Mercurial > repos > fubar > tool_factory_2

annotate toolfactory/tfworkflowsample.ga @ 36:ce2b1f8ea68d draft

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passes flake8 tests finally :)
author fubar
date Mon, 10 Aug 2020 23:24:41 -0400
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children
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36
ce2b1f8ea68d passes flake8 tests finally :)
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1 {
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2 "a_galaxy_workflow": "true",
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3 "annotation": "",
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4 "format-version": "0.1",
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5 "name": "workflow to generate a bunch of sample toolfactory tools",
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6 "steps": {
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7 "0": {
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8 "annotation": "",
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9 "content_id": null,
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10 "errors": null,
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11 "id": 0,
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12 "input_connections": {},
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13 "inputs": [
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14 {
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15 "description": "",
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16 "name": "rgToolFactory2.py"
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17 }
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18 ],
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19 "label": "rgToolFactory2.py",
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20 "name": "Input dataset",
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21 "outputs": [],
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22 "position": {
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23 "bottom": 235.25,
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24 "height": 81,
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25 "left": 711.84375,
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26 "right": 911.84375,
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27 "top": 154.25,
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28 "width": 200,
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29 "x": 711.84375,
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30 "y": 154.25
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31 },
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32 "tool_id": null,
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33 "tool_state": "{\"optional\": false}",
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34 "tool_version": null,
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35 "type": "data_input",
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36 "uuid": "b717b6ee-51d0-415d-876d-f19b42f67666",
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37 "workflow_outputs": [
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38 {
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39 "label": null,
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40 "output_name": "output",
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41 "uuid": "09acd6fd-4e2b-44a8-8757-35eca8d0de89"
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42 }
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43 ]
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44 },
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45 "1": {
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46 "annotation": "",
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47 "content_id": null,
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48 "errors": null,
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49 "id": 1,
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50 "input_connections": {},
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51 "inputs": [
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52 {
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53 "description": "",
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54 "name": "README.md"
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55 }
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56 ],
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57 "label": "README.md",
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58 "name": "Input dataset",
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59 "outputs": [],
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60 "position": {
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61 "bottom": 760.25,
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62 "height": 61,
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63 "left": 711.84375,
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64 "right": 911.84375,
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65 "top": 699.25,
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66 "width": 200,
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67 "x": 711.84375,
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68 "y": 699.25
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69 },
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70 "tool_id": null,
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71 "tool_state": "{\"optional\": false}",
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72 "tool_version": null,
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73 "type": "data_input",
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74 "uuid": "8aefae07-4fd1-44a6-bea2-5d377567ac27",
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75 "workflow_outputs": [
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76 {
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77 "label": null,
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78 "output_name": "output",
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79 "uuid": "5f8453d0-abd1-41d9-a4a7-1f8b82f1f095"
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80 }
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81 ]
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82 },
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83 "2": {
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84 "annotation": "",
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85 "content_id": null,
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86 "errors": null,
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87 "id": 2,
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88 "input_connections": {},
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89 "inputs": [
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90 {
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91 "description": "",
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92 "name": "testtext"
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93 }
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94 ],
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95 "label": "testtext",
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96 "name": "Input dataset",
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97 "outputs": [],
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98 "position": {
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99 "bottom": 235.25,
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100 "height": 61,
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101 "left": 989.84375,
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102 "right": 1189.84375,
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103 "top": 174.25,
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104 "width": 200,
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105 "x": 989.84375,
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106 "y": 174.25
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107 },
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108 "tool_id": null,
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109 "tool_state": "{\"optional\": false}",
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110 "tool_version": null,
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111 "type": "data_input",
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112 "uuid": "02a35533-a67b-44c0-bce8-96a8adddc5a9",
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113 "workflow_outputs": [
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114 {
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115 "label": null,
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116 "output_name": "output",
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117 "uuid": "abe4a1b1-2c0b-44d1-95f8-4f9bb38e9daa"
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118 }
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119 ]
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120 },
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121 "3": {
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122 "annotation": "",
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123 "content_id": "rgTF2",
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124 "errors": null,
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125 "id": 3,
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126 "input_connections": {
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127 "ppass|history_inputs_0|input_files": {
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128 "id": 1,
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129 "output_name": "output"
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130 }
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131 },
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132 "inputs": [],
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133 "label": null,
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134 "name": "toolfactory",
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135 "outputs": [
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136 {
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137 "name": "ToolFactory_Outputs",
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138 "type": "input"
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139 },
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140 {
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141 "name": "new_tool",
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142 "type": "tgz"
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143 }
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144 ],
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145 "position": {
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146 "bottom": 636.25,
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147 "height": 222,
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148 "left": 989.84375,
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149 "right": 1189.84375,
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150 "top": 414.25,
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151 "width": 200,
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152 "x": 989.84375,
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153 "y": 414.25
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154 },
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155 "post_job_actions": {},
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156 "tool_id": "rgTF2",
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157 "tool_state": "{\"__input_ext\": \"txt\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"bash\", \"__current_case__\": 5, \"interpreter_version\": \"\", \"exe_package_version\": \"\", \"dynScript\": \"rev | tac\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"tacrev\", \"help_text\": \"**What it Does**\", \"citations\": []}, \"ppass\": {\"parampass\": \"0\", \"__current_case__\": 2, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"txt\"], \"input_label\": \"input file\", \"input_help\": \"parameter_help\", \"input_CL\": \"1\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"outfile\", \"history_format\": \"txt\", \"history_CL\": \"2\"}]}, \"tool_name\": \"tacrev\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
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158 "tool_version": "2.00",
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159 "type": "tool",
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160 "uuid": "8fab16a0-5303-4e5c-8bf6-d6ebc70aa9af",
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161 "workflow_outputs": [
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162 {
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163 "label": null,
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164 "output_name": "ToolFactory_Outputs",
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165 "uuid": "68d1a0b8-d897-48e9-a304-25d289e139e9"
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166 },
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167 {
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168 "label": null,
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169 "output_name": "new_tool",
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170 "uuid": "8669863e-a1a5-4ed6-a412-c7f341f66176"
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171 }
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172 ]
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173 },
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174 "4": {
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175 "annotation": "",
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176 "content_id": "rgTF2",
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177 "errors": null,
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178 "id": 4,
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179 "input_connections": {
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180 "ppass|history_inputs_0|input_files": {
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181 "id": 1,
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182 "output_name": "output"
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183 }
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184 },
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185 "inputs": [],
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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193 {
ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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parents:
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ce2b1f8ea68d passes flake8 tests finally :)
fubar
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ce2b1f8ea68d passes flake8 tests finally :)
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parents:
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ce2b1f8ea68d passes flake8 tests finally :)
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parents:
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246 {
ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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parents:
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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295 {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
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348 {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
349 "name": "ToolFactory_Outputs",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
350 "type": "input"
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
351 },
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
352 {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
353 "name": "new_tool",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
354 "type": "tgz"
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
355 }
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
356 ],
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
357 "position": {
ce2b1f8ea68d passes flake8 tests finally :)
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parents:
diff changeset
358 "bottom": 376.25,
ce2b1f8ea68d passes flake8 tests finally :)
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parents:
diff changeset
359 "height": 222,
ce2b1f8ea68d passes flake8 tests finally :)
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parents:
diff changeset
360 "left": 1267.84375,
ce2b1f8ea68d passes flake8 tests finally :)
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parents:
diff changeset
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ce2b1f8ea68d passes flake8 tests finally :)
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parents:
diff changeset
362 "top": 154.25,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
363 "width": 200,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
364 "x": 1267.84375,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
365 "y": 154.25
ce2b1f8ea68d passes flake8 tests finally :)
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parents:
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366 },
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
367 "post_job_actions": {},
ce2b1f8ea68d passes flake8 tests finally :)
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parents:
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368 "tool_id": "rgTF2",
ce2b1f8ea68d passes flake8 tests finally :)
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369 "tool_state": "{\"__input_ext\": \"txt\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"system\", \"__current_case__\": 1, \"exe_package\": \"sed\", \"exe_package_version\": \"\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"sed runner\", \"help_text\": \"sed '/old/new/g input.txt\", \"citations\": []}, \"ppass\": {\"parampass\": \"positional\", \"__current_case__\": 1, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"txt\"], \"input_label\": \"input text\", \"input_help\": \"parameter_help\", \"input_CL\": \"3\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"output\", \"history_format\": \"txt\", \"history_CL\": \"STDOUT\"}], \"edit_params\": \"yes\", \"additional_parameters\": [{\"__index__\": 0, \"param_name\": \"sedstring\", \"param_type\": \"text\", \"param_value\": \"s/Old/New/g\", \"param_label\": \"parameter_label\", \"param_help\": \"parameter_help\", \"param_CL\": \"1\"}]}, \"tool_name\": \"sedtest\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
370 "tool_version": "2.00",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
371 "type": "tool",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
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372 "uuid": "e26df7b6-3899-42fb-8efc-5f13d53668f8",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
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373 "workflow_outputs": [
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
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374 {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
375 "label": null,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
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376 "output_name": "ToolFactory_Outputs",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
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377 "uuid": "0a819390-acd4-4be6-aac9-ec3322302b0f"
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
378 },
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
379 {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
380 "label": null,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
381 "output_name": "new_tool",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
382 "uuid": "f7555059-144d-4f64-a303-b70d189e6e35"
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
383 }
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
384 ]
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
385 },
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
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386 "8": {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
387 "annotation": "",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
388 "content_id": "rgTF2",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
389 "errors": null,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
390 "id": 8,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
391 "input_connections": {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
392 "ppass|history_inputs_0|input_files": {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
393 "id": 5,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
394 "output_name": "new_tool"
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
395 }
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
396 },
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
397 "inputs": [],
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
398 "label": null,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
399 "name": "toolfactory",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
400 "outputs": [
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
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401 {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
402 "name": "ToolFactory_Outputs",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
403 "type": "input"
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
404 },
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
405 {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
406 "name": "new_tool",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
407 "type": "tgz"
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
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408 }
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
409 ],
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
410 "position": {
ce2b1f8ea68d passes flake8 tests finally :)
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parents:
diff changeset
411 "bottom": 1271.25,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
412 "height": 242,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
413 "left": 1267.84375,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
414 "right": 1467.84375,
ce2b1f8ea68d passes flake8 tests finally :)
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parents:
diff changeset
415 "top": 1029.25,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
416 "width": 200,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
417 "x": 1267.84375,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
418 "y": 1029.25
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
419 },
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
420 "post_job_actions": {},
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
421 "tool_id": "rgTF2",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
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422 "tool_state": "{\"__input_ext\": \"tgz\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"python\", \"__current_case__\": 2, \"interpreter_version\": \"\", \"exe_package_version\": \"\", \"dynScript\": \"import argparse\\nimport tarfile\\nimport os\\nimport tempfile\\nimport subprocess\\n\\n\\\"\\\"\\\"\\nplanemo test --no_cleanup --no_dependency_resolution --skip_venv --galaxy_root ~/galaxy ~/galaxy/tools/tool_makers/pyrevargparse/ &> pyrevargparse\\n\\\"\\\"\\\"\\n\\nparser = argparse.ArgumentParser()\\na = parser.add_argument\\na('--tooltgz',default='')\\na('--report',default=None)\\na('--toolout',default=None)\\na('--galaxy_root',default=None)\\nargs = parser.parse_args()\\ntoolname = args.toolout.split(os.sep)[-1]\\ntoolpath = os.path.join(args.galaxy_root,args.toolout)\\ntf = tarfile.open(args.tooltgz,\\\"r:gz\\\")\\ntf.extractall(toolpath)\\ncl = \\\"planemo test --skip_venv --galaxy_root %s %s\\\" % (args.galaxy_root,toolpath)\\ncll = cl.split(' ')\\nsto = open(args.report, 'w')\\np = subprocess.run(cll, shell=False, stdout=sto)\\nretval = p.returncode\\nsto.close()\\n\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"Tool to test toolshed tool archives generated by the tool factory.\", \"help_text\": \"**What it Does**\\n\\nGiven a toolshed tgz file generated by a tool factory run, this will unpack it and run planemo test, returning the planemo stdout as a report\\nIt was generated using the tool factory.\", \"citations\": []}, \"ppass\": {\"parampass\": \"argparse\", \"__current_case__\": 0, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"tgz\"], \"input_label\": \"tool toolshed tgz archive from history\", \"input_help\": \"Run planemo test on a tool shed tool archive tgz format file generated by the ToolFactory or Planemo\", \"input_CL\": \"tooltgz\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"report\", \"history_format\": \"txt\", \"history_CL\": \"report\"}], \"edit_params\": \"yes\", \"additional_parameters\": [{\"__index__\": 0, \"param_name\": \"toolout\", \"param_type\": \"text\", \"param_value\": \"tools/toolmakers/planemotest\", \"param_label\": \"output path under galaxy root\", \"param_help\": \"This is where the tgz file will be extracted and tested by planemo\", \"param_CL\": \"toolout\"}, {\"__index__\": 1, \"param_name\": \"galaxy_root\", \"param_type\": \"text\", \"param_value\": \"/home/ross/galaxy\", \"param_label\": \"your galaxy root to use for running planemo\", \"param_help\": \"This will form the galaxy_root parameter for running planemo using an existing Galaxy source tree, and the tgz will be extracted at a path relative to that root\", \"param_CL\": \"galaxy_root\"}]}, \"tool_name\": \"planemotest\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
423 "tool_version": "2.00",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
424 "type": "tool",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
425 "uuid": "c72a7aae-3801-431b-a331-be6938d34fbd",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
426 "workflow_outputs": [
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
427 {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
428 "label": null,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
429 "output_name": "ToolFactory_Outputs",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
430 "uuid": "75aa9815-5bd6-44a7-8210-889d3b7e5027"
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
431 },
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
432 {
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
433 "label": null,
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
434 "output_name": "new_tool",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
435 "uuid": "744499de-5d7e-4415-b427-315057c81ebc"
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
436 }
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
437 ]
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
438 }
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
439 },
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
440 "tags": [],
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
441 "uuid": "490d9c7f-eea3-4616-a8b7-13510da0430b",
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
diff changeset
442 "version": 1
ce2b1f8ea68d passes flake8 tests finally :)
fubar
parents:
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443 }