Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/prov/dot.py @ 3:758bc20232e8 draft

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"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:20:52 -0400
parents 26e78fe6e8c4
children
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1 """Graphical visualisation support for prov.model.
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2
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3 This module produces graphical visualisation for provenanve graphs.
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4 Requires pydot module and Graphviz.
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5
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6 References:
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7
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8 * pydot homepage: https://github.com/erocarrera/pydot
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9 * Graphviz: http://www.graphviz.org/
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10 * DOT Language: http://www.graphviz.org/doc/info/lang.html
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11
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12 .. moduleauthor:: Trung Dong Huynh <trungdong@donggiang.com>
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13 """
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14 from __future__ import (absolute_import, division, print_function,
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15 unicode_literals)
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16
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17 try:
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18 from html import escape
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19 except ImportError:
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20 from cgi import escape
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21 from datetime import datetime
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22 import pydot
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23 import six
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24
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25 from prov.model import (
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26 PROV_ACTIVITY, PROV_AGENT, PROV_ALTERNATE, PROV_ASSOCIATION,
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27 PROV_ATTRIBUTION, PROV_BUNDLE, PROV_COMMUNICATION, PROV_DERIVATION,
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28 PROV_DELEGATION, PROV_ENTITY, PROV_GENERATION, PROV_INFLUENCE,
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29 PROV_INVALIDATION, PROV_END, PROV_MEMBERSHIP, PROV_MENTION,
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30 PROV_SPECIALIZATION, PROV_START, PROV_USAGE, Identifier,
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31 PROV_ATTRIBUTE_QNAMES, sorted_attributes, ProvException
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32 )
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33
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34 __author__ = 'Trung Dong Huynh'
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35 __email__ = 'trungdong@donggiang.com'
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36
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37
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38 # Visual styles for various elements (nodes) and relations (edges)
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39 # see http://graphviz.org/content/attrs
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40 DOT_PROV_STYLE = {
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41 # Generic node
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42 0: {
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43 'shape': 'oval', 'style': 'filled',
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44 'fillcolor': 'lightgray', 'color': 'dimgray'
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45 },
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46 # Elements
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47 PROV_ENTITY: {
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48 'shape': 'oval', 'style': 'filled',
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49 'fillcolor': '#FFFC87', 'color': '#808080'
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50 },
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51 PROV_ACTIVITY: {
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52 'shape': 'box', 'style': 'filled',
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53 'fillcolor': '#9FB1FC', 'color': '#0000FF'
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54 },
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55 PROV_AGENT: {
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56 'shape': 'house', 'style': 'filled',
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57 'fillcolor': '#FED37F'
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58 },
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59 PROV_BUNDLE: {
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60 'shape': 'folder', 'style': 'filled',
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61 'fillcolor': 'aliceblue'
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62 },
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63 # Relations
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64 PROV_GENERATION: {
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65 'label': 'wasGeneratedBy', 'fontsize': '10.0',
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66 'color': 'darkgreen', 'fontcolor': 'darkgreen'
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67 },
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68 PROV_USAGE: {
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69 'label': 'used', 'fontsize': '10.0',
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70 'color': 'red4', 'fontcolor': 'red'
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71 },
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72 PROV_COMMUNICATION: {
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73 'label': 'wasInformedBy', 'fontsize': '10.0'
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74 },
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75 PROV_START: {
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76 'label': 'wasStartedBy', 'fontsize': '10.0'
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77 },
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78 PROV_END: {
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79 'label': 'wasEndedBy', 'fontsize': '10.0'
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80 },
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81 PROV_INVALIDATION: {
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82 'label': 'wasInvalidatedBy', 'fontsize': '10.0'
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83 },
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84 PROV_DERIVATION: {
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85 'label': 'wasDerivedFrom', 'fontsize': '10.0'
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86 },
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87 PROV_ATTRIBUTION: {
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88 'label': 'wasAttributedTo', 'fontsize': '10.0',
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89 'color': '#FED37F'
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90 },
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91 PROV_ASSOCIATION: {
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92 'label': 'wasAssociatedWith', 'fontsize': '10.0',
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93 'color': '#FED37F'
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94 },
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95 PROV_DELEGATION: {
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96 'label': 'actedOnBehalfOf', 'fontsize': '10.0',
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97 'color': '#FED37F'
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98 },
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99 PROV_INFLUENCE: {
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100 'label': 'wasInfluencedBy', 'fontsize': '10.0',
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101 'color': 'grey'
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102 },
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103 PROV_ALTERNATE: {
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104 'label': 'alternateOf', 'fontsize': '10.0'
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105 },
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106 PROV_SPECIALIZATION: {
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107 'label': 'specializationOf', 'fontsize': '10.0'
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108 },
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109 PROV_MENTION: {
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110 'label': 'mentionOf', 'fontsize': '10.0'
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111 },
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112 PROV_MEMBERSHIP: {
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113 'label': 'hadMember', 'fontsize': '10.0'
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114 },
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115 }
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116
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117 ANNOTATION_STYLE = {
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118 'shape': 'note', 'color': 'gray',
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119 'fontcolor': 'black', 'fontsize': '10'
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120 }
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121 ANNOTATION_LINK_STYLE = {
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122 'arrowhead': 'none', 'style': 'dashed',
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123 'color': 'gray'
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124 }
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125 ANNOTATION_START_ROW = '<<TABLE cellpadding=\"0\" border=\"0\">'
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126 ANNOTATION_ROW_TEMPLATE = """ <TR>
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127 <TD align=\"left\" href=\"%s\">%s</TD>
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128 <TD align=\"left\"%s>%s</TD>
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129 </TR>"""
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130 ANNOTATION_END_ROW = ' </TABLE>>'
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131
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132
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133 def htlm_link_if_uri(value):
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134 try:
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135 uri = value.uri
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136 return '<a href="%s">%s</a>' % (uri, six.text_type(value))
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137 except AttributeError:
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138 return six.text_type(value)
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139
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140
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141 def prov_to_dot(bundle, show_nary=True, use_labels=False,
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142 direction='BT',
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143 show_element_attributes=True, show_relation_attributes=True):
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144 """
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145 Convert a provenance bundle/document into a DOT graphical representation.
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146
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147 :param bundle: The provenance bundle/document to be converted.
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148 :type bundle: :class:`ProvBundle`
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149 :param show_nary: shows all elements in n-ary relations.
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150 :type show_nary: bool
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151 :param use_labels: uses the prov:label property of an element as its name (instead of its identifier).
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152 :type use_labels: bool
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153 :param direction: specifies the direction of the graph. Valid values are "BT" (default), "TB", "LR", "RL".
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154 :param show_element_attributes: shows attributes of elements.
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155 :type show_element_attributes: bool
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156 :param show_relation_attributes: shows attributes of relations.
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157 :type show_relation_attributes: bool
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158 :returns: :class:`pydot.Dot` -- the Dot object.
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159 """
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160 if direction not in {'BT', 'TB', 'LR', 'RL'}:
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161 # Invalid direction is provided
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162 direction = 'BT' # reset it to the default value
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163 maindot = pydot.Dot(graph_type='digraph', rankdir=direction, charset='utf-8')
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164
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165 node_map = {}
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166 count = [0, 0, 0, 0] # counters for node ids
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167
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168 def _bundle_to_dot(dot, bundle):
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169 def _attach_attribute_annotation(node, record):
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170 # Adding a node to show all attributes
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171 attributes = list(
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172 (attr_name, value) for attr_name, value in record.attributes
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173 if attr_name not in PROV_ATTRIBUTE_QNAMES
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174 )
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175
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176 if not attributes:
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177 return # No attribute to display
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178
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179 # Sort the attributes.
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180 attributes = sorted_attributes(record.get_type(), attributes)
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181
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182 ann_rows = [ANNOTATION_START_ROW]
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183 ann_rows.extend(
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184 ANNOTATION_ROW_TEMPLATE % (
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185 attr.uri, escape(six.text_type(attr)),
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186 ' href=\"%s\"' % value.uri if isinstance(value, Identifier)
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187 else '',
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188 escape(six.text_type(value)
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189 if not isinstance(value, datetime) else
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190 six.text_type(value.isoformat())))
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191 for attr, value in attributes
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192 )
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193 ann_rows.append(ANNOTATION_END_ROW)
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194 count[3] += 1
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195 annotations = pydot.Node(
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196 'ann%d' % count[3], label='\n'.join(ann_rows),
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197 **ANNOTATION_STYLE
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198 )
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199 dot.add_node(annotations)
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200 dot.add_edge(pydot.Edge(annotations, node, **ANNOTATION_LINK_STYLE))
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201
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202 def _add_bundle(bundle):
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203 count[2] += 1
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204 subdot = pydot.Cluster(
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205 graph_name='c%d' % count[2], URL='"%s"' % bundle.identifier.uri
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206 )
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207 if use_labels:
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208 if bundle.label == bundle.identifier:
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209 bundle_label = '"%s"' % six.text_type(bundle.label)
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210 else:
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211 # Fancier label if both are different. The label will be
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212 # the main node text, whereas the identifier will be a
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213 # kind of subtitle.
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214 bundle_label = ('<%s<br />'
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215 '<font color="#333333" point-size="10">'
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216 '%s</font>>')
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217 bundle_label = bundle_label % (
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218 six.text_type(bundle.label),
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219 six.text_type(bundle.identifier)
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220 )
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221 subdot.set_label('"%s"' % six.text_type(bundle_label))
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222 else:
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223 subdot.set_label('"%s"' % six.text_type(bundle.identifier))
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224 _bundle_to_dot(subdot, bundle)
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225 dot.add_subgraph(subdot)
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226 return subdot
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227
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228 def _add_node(record):
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229 count[0] += 1
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230 node_id = 'n%d' % count[0]
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231 if use_labels:
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232 if record.label == record.identifier:
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233 node_label = '"%s"' % six.text_type(record.label)
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234 else:
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235 # Fancier label if both are different. The label will be
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236 # the main node text, whereas the identifier will be a
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237 # kind of subtitle.
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238 node_label = ('<%s<br />'
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239 '<font color="#333333" point-size="10">'
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240 '%s</font>>')
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241 node_label = node_label % (six.text_type(record.label),
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242 six.text_type(record.identifier))
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243 else:
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244 node_label = '"%s"' % six.text_type(record.identifier)
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245
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246 uri = record.identifier.uri
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247 style = DOT_PROV_STYLE[record.get_type()]
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248 node = pydot.Node(
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249 node_id, label=node_label, URL='"%s"' % uri, **style
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250 )
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251 node_map[uri] = node
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252 dot.add_node(node)
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253
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254 if show_element_attributes:
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255 _attach_attribute_annotation(node, rec)
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256 return node
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257
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258 def _add_generic_node(qname):
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259 count[0] += 1
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260 node_id = 'n%d' % count[0]
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261 node_label = '"%s"' % six.text_type(qname)
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262
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263 uri = qname.uri
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264 style = DOT_PROV_STYLE[0]
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265 node = pydot.Node(
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266 node_id, label=node_label, URL='"%s"' % uri, **style
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267 )
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268 node_map[uri] = node
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269 dot.add_node(node)
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270 return node
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271
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272 def _get_bnode():
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273 count[1] += 1
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274 bnode_id = 'b%d' % count[1]
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275 bnode = pydot.Node(
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276 bnode_id, label='""', shape='point', color='gray'
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277 )
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278 dot.add_node(bnode)
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279 return bnode
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280
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281 def _get_node(qname):
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282 if qname is None:
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283 return _get_bnode()
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284 uri = qname.uri
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285 if uri not in node_map:
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286 _add_generic_node(qname)
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287 return node_map[uri]
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288
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289 records = bundle.get_records()
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290 relations = []
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291 for rec in records:
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292 if rec.is_element():
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293 _add_node(rec)
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294 else:
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295 # Saving the relations for later processing
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296 relations.append(rec)
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297
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298 if not bundle.is_bundle():
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299 for bundle in bundle.bundles:
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300 _add_bundle(bundle)
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301
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302 for rec in relations:
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303 args = rec.args
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304 # skipping empty records
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305 if not args:
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306 continue
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307 # picking element nodes
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308 nodes = [
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309 value for attr_name, value in rec.formal_attributes
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310 if attr_name in PROV_ATTRIBUTE_QNAMES
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311 ]
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312 other_attributes = [
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313 (attr_name, value) for attr_name, value in rec.attributes
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314 if attr_name not in PROV_ATTRIBUTE_QNAMES
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315 ]
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316 add_attribute_annotation = (
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317 show_relation_attributes and other_attributes
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318 )
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319 add_nary_elements = len(nodes) > 2 and show_nary
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320 style = DOT_PROV_STYLE[rec.get_type()]
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321 if len(nodes) < 2: # too few elements for a relation?
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322 continue # cannot draw this
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323
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324 if add_nary_elements or add_attribute_annotation:
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325 # a blank node for n-ary relations or the attribute annotation
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326 bnode = _get_bnode()
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327
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328 # the first segment
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329 dot.add_edge(
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330 pydot.Edge(
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331 _get_node(nodes[0]), bnode, arrowhead='none', **style
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332 )
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333 )
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334 style = dict(style) # copy the style
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335 del style['label'] # not showing label in the second segment
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336 # the second segment
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337 dot.add_edge(pydot.Edge(bnode, _get_node(nodes[1]), **style))
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338 if add_nary_elements:
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339 style['color'] = 'gray' # all remaining segment to be gray
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340 for node in nodes[2:]:
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341 if node is not None:
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342 dot.add_edge(
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343 pydot.Edge(bnode, _get_node(node), **style)
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344 )
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345 if add_attribute_annotation:
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346 _attach_attribute_annotation(bnode, rec)
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347 else:
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348 # show a simple binary relations with no annotation
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349 dot.add_edge(
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350 pydot.Edge(
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351 _get_node(nodes[0]), _get_node(nodes[1]), **style
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352 )
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353 )
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354
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355 try:
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356 unified = bundle.unified()
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357 except ProvException:
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358 # Could not unify this bundle
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359 # try the original document anyway
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360 unified = bundle
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361
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362 _bundle_to_dot(maindot, unified)
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363 return maindot