Mercurial > repos > fubar > tool_factory_2

annotate toolfactory/galaxyxml/tool/parameters/__init__.py @ 35:5d38cb3d9be8 draft

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added patched galaxyxml code temporarily until PR accepted
author fubar
date Sat, 08 Aug 2020 19:55:55 -0400
parents
children ce2b1f8ea68d
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35
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1 from builtins import str
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2 from builtins import object
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3 from lxml import etree
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4 from galaxyxml import Util
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5
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6
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7 class XMLParam(object):
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8 name = 'node'
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9
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10 def __init__(self, *args, **kwargs):
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11 # http://stackoverflow.com/a/12118700
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12 self.children = []
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13 kwargs = {k: v for k, v in list(kwargs.items()) if v is not None}
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14 kwargs = Util.coerce(kwargs, kill_lists=True)
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15 kwargs = Util.clean_kwargs(kwargs, final=True)
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16 self.node = etree.Element(self.name, **kwargs)
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17
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18 def append(self, sub_node):
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19 if self.acceptable_child(sub_node):
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20 # If one of ours, they aren't etree nodes, they're custom objects
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21 if issubclass(type(sub_node), XMLParam):
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22 self.node.append(sub_node.node)
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23 self.children.append(sub_node)
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24 else:
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25 raise Exception("Child was unacceptable to parent (%s is not appropriate for %s)" % (
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26 type(self), type(sub_node)))
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27 else:
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28 raise Exception("Child was unacceptable to parent (%s is not appropriate for %s)" % (
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29 type(self), type(sub_node)))
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30
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31 def validate(self):
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32 # Very few need validation, but some nodes we may want to have
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33 # validation routines on. Should only be called when DONE.
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34 for child in self.children:
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35 # If any child fails to validate return false.
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36 if not child.validate():
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37 return False
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38 return True
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39
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40 def cli(self):
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41 lines = []
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42 for child in self.children:
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43 lines.append(child.command_line())
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44 # lines += child.command_line()
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45 return '\n'.join(lines)
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46
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47 def command_line(self):
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48 return None
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49
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50
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51 class RequestParamTranslation(XMLParam):
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52 name = 'request_param_translation'
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53
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54 def __init__(self, **kwargs):
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55 self.node = etree.Element(self.name)
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56
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57 def acceptable_child(self, child):
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58 return isinstance(child, RequestParamTranslation)
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59
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60
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61 class RequestParam(XMLParam):
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62 name = 'request_param'
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63
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64 def __init__(self, galaxy_name, remote_name, missing, **kwargs):
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65 # TODO: bulk copy locals into self.attr?
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66 self.galaxy_name = galaxy_name
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67 # http://stackoverflow.com/a/1408860
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68 params = Util.clean_kwargs(locals().copy())
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69 super(RequestParam, self).__init__(**params)
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70
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71 def acceptable_child(self, child):
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72 return isinstance(child, AppendParam) and self.galaxy_name == "URL"
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73
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74
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75 class AppendParam(XMLParam):
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76 name = 'append_param'
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77
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78 def __init__(self, separator="&", first_separator="?", join="=", **kwargs):
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79 params = Util.clean_kwargs(locals().copy())
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80 super(AppendParam, self).__init__(**params)
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81
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82 def acceptable_child(self, child):
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83 return isinstance(child, AppendParamValue)
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84
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85
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86 class AppendParamValue(XMLParam):
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87 name = 'value'
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88
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89 def __init__(self, name="_export", missing="1", **kwargs):
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90 params = Util.clean_kwargs(locals().copy())
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91 super(AppendParamValue, self).__init__(**params)
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92
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93 def acceptable_child(self, child):
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94 return False
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95
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96
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97 class EdamOperations(XMLParam):
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98 name = 'edam_operations'
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99
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100 def acceptable_child(self, child):
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101 return issubclass(type(child), EdamOperation)
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102
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103 def has_operation(self, edam_operation):
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104 """
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105 Check the presence of a given edam_operation.
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106
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107 :type edam_operation: STRING
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108 """
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109 for operation in self.children:
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110 if operation.node.text == edam_operation:
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111 return True
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112 return False
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113
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114
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115 class EdamOperation(XMLParam):
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116 name = 'edam_operation'
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117
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118 def __init__(self, value):
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119 super(EdamOperation, self).__init__()
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120 self.node.text = str(value)
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121
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122
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123 class EdamTopics(XMLParam):
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124 name = 'edam_topics'
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125
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126 def acceptable_child(self, child):
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127 return issubclass(type(child), EdamTopic)
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128
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129 def has_topic(self, edam_topic):
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130 """
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131 Check the presence of a given edam_topic.
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132
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133 :type edam_topic: STRING
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134 """
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135 for topic in self.children:
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136 if topic.node.text == edam_topic:
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137 return True
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138 return False
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139
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140
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141 class EdamTopic(XMLParam):
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142 name = 'edam_topic'
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143
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144 def __init__(self, value):
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145 super(EdamTopic, self).__init__()
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146 self.node.text = str(value)
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147
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148
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149 class Requirements(XMLParam):
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150 name = 'requirements'
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151 # This bodes to be an issue -__-
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152
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153 def acceptable_child(self, child):
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154 return issubclass(type(child), Requirement) or issubclass(type(child), Container)
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155
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156
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157 class Requirement(XMLParam):
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158 name = 'requirement'
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159
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160 def __init__(self, type, value, version=None, **kwargs):
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161 params = Util.clean_kwargs(locals().copy())
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162 passed_kwargs = {}
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163 passed_kwargs['version'] = params['version']
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164 passed_kwargs['type'] = params['type']
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165 super(Requirement, self).__init__(**passed_kwargs)
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166 self.node.text = str(value)
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167
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168
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169 class Container(XMLParam):
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170 name = 'container'
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171
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172 def __init__(self, type, value, **kwargs):
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173 params = Util.clean_kwargs(locals().copy())
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174 passed_kwargs = {}
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175 passed_kwargs['type'] = params['type']
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176 super(Container, self).__init__(**passed_kwargs)
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177 self.node.text = str(value)
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178
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179
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180 class Configfiles(XMLParam):
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181 name = 'configfiles'
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182
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183 def acceptable_child(self, child):
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184 return issubclass(type(child), Configfile) or issubclass(type(child), ConfigfileDefaultInputs)
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185
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186
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187 class Configfile(XMLParam):
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188 name = 'configfile'
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189
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190 def __init__(self, name, text, **kwargs):
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191 params = Util.clean_kwargs(locals().copy())
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192 passed_kwargs = {}
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193 passed_kwargs['name'] = params['name']
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194 super(Configfile, self).__init__(**passed_kwargs)
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195 self.node.text = etree.CDATA(str(text))
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196
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197
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198 class ConfigfileDefaultInputs(XMLParam):
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199 name = 'inputs'
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200
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201 def __init__(self, name, **kwargs):
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202 params = Util.clean_kwargs(locals().copy())
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203 passed_kwargs = {}
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204 passed_kwargs['name'] = params['name']
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205 super(ConfigfileDefaultInputs, self).__init__(**passed_kwargs)
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206
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207
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208 class Inputs(XMLParam):
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209 name = 'inputs'
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210 # This bodes to be an issue -__-
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211
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212 def __init__(self, action=None, check_value=None, method=None,
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213 target=None, nginx_upload=None, **kwargs):
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214 params = Util.clean_kwargs(locals().copy())
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215 super(Inputs, self).__init__(**params)
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216
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217 def acceptable_child(self, child):
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218 return issubclass(type(child), InputParameter)
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219
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220
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221 class InputParameter(XMLParam):
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222
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223 def __init__(self, name, **kwargs):
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224 # TODO: look at
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225 self.mako_identifier = name
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226 # We use kwargs instead of the usual locals(), so manually copy the
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227 # name to kwargs
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228 if name is not None:
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229 kwargs['name'] = name
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230
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231 # Handle positional parameters
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232 if 'positional' in kwargs and kwargs['positional']:
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233 self.positional = True
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234 else:
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235 self.positional = False
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236
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237 if 'num_dashes' in kwargs:
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238 self.num_dashes = kwargs['num_dashes']
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239 del kwargs['num_dashes']
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240 else:
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241 self.num_dashes = 0
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242
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243 self.space_between_arg = " "
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244
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245 # Not sure about this :(
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246 # https://wiki.galaxyproject.org/Tools/BestPractices#Parameter_help
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247 if 'label' in kwargs:
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248 # TODO: replace with positional attribute
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249 if len(self.flag()) > 0:
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250 if kwargs['label'] is None:
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251 kwargs[
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252 'label'] = 'Author did not provide help for this parameter... '
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253 if not self.positional:
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254 kwargs['argument'] = self.flag()
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255
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256 super(InputParameter, self).__init__(**kwargs)
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257
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258 def command_line(self):
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259 before = self.command_line_before()
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260 cli = self.command_line_actual()
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261 after = self.command_line_after()
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262
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263 complete = [x for x in (before, cli, after) if x is not None]
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264 return '\n'.join(complete)
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265
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266 def command_line_before(self):
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267 try:
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268 return self.command_line_before_override
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269 except Exception:
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270 return None
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271
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272 def command_line_after(self):
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273 try:
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274 return self.command_line_after_override
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275 except Exception:
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276 return None
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277
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278 def command_line_actual(self):
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279 try:
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280 return self.command_line_override
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281 except Exception:
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282 if self.positional:
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283 return self.mako_name()
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284 else:
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285 return "%s%s%s" % (self.flag(), self.space_between_arg, self.mako_name())
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286
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287 def mako_name(self):
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288 # TODO: enhance logic to check up parents for things like
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289 # repeat>condotion>param
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290 return '$' + self.mako_identifier
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291
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292 def flag(self):
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293 flag = '-' * self.num_dashes
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294 return flag + self.mako_identifier
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295
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296
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297 class Section(InputParameter):
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298 name = 'section'
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299
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300 def __init__(self, name, title, expanded=None, help=None, **kwargs):
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301 params = Util.clean_kwargs(locals().copy())
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302 super(Section, self).__init__(**params)
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303
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304 def acceptable_child(self, child):
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305 return issubclass(type(child), InputParameter)
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306
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307
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308 class Repeat(InputParameter):
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309 name = 'repeat'
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310
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311 def __init__(self, name, title, min=None, max=None, default=None,
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312 **kwargs):
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313 params = Util.clean_kwargs(locals().copy())
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314 # Allow overriding
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315 self.command_line_before_override = '#for $i in $%s:' % name
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316 self.command_line_after_override = '#end for'
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317 # self.command_line_override
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318 super(Repeat, self).__init__(**params)
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319
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320 def acceptable_child(self, child):
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321 return issubclass(type(child), InputParameter)
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322
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323 def command_line_actual(self):
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324 if hasattr(self, 'command_line_override'):
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325 return self.command_line_override
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326 else:
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327 return "%s" % self.mako_name()
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328
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329
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330 class Conditional(InputParameter):
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331 name = 'conditional'
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332
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333 def __init__(self, name, **kwargs):
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334 params = Util.clean_kwargs(locals().copy())
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335 super(Conditional, self).__init__(**params)
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336
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337 def acceptable_child(self, child):
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338 return issubclass(type(child), InputParameter) \
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339 and not isinstance(child, Conditional)
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340
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341 def validate(self):
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342 # Find a way to check if one of the kids is a WHEN
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343 pass
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344
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345
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346 class When(InputParameter):
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347 name = 'when'
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348
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349 def __init__(self, value):
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350 params = Util.clean_kwargs(locals().copy())
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351 super(When, self).__init__(None, **params)
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352
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353 def acceptable_child(self, child):
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354 return issubclass(type(child), InputParameter)
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355
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356
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357 class Param(InputParameter):
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358 name = 'param'
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359
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360 # This...isn't really valid as-is, and shouldn't be used.
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361 def __init__(self, name, optional=None, label=None, help=None, **kwargs):
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362 params = Util.clean_kwargs(locals().copy())
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363 params['type'] = self.type
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364 super(Param, self).__init__(**params)
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365
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366 if type(self) == Param:
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367 raise Exception(
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368 "Param class is not an actual parameter type, use a subclass of Param")
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369
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370 def acceptable_child(self, child):
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371 return issubclass(type(child, InputParameter) or isinstance(child), ValidatorParam)
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372
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373
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374 class TextParam(Param):
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375 type = 'text'
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376
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377 def __init__(self, name, optional=None, label=None, help=None,
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378 value=None, **kwargs):
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379 params = Util.clean_kwargs(locals().copy())
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380 super(TextParam, self).__init__(**params)
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381
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382 def command_line_actual(self):
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383 try:
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384 return self.command_line_override
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385 except Exception:
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386 if self.positional:
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387 return self.mako_name()
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388 else:
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389 return f"{self.flag}{self.space_between_arg}'{self.mako_name()}'"
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390
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391
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392 class _NumericParam(Param):
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393
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394 def __init__(self, name, value, optional=None, label=None, help=None,
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395 min=None, max=None, **kwargs):
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396 params = Util.clean_kwargs(locals().copy())
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397 super(_NumericParam, self).__init__(**params)
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398
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399
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400 class IntegerParam(_NumericParam):
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401 type = 'integer'
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402
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403
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404 class FloatParam(_NumericParam):
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405 type = 'float'
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406
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407
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408 class BooleanParam(Param):
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409 type = 'boolean'
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410
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411 def __init__(self, name, optional=None, label=None, help=None,
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412 checked=False, truevalue=None, falsevalue=None, **kwargs):
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413 params = Util.clean_kwargs(locals().copy())
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414
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415 super(BooleanParam, self).__init__(**params)
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416 if truevalue is None:
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417 # If truevalue and falsevalue are None, then we use "auto", the IUC
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418 # recommended default.
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419 #
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420 # truevalue is set to the parameter's value, and falsevalue is not.
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421 #
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422 # Unfortunately, mako_identifier is set as a result of the super
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423 # call, which we shouldn't call TWICE, so we'll just hack around this :(
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424 # params['truevalue'] = '%s%s' % (self.)
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425 self.node.attrib['truevalue'] = self.flag()
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426
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427 if falsevalue is None:
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428 self.node.attrib['falsevalue'] = ""
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429
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430 def command_line_actual(self):
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431 if hasattr(self, 'command_line_override'):
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432 return self.command_line_override
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433 else:
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434 return "%s" % self.mako_name()
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435
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436
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437 class DataParam(Param):
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438 type = 'data'
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439
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440 def __init__(self, name, optional=None, label=None, help=None, format=None,
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441 multiple=None, **kwargs):
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442 params = Util.clean_kwargs(locals().copy())
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443 super(DataParam, self).__init__(**params)
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444
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445
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446 class SelectParam(Param):
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447 type = 'select'
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448
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449 def __init__(self, name, optional=None, label=None, help=None,
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450 data_ref=None, display=None, multiple=None, options=None,
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451 default=None, **kwargs):
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452 params = Util.clean_kwargs(locals().copy())
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453 del params['options']
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454 del params['default']
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455
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456 super(SelectParam, self).__init__(**params)
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457
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458 if options is not None and default is not None:
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459 if default not in options:
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460 raise Exception("Specified a default that isn't in options")
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461
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462 if options:
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463 for k, v in list(sorted(options.items())):
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464 selected = (k == default)
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465 self.append(SelectOption(k, v, selected=selected))
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466
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467 def acceptable_child(self, child):
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468 return issubclass(type(child), SelectOption) \
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469 or issubclass(type(child), Options)
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470
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471
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472 class SelectOption(InputParameter):
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473 name = 'option'
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474
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475 def __init__(self, value, text, selected=False, **kwargs):
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476 params = Util.clean_kwargs(locals().copy())
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477
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478 passed_kwargs = {}
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479 if selected:
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480 passed_kwargs['selected'] = "true"
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481 passed_kwargs['value'] = params['value']
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482
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483 super(SelectOption, self).__init__(None, **passed_kwargs)
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484 self.node.text = str(text)
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485
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486
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487 class Options(InputParameter):
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488 name = 'options'
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489
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490 def __init__(self, from_dataset=None, from_file=None, from_data_table=None,
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491 from_parameter=None, **kwargs):
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492 params = Util.clean_kwargs(locals().copy())
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493 super(Options, self).__init__(None, **params)
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494
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495 def acceptable_child(self, child):
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496 return issubclass(type(child), Column) or issubclass(type(child), Filter)
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497
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498
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499 class Column(InputParameter):
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500 name = 'column'
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501
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502 def __init__(self, name, index, **kwargs):
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503 params = Util.clean_kwargs(locals().copy())
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504 super(Column, self).__init__(**params)
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505
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506
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507 class Filter(InputParameter):
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508 name = 'filter'
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509
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510 def __init__(self, type, column=None, name=None, ref=None, key=None,
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511 multiple=None, separator=None, keep=None, value=None,
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512 ref_attribute=None, index=None, **kwargs):
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513 params = Util.clean_kwargs(locals().copy())
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514 super(Filter, self).__init__(**params)
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515
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516
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517 class ValidatorParam(InputParameter):
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518 name = 'validator'
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519
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520 def __init__(self, type, message=None, filename=None, metadata_name=None,
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521 metadata_column=None, line_startswith=None, min=None,
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522 max=None, **kwargs):
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523 params = Util.clean_kwargs(locals().copy())
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diff changeset
524 super(ValidatorParam, self).__init__(**params)
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525
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526
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527 class Outputs(XMLParam):
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528 name = 'outputs'
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529
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530 def acceptable_child(self, child):
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531 return isinstance(child, OutputData) or isinstance(child, OutputCollection)
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532
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533
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534 class OutputData(XMLParam):
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diff changeset
535 """Copypasta of InputParameter, needs work
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536 """
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537 name = 'data'
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538
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539 def __init__(self, name, format, format_source=None, metadata_source=None,
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540 label=None, from_work_dir=None, hidden=False, **kwargs):
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diff changeset
541 # TODO: validate format_source&metadata_source against something in the
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542 # XMLParam children tree.
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543 self.mako_identifier = name
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544 if 'num_dashes' in kwargs:
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545 self.num_dashes = kwargs['num_dashes']
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546 del kwargs['num_dashes']
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547 else:
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548 self.num_dashes = 0
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549 self.space_between_arg = " "
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550 params = Util.clean_kwargs(locals().copy())
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551
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552 super(OutputData, self).__init__(**params)
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553
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554 def command_line(self):
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555 if hasattr(self, 'command_line_override'):
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556 return self.command_line_override
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557 else:
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558 return "%s%s%s" % (self.flag(), self.space_between_arg, self.mako_name())
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559
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560 def mako_name(self):
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561 return '$' + self.mako_identifier
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562
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563 def flag(self):
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564 flag = '-' * self.num_dashes
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565 return flag + self.mako_identifier
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566
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567 def acceptable_child(self, child):
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568 return isinstance(child, OutputFilter) or \
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569 isinstance(child, ChangeFormat) or \
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570 isinstance(child, DiscoverDatasets)
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571
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572
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573 class OutputFilter(XMLParam):
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574 name = 'filter'
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575
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576 def __init__(self, text, **kwargs):
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577 params = Util.clean_kwargs(locals().copy())
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578 del params['text']
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579 super(OutputFilter, self).__init__(**params)
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580 self.node.text = text
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581
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582 def acceptable_child(self, child):
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583 return False
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584
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585
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586 class ChangeFormat(XMLParam):
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587 name = 'change_format'
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588
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589 def __init__(self, **kwargs):
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590 params = Util.clean_kwargs(locals().copy())
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591 super(ChangeFormat, self).__init__(**params)
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592
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593 def acceptable_child(self, child):
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594 return isinstance(child, ChangeFormatWhen)
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595
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596
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597 class ChangeFormatWhen(XMLParam):
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598 name = 'when'
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599
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600 def __init__(self, input, format, value, **kwargs):
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601 params = Util.clean_kwargs(locals().copy())
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602 super(ChangeFormatWhen, self).__init__(**params)
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603
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604 def acceptable_child(self, child):
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605 return False
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606
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607
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608 class OutputCollection(XMLParam):
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609 name = 'collection'
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610
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611 def __init__(self, name, type=None, label=None, format_source=None,
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612 type_source=None, structured_like=None, inherit_format=None, **kwargs):
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613 params = Util.clean_kwargs(locals().copy())
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614 super(OutputCollection, self).__init__(**params)
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615
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616 def acceptable_child(self, child):
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617 return isinstance(child, OutputData) or isinstance(child, OutputFilter) \
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parents:
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618 or isinstance(child, DiscoverDatasets)
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619
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620
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621 class DiscoverDatasets(XMLParam):
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622 name = 'discover_datasets'
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623
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624 def __init__(self, pattern, directory=None, format=None, ext=None,
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625 visible=None, **kwargs):
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626 params = Util.clean_kwargs(locals().copy())
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627 super(DiscoverDatasets, self).__init__(**params)
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628
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629
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630 class Tests(XMLParam):
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631 name = 'tests'
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632
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633 def acceptable_child(self, child):
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634 return issubclass(type(child), Test)
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635
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636
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637 class Test(XMLParam):
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diff changeset
638 name = 'test'
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639
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diff changeset
640 def acceptable_child(self, child):
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diff changeset
641 return isinstance(child, TestParam) or isinstance(child, TestOutput)
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diff changeset
642
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643
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644 class TestParam(XMLParam):
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645 name = 'param'
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646
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647 def __init__(self, name, value=None, ftype=None, dbkey=None, **kwargs):
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diff changeset
648 params = Util.clean_kwargs(locals().copy())
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diff changeset
649 super(TestParam, self).__init__(**params)
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650
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651
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652 class TestOutput(XMLParam):
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diff changeset
653 name = 'output'
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diff changeset
654
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655 def __init__(self, name=None, file=None, ftype=None, sort=None, value=None,
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656 md5=None, checksum=None, compare=None, lines_diff=None,
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657 delta=None, **kwargs):
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diff changeset
658 params = Util.clean_kwargs(locals().copy())
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diff changeset
659 super(TestOutput, self).__init__(**params)
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diff changeset
660
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
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diff changeset
661
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diff changeset
662 class Citations(XMLParam):
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diff changeset
663 name = 'citations'
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diff changeset
664
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
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665 def acceptable_child(self, child):
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diff changeset
666 return issubclass(type(child), Citation)
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diff changeset
667
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diff changeset
668 def has_citation(self, type, value):
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diff changeset
669 """
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diff changeset
670 Check the presence of a given citation.
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diff changeset
671
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diff changeset
672 :type type: STRING
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diff changeset
673 :type value: STRING
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diff changeset
674 """
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parents:
diff changeset
675 for citation in self.children:
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diff changeset
676 if citation.node.attrib['type'] == type and citation.node.text == value:
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677 return True
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diff changeset
678 return False
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diff changeset
679
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diff changeset
680
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681 class Citation(XMLParam):
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diff changeset
682 name = 'citation'
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diff changeset
683
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diff changeset
684 def __init__(self, type, value):
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diff changeset
685 passed_kwargs = {}
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686 passed_kwargs['type'] = type
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687 super(Citation, self).__init__(**passed_kwargs)
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diff changeset
688 self.node.text = str(value)