(
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69 self.target_dir, "src", "main", "java", rel_package_dir
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70 )
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71 self.test_src_dir = os.path.join(
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72 self.target_dir, "src", "test", "java", rel_package_dir
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73 )
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74 self.test_resources_dir = os.path.join(
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75 self.target_dir, "src", "test", "resources", rel_package_dir
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76 )
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77
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78 def prologue(self): # type: () -> None
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79 for src_dir in [self.main_src_dir, self.test_src_dir]:
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80 _safe_makedirs(src_dir)
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81
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82 for primitive in itervalues(self.prims):
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83 self.declare_type(primitive)
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84
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85 @staticmethod
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86 def property_name(name): # type: (Text) -> Text
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87 avn = schema.avro_name(name)
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88 return avn
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89
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90 @staticmethod
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91 def safe_name(name): # type: (Text) -> Text
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92 avn = JavaCodeGen.property_name(name)
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93 if avn in ("class", "extends", "abstract", "default", "package"):
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94 # reserved words
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95 avn = avn + "_"
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96 return avn
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97
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98 def interface_name(self, n):
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99 # type: (Text) -> Text
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100 return self.safe_name(n)
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101
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102 def begin_class(
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103 self,
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104 classname, # type: Text
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105 extends, # type: MutableSequence[Text]
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106 doc, # type: Text
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107 abstract, # type: bool
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108 field_names, # type: MutableSequence[Text]
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109 idfield, # type: Text
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110 ): # type: (...) -> None
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111 cls = self.interface_name(classname)
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112 self.current_class = cls
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113 self.current_class_is_abstract = abstract
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114 self.current_loader = cStringIO()
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115 self.current_fieldtypes = {} # type: Dict[Text, TypeDef]
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116 self.current_fields = cStringIO()
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117 interface_doc_str = u"* Auto-generated interface for <I>%s</I><BR>" % classname
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118 if not abstract:
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119 implemented_by = u"This interface is implemented by {{@link {}Impl}}<BR>"
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120 interface_doc_str += implemented_by.format(cls)
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121 interface_doc_str += doc_to_doc_string(doc)
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122 class_doc_str = u"* Auto-generated class implementation for <I>{}</I><BR>".format(
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123 classname
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124 )
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125 class_doc_str += doc_to_doc_string(doc)
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126 with open(os.path.join(self.main_src_dir, "{}.java".format(cls)), "w") as f:
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127
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128 if extends:
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129 ext = (
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130 "extends "
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131 + ", ".join(self.interface_name(e) for e in extends)
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132 + ", Savable"
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133 )
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134 else:
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135 ext = "extends Savable"
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136 f.write(
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137 """package {package};
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138
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139 import {package}.utils.Savable;
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140
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141 /**
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142 {interface_doc_str}
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143 */
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144 public interface {cls} {ext} {{""".format(
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145 package=self.package,
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146 cls=cls,
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147 ext=ext,
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148 interface_doc_str=interface_doc_str,
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149 )
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150 )
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151
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152 if self.current_class_is_abstract:
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153 return
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154
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155 with open(os.path.join(self.main_src_dir, "{}Impl.java".format(cls)), "w") as f:
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156 f.write(
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157 """package {package};
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158
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159 import {package}.utils.LoaderInstances;
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160 import {package}.utils.LoadingOptions;
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161 import {package}.utils.LoadingOptionsBuilder;
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162 import {package}.utils.SavableImpl;
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163 import {package}.utils.ValidationException;
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164
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165 /**
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166 {class_doc_str}
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167 */
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168 public class {cls}Impl extends SavableImpl implements {cls} {{
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169 private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build();
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170 private java.util.Map<String, Object> extensionFields_ =
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171 new java.util.HashMap<String, Object>();
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172 """.format(
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173 package=self.package, cls=cls, class_doc_str=class_doc_str
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174 )
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175 )
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176 self.current_loader.write(
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177 """
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178 /**
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179 * Used by {{@link {package}.utils.RootLoader}} to construct instances of {cls}Impl.
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180 *
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181 * @param __doc_ Document fragment to load this record object from (presumably a
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182 {{@link java.util.Map}}).
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183 * @param __baseUri_ Base URI to generate child document IDs against.
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184 * @param __loadingOptions Context for loading URIs and populating objects.
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185 * @param __docRoot_ ID at this position in the document (if available) (maybe?)
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186 * @throws ValidationException If the document fragment is not a {{@link java.util.Map}}
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187 * or validation of fields fails.
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188 */
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189 public {cls}Impl(
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190 final Object __doc_,
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191 final String __baseUri_,
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192 LoadingOptions __loadingOptions,
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193 final String __docRoot_) {{
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194 super(__doc_, __baseUri_, __loadingOptions, __docRoot_);
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195 // Prefix plumbing variables with '__' to reduce likelihood of collision with
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196 // generated names.
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197 String __baseUri = __baseUri_;
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198 String __docRoot = __docRoot_;
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199 if (!(__doc_ instanceof java.util.Map)) {{
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200 throw new ValidationException("{cls}Impl called on non-map");
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201 }}
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202 final java.util.Map<String, Object> __doc = (java.util.Map<String, Object>) __doc_;
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203 final java.util.List<ValidationException> __errors =
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204 new java.util.ArrayList<ValidationException>();
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205 if (__loadingOptions != null) {{
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206 this.loadingOptions_ = __loadingOptions;
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207 }}
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208 """.format(
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209 cls=cls, package=self.package
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210 )
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211 )
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212
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213 def end_class(self, classname, field_names):
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214 # type: (Text, List[Text]) -> None
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215 with open(
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216 os.path.join(self.main_src_dir, "{}.java".format(self.current_class)), "a"
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217 ) as f:
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218 f.write(
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219 """
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220 }
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221 """
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222 )
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223 if self.current_class_is_abstract:
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224 return
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225
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226 self.current_loader.write(
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227 """ if (!__errors.isEmpty()) {
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228 throw new ValidationException("Trying 'RecordField'", __errors);
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229 }
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230 """
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231 )
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232 for fieldname in field_names:
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233 fieldtype = self.current_fieldtypes.get(fieldname)
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234 if fieldtype is None:
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235 continue
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236 self.current_loader.write(
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237 """ this.{safename} = ({type}) {safename};
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238 """.format(
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239 safename=self.safe_name(fieldname), type=fieldtype.instance_type
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240 )
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241 )
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242
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243 self.current_loader.write(""" }""")
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244
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245 with open(
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246 os.path.join(self.main_src_dir, "{}Impl.java".format(self.current_class)),
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247 "a",
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248 ) as f:
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249 f.write(self.current_fields.getvalue())
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250 f.write(self.current_loader.getvalue())
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251 f.write(
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252 """
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253 }
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254 """
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255 )
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256
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257 prims = {
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258 u"http://www.w3.org/2001/XMLSchema#string": TypeDef(
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259 instance_type="String",
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260 init="new PrimitiveLoader<String>(String.class)",
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261 name="StringInstance",
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262 loader_type="Loader<String>",
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263 ),
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264 u"http://www.w3.org/2001/XMLSchema#int": TypeDef(
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265 instance_type="Integer",
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266 init="new PrimitiveLoader<Integer>(Integer.class)",
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267 name="IntegerInstance",
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268 loader_type="Loader<Integer>",
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269 ),
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270 u"http://www.w3.org/2001/XMLSchema#long": TypeDef(
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271 instance_type="Long",
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272 name="LongInstance",
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273 loader_type="Loader<Long>",
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274 init="new PrimitiveLoader<Long>(Long.class)",
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275 ),
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276 u"http://www.w3.org/2001/XMLSchema#float": TypeDef(
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277 instance_type="Float",
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278 name="FloatInstance",
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279 loader_type="Loader<Float>",
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280 init="new PrimitiveLoader<Float>(Float.class)",
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281 ),
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282 u"http://www.w3.org/2001/XMLSchema#double": TypeDef(
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283 instance_type="Double",
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284 name="DoubleInstance",
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285 loader_type="Loader<Double>",
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286 init="new PrimitiveLoader<Double>(Double.class)",
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287 ),
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288 u"http://www.w3.org/2001/XMLSchema#boolean": TypeDef(
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289 instance_type="Boolean",
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290 name="BooleanInstance",
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291 loader_type="Loader<Boolean>",
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292 init="new PrimitiveLoader<Boolean>(Boolean.class)",
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293 ),
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294 u"https://w3id.org/cwl/salad#null": TypeDef(
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295 instance_type="Object",
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296 name="NullInstance",
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297 loader_type="Loader<Object>",
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298 init="new NullLoader()",
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299 ),
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300 u"https://w3id.org/cwl/salad#Any": TypeDef(
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301 instance_type="Object",
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302 name="AnyInstance",
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303 init="new AnyLoader()",
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304 loader_type="Loader<Object>",
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305 ),
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306 }
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307
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308 def type_loader(self, type_declaration):
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309 # type: (Union[List[Any], Dict[Text, Any], Text]) -> TypeDef
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310 if isinstance(type_declaration, MutableSequence):
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311 sub = [self.type_loader(i) for i in type_declaration]
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312 if len(sub) < 2:
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313 return sub[0]
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314
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315 if len(sub) == 2:
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316 type_1 = sub[0]
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317 type_2 = sub[1]
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318 type_1_name = type_1.name
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319 type_2_name = type_2.name
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320 if type_1_name == "NullInstance" or type_2_name == "NullInstance":
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321 non_null_type = type_1 if type_1.name != "NullInstance" else type_2
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322 return self.declare_type(
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323 TypeDef(
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324 instance_type="java.util.Optional<{}>".format(
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325 non_null_type.instance_type
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326 ),
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327 init="new OptionalLoader({})".format(non_null_type.name),
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328 name="optional_{}".format(non_null_type.name),
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329 loader_type="Loader<java.util.Optional<{}>>".format(
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330 non_null_type.instance_type
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331 ),
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332 )
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333 )
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334 if (
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335 type_1_name == "array_of_{}".format(type_2_name)
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336 or type_2_name == "array_of_{}".format(type_1_name)
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337 ) and USE_ONE_OR_LIST_OF_TYPES:
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338 if type_1_name == "array_of_{}".format(type_2_name):
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339 single_type = type_2
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340 array_type = type_1
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341 else:
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342 single_type = type_1
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343 array_type = type_2
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344 fqclass = "{}.{}".format(self.package, single_type.instance_type)
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345 return self.declare_type(
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346 TypeDef(
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347 instance_type="{}.utils.OneOrListOf<{}>".format(
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348 self.package, fqclass
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349 ),
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350 init="new OneOrListOfLoader<{}>({}, {})".format(
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351 fqclass, single_type.name, array_type.name
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352 ),
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353 name="one_or_array_of_{}".format(single_type.name),
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354 loader_type="Loader<{}.utils.OneOrListOf<{}>>".format(
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355 self.package, fqclass
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356 ),
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357 )
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358 )
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359 return self.declare_type(
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360 TypeDef(
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361 instance_type="Object",
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362 init="new UnionLoader(new Loader[] {{ {} }})".format(
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363 ", ".join(s.name for s in sub)
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364 ),
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365 name="union_of_{}".format("_or_".join(s.name for s in sub)),
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366 loader_type="Loader<Object>",
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367 )
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368 )
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369 if isinstance(type_declaration, MutableMapping):
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370 if type_declaration["type"] in (
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371 "array",
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372 "https://w3id.org/cwl/salad#array",
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373 ):
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374 i = self.type_loader(type_declaration["items"])
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375 return self.declare_type(
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376 TypeDef(
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377 # special doesn't work out with subclassing, gotta be more clever
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378 # instance_type="List<{}>".format(i.instance_type),
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379 instance_type="java.util.List<Object>",
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380 name="array_of_{}".format(i.name),
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381 init="new ArrayLoader({})".format(i.name),
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382 loader_type="Loader<java.util.List<{}>>".format(
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383 i.instance_type
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384 ),
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385 )
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386 )
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387 if type_declaration["type"] in ("enum", "https://w3id.org/cwl/salad#enum"):
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388 return self.type_loader_enum(type_declaration)
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389 if type_declaration["type"] in (
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390 "record",
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391 "https://w3id.org/cwl/salad#record",
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392 ):
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393 is_abstract = type_declaration.get("abstract", False)
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394 fqclass = "{}.{}".format(
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395 self.package, self.safe_name(type_declaration["name"])
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396 )
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397 return self.declare_type(
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398 TypeDef(
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399 instance_type=self.safe_name(type_declaration["name"]),
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400 name=self.safe_name(type_declaration["name"]),
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401 init="new RecordLoader<{clazz}>({clazz}{ext}.class)".format(
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402 clazz=fqclass, ext="Impl" if not is_abstract else "",
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403 ),
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404 loader_type="Loader<{}>".format(fqclass),
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405 )
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406 )
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407 raise SchemaException("wft {}".format(type_declaration["type"]))
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408 if type_declaration in self.prims:
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409 return self.prims[type_declaration]
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410 return self.collected_types[self.safe_name(type_declaration)]
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411
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412 def type_loader_enum(self, type_declaration):
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413 # type: (Dict[Text, Any]) -> TypeDef
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414 symbols = [self.property_name(sym) for sym in type_declaration["symbols"]]
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415 for sym in symbols:
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416 self.add_vocab(shortname(sym), sym)
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417 clazz = self.safe_name(type_declaration["name"])
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418 symbols_decl = 'new String[] {{"{}"}}'.format(
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419 '", "'.join(sym for sym in symbols)
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420 )
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421 enum_path = os.path.join(self.main_src_dir, "{}.java".format(clazz))
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422 with open(enum_path, "w") as f:
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423 f.write(
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424 """package {package};
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425
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426 import {package}.utils.ValidationException;
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427
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428 public enum {clazz} {{
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429 """.format(
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430 package=self.package, clazz=clazz
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431 )
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432 )
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433 for i, sym in enumerate(symbols):
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434 suffix = "," if i < (len(symbols) - 1) else ";"
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435 const = self.safe_name(sym).replace("-", "_").replace(".", "_").upper()
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436 f.write(
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437 """ {const}("{val}"){suffix}\n""".format(
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438 const=const, val=sym, suffix=suffix
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439 )
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440 )
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441 f.write(
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442 """
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443 private static String[] symbols = {symbols_decl};
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444 private String docVal;
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445
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446 private {clazz}(final String docVal) {{
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447 this.docVal = docVal;
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448 }}
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449
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450 public static {clazz} fromDocumentVal(final String docVal) {{
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451 for(final {clazz} val : {clazz}.values()) {{
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parents:
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452 if(val.docVal.equals(docVal)) {{
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453 return val;
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454 }}
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455 }}
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456 throw new ValidationException(String.format("Expected one of %s", {clazz}.symbols, docVal));
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457 }}
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458 }}
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459 """.format(
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diff changeset
460 clazz=clazz, symbols_decl=symbols_decl
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diff changeset
461 )
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462 )
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463 return self.declare_type(
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diff changeset
464 TypeDef(
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diff changeset
465 instance_type=clazz,
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diff changeset
466 name=self.safe_name(type_declaration["name"]),
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467 loader_type="Loader<{clazz}>".format(clazz=clazz),
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468 init="new EnumLoader({clazz}.class)".format(clazz=clazz),
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469 )
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470 )
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471
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472 def declare_field(self, name, fieldtype, doc, optional):
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473 # type: (Text, TypeDef, Text, bool) -> None
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474 fieldname = name
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475 property_name = self.property_name(fieldname)
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diff changeset
476 cap_case_property_name = property_name[0].upper() + property_name[1:]
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parents:
diff changeset
477 if cap_case_property_name == "Class":
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diff changeset
478 cap_case_property_name = "Class_"
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diff changeset
479
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480 safename = self.safe_name(fieldname)
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diff changeset
481 self.current_fieldtypes[property_name] = fieldtype
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diff changeset
482 getter_doc_str = """ /**
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parents:
diff changeset
483 * Getter for property <I>{fieldname}</I><BR>
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diff changeset
484 {field_doc_str}
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diff changeset
485 */
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486 """.format(
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diff changeset
487 fieldname=fieldname, field_doc_str=doc_to_doc_string(doc, indent_level=1)
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488 )
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489 with open(
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diff changeset
490 os.path.join(self.main_src_dir, "{}.java".format(self.current_class)), "a"
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parents:
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491 ) as f:
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diff changeset
492 f.write(
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diff changeset
493 """
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parents:
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494 {getter_doc_str}
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parents:
diff changeset
495 {type} get{capfieldname}();""".format(
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parents:
diff changeset
496 getter_doc_str=getter_doc_str,
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diff changeset
497 capfieldname=cap_case_property_name,
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diff changeset
498 type=fieldtype.instance_type,
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499 )
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parents:
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500 )
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501
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502 if self.current_class_is_abstract:
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parents:
diff changeset
503 return
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504
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505 self.current_fields.write(
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diff changeset
506 """
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507 private {type} {safename};
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508
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parents:
diff changeset
509 {getter_doc_str}
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diff changeset
510 public {type} get{capfieldname}() {{
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parents:
diff changeset
511 return this.{safename};
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parents:
diff changeset
512 }}
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parents:
diff changeset
513 """.format(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
514 safename=safename,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
515 capfieldname=cap_case_property_name,
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parents:
diff changeset
516 getter_doc_str=getter_doc_str,
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parents:
diff changeset
517 type=fieldtype.instance_type,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
518 )
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
519 )
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parents:
diff changeset
520
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
521 self.current_loader.write(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
522 """ {type} {safename};
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
523 """.format(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
524 type=fieldtype.instance_type, safename=safename
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
525 )
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
526 )
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
527 if optional:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
528 self.current_loader.write(
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parents:
diff changeset
529 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
530 if (__doc.containsKey("{fieldname}")) {{
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
531 """.format(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
532 fieldname=property_name
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parents:
diff changeset
533 )
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parents:
diff changeset
534 )
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parents:
diff changeset
535 spc = " "
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
536 else:
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parents:
diff changeset
537 spc = ""
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parents:
diff changeset
538
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parents:
diff changeset
539 self.current_loader.write(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
540 """{spc} try {{
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
541 {spc} {safename} =
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parents:
diff changeset
542 {spc} LoaderInstances
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parents:
diff changeset
543 {spc} .{fieldtype}
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parents:
diff changeset
544 {spc} .loadField(__doc.get("{fieldname}"), __baseUri, __loadingOptions);
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
545 {spc} }} catch (ValidationException e) {{
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
546 {spc} {safename} = null; // won't be used but prevents compiler from complaining.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
547 {spc} final String __message = "the `{fieldname}` field is not valid because:";
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
548 {spc} __errors.add(new ValidationException(__message, e));
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parents:
diff changeset
549 {spc} }}
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parents:
diff changeset
550 """.format(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
551 fieldtype=fieldtype.name,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
552 safename=safename,
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parents:
diff changeset
553 fieldname=property_name,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
554 spc=spc,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
555 )
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
556 )
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
557
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
558 if optional:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
559 self.current_loader.write(
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parents:
diff changeset
560 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
561 }} else {{
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
562 {safename} = null;
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
563 }}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
564 """.format(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
565 safename=safename
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
566 )
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
567 )
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
568
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
569 def declare_id_field(self, name, fieldtype, doc, optional):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
570 # type: (Text, TypeDef, Text, bool) -> None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
571 if self.current_class_is_abstract:
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parents:
diff changeset
572 return
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parents:
diff changeset
573
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
574 self.declare_field(name, fieldtype, doc, True)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
575 if optional:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
576 set_uri = """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
577 if ({safename} == null) {{
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
578 if (__docRoot != null) {{
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
579 {safename} = java.util.Optional.of(__docRoot);
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
580 }} else {{
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
581 {safename} = java.util.Optional.of("_:" + java.util.UUID.randomUUID().toString());
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
582 }}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
583 }}
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parents:
diff changeset
584 __baseUri = (String) {safename}.orElse(null);
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
585 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
586 else:
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parents:
diff changeset
587 set_uri = """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
588 if ({safename} == null) {{
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
589 if (__docRoot != null) {{
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
590 {safename} = __docRoot;
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parents:
diff changeset
591 }} else {{
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
592 throw new ValidationException("Missing {fieldname}");
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
593 }}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
594 }}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
595 __baseUri = (String) {safename};
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parents:
diff changeset
596 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
597 self.current_loader.write(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
598 set_uri.format(safename=self.safe_name(name), fieldname=shortname(name))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
599 )
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
600
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
601 def uri_loader(self, inner, scoped_id, vocab_term, ref_scope):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
602 # type: (TypeDef, bool, bool, Union[int, None]) -> TypeDef
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
603 assert inner is not None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
604 instance_type = inner.instance_type or "Object"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
605 return self.declare_type(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
606 TypeDef(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
607 instance_type=instance_type, # ?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
608 name="uri_{}_{}_{}_{}".format(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
609 inner.name, scoped_id, vocab_term, ref_scope
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
610 ),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
611 init="new UriLoader({}, {}, {}, {})".format(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
612 inner.name,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
613 self.to_java(scoped_id),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
614 self.to_java(vocab_term),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
615 self.to_java(ref_scope),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
616 ),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
617 is_uri=True,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
618 scoped_id=scoped_id,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
619 ref_scope=ref_scope,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
620 loader_type="Loader<{}>".format(instance_type),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
621 )
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
622 )
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
623
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
624 def idmap_loader(self, field, inner, map_subject, map_predicate):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
625 # type: (Text, TypeDef, Text, Union[Text, None]) -> TypeDef
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
626 assert inner is not None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
627 instance_type = inner.instance_type or "Object"
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parents:
diff changeset
628 return self.declare_type(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
629 TypeDef(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
630 instance_type=instance_type,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
631 name="idmap_{}_{}".format(self.safe_name(field), inner.name),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
632 init='new IdMapLoader({}, "{}", "{}")'.format(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
633 inner.name, map_subject, map_predicate
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
634 ),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
635 loader_type="Loader<{}>".format(instance_type),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
636 )
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
637 )
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
638
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
639 def typedsl_loader(self, inner, ref_scope):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
640 # type: (TypeDef, Union[int, None]) -> TypeDef
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parents:
diff changeset
641 assert inner is not None
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642 instance_type = inner.instance_type or "Object"
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parents:
diff changeset
643 return self.declare_type(
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parents:
diff changeset
644 TypeDef(
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645 instance_type=instance_type,
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diff changeset
646 name="typedsl_{}_{}".format(inner.name, ref_scope),
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647 init="new TypeDslLoader({}, {})".format(inner.name, ref_scope),
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diff changeset
648 loader_type="Loader<{}>".format(instance_type),
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649 )
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parents:
diff changeset
650 )
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diff changeset
651
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parents:
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652 return inner
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parents:
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653
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654 def to_java(self, val): # type: (Any) -> Any
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parents:
diff changeset
655 if val is True:
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656 return "true"
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657 elif val is None:
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658 return "null"
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659 elif val is False:
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parents:
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660 return "false"
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661 return val
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662
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663 def epilogue(self, root_loader): # type: (TypeDef) -> None
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664 pd = u"This project contains Java objects and utilities "
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665 pd = pd + ' auto-generated by <a href="https://github.com/'
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666 pd = pd + 'common-workflow-language/schema_salad">Schema Salad</a>'
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667 pd = pd + " for parsing documents corresponding to the "
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668 pd = pd + str(self.base_uri) + " schema."
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669
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670 template_vars = dict(
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671 base_uri=self.base_uri,
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672 package=self.package,
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673 group_id=self.package,
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674 artifact_id=self.artifact,
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675 version="0.0.1-SNAPSHOT",
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diff changeset
676 project_name=self.package,
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diff changeset
677 project_description=pd,
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diff changeset
678 license_name="Apache License, Version 2.0",
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diff changeset
679 license_url="https://www.apache.org/licenses/LICENSE-2.0.txt",
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diff changeset
680 ) # type: MutableMapping[Text, Text]
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681
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682 def template_from_resource(resource):
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parents:
diff changeset
683 # type: (str) -> string.Template
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diff changeset
684 template_str = pkg_resources.resource_string(
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diff changeset
685 __name__, "java/%s" % resource
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parents:
diff changeset
686 ).decode("utf-8")
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diff changeset
687 template = string.Template(template_str)
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parents:
diff changeset
688 return template
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diff changeset
689
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diff changeset
690 def expand_resource_template_to(resource, path):
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diff changeset
691 # type: (str, str) -> None
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parents:
diff changeset
692 template = template_from_resource(resource)
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parents:
diff changeset
693 src = template.safe_substitute(template_vars)
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parents:
diff changeset
694 _ensure_directory_and_write(path, src)
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diff changeset
695
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diff changeset
696 expand_resource_template_to("pom.xml", os.path.join(self.target_dir, "pom.xml"))
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diff changeset
697 expand_resource_template_to(
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parents:
diff changeset
698 "gitignore", os.path.join(self.target_dir, ".gitignore")
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diff changeset
699 )
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parents:
diff changeset
700 expand_resource_template_to(
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parents:
diff changeset
701 "package.html", os.path.join(self.main_src_dir, "package.html")
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diff changeset
702 )
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parents:
diff changeset
703 expand_resource_template_to(
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diff changeset
704 "overview.html",
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parents:
diff changeset
705 os.path.join(self.target_dir, "src", "main", "javadoc", "overview.html"),
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parents:
diff changeset
706 )
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parents:
diff changeset
707 expand_resource_template_to(
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parents:
diff changeset
708 "MANIFEST.MF",
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parents:
diff changeset
709 os.path.join(
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parents:
diff changeset
710 self.target_dir, "src", "main", "resources", "META-INF", "MANIFEST.MF"
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diff changeset
711 ),
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parents:
diff changeset
712 )
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parents:
diff changeset
713 expand_resource_template_to(
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parents:
diff changeset
714 "README.md", os.path.join(self.target_dir, "README.md"),
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parents:
diff changeset
715 )
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diff changeset
716
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parents:
diff changeset
717 vocab = ""
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parents:
diff changeset
718 rvocab = ""
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parents:
diff changeset
719 for k in sorted(self.vocab.keys()):
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parents:
diff changeset
720 vocab += """ vocab.put("{}", "{}");\n""".format(k, self.vocab[k])
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parents:
diff changeset
721 rvocab += """ rvocab.put("{}", "{}");\n""".format(self.vocab[k], k)
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diff changeset
722
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parents:
diff changeset
723 loader_instances = ""
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parents:
diff changeset
724 for _, collected_type in iteritems(self.collected_types):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
725 loader_instances += " public static {} {} = {};\n".format(
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shellac
parents:
diff changeset
726 collected_type.loader_type, collected_type.name, collected_type.init
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parents:
diff changeset
727 )
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parents:
diff changeset
728
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parents:
diff changeset
729 example_tests = ""
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parents:
diff changeset
730 if self.examples:
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parents:
diff changeset
731 _safe_makedirs(self.test_resources_dir)
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parents:
diff changeset
732 utils_resources = os.path.join(self.test_resources_dir, "utils")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
733 if os.path.exists(utils_resources):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
734 shutil.rmtree(utils_resources)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
735 shutil.copytree(self.examples, utils_resources)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
736 for example_name in os.listdir(self.examples):
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parents:
diff changeset
737 if example_name.startswith("valid"):
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parents:
diff changeset
738 basename = os.path.basename(example_name).split(".", 1)[0]
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parents:
diff changeset
739 example_tests += """
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parents:
diff changeset
740 @org.junit.Test
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parents:
diff changeset
741 public void test{basename}ByString() throws Exception {{
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
742 String path = java.nio.file.Paths.get(".").toAbsolutePath().normalize().toString();
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
743 String baseUri = Uris.fileUri(path) + "/";
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parents:
diff changeset
744 java.net.URL url = getClass().getResource("{example_name}");
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
745 java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI());
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parents:
diff changeset
746 String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8");
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
747 RootLoader.loadDocument(yaml, baseUri);
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parents:
diff changeset
748 }}
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diff changeset
749
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parents:
diff changeset
750 @org.junit.Test
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parents:
diff changeset
751 public void test{basename}ByPath() throws Exception {{
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parents:
diff changeset
752 java.net.URL url = getClass().getResource("{example_name}");
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parents:
diff changeset
753 java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI());
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parents:
diff changeset
754 RootLoader.loadDocument(resPath);
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parents:
diff changeset
755 }}
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parents:
diff changeset
756
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parents:
diff changeset
757 @org.junit.Test
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parents:
diff changeset
758 public void test{basename}ByMap() throws Exception {{
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shellac
parents:
diff changeset
759 java.net.URL url = getClass().getResource("{example_name}");
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parents:
diff changeset
760 java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI());
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parents:
diff changeset
761 String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8");
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parents:
diff changeset
762 java.util.Map<String, Object> doc;
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
763 doc = (java.util.Map<String, Object>) YamlUtils.mapFromString(yaml);
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parents:
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764 RootLoader.loadDocument(doc);
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765 }}""".format(
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766 basename=basename, example_name=example_name,
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767 )
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768
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769 template_args = dict(
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770 package=self.package,
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771 vocab=vocab,
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772 rvocab=rvocab,
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773 loader_instances=loader_instances,
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774 root_loader_name=root_loader.name,
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775 root_loader_instance_type=root_loader.instance_type or "Object",
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776 example_tests=example_tests,
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777 ) # type: MutableMapping[Text, Text]
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778
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779 util_src_dirs = {
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780 "main_utils": self.main_src_dir,
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781 "test_utils": self.test_src_dir,
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782 }
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783 for (util_src, util_target) in util_src_dirs.items():
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784 for util in pkg_resources.resource_listdir(__name__, "java/%s" % util_src):
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785 src_path = os.path.join(util_target, "utils", util)
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786 src_template = template_from_resource(os.path.join(util_src, util))
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787 src = src_template.safe_substitute(template_args)
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788 _ensure_directory_and_write(src_path, src)