Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/gxformat2/export.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 """Functionality for converting a standard Galaxy workflow into a format 2 workflow.""" |
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2 import argparse |
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3 import json |
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4 import sys |
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5 from collections import OrderedDict |
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6 |
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7 from ._labels import Labels |
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8 from .model import native_input_to_format2_type |
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9 from .yaml import ordered_dump |
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10 |
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11 SCRIPT_DESCRIPTION = """ |
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12 Convert a native Galaxy workflow description into a Format 2 description. |
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13 """ |
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14 |
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15 |
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16 def _copy_common_properties(from_native_step, to_format2_step): |
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17 annotation = from_native_step.get("annotation", "") |
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18 if annotation: |
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19 to_format2_step["doc"] = annotation |
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20 position = from_native_step.get("position", None) |
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21 if position: |
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22 to_format2_step["position"] = position |
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23 |
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24 |
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25 def from_galaxy_native(format2_dict, tool_interface=None, json_wrapper=False): |
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26 """Convert native .ga workflow definition to a format2 workflow. |
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27 |
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28 This is highly experimental and currently broken. |
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29 """ |
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30 data = OrderedDict() |
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31 data['class'] = 'GalaxyWorkflow' |
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32 _copy_common_properties(format2_dict, data) |
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33 if "name" in format2_dict: |
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34 data["label"] = format2_dict.pop("name") |
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35 for top_level_key in ['tags', 'uuid', 'report']: |
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36 value = format2_dict.get(top_level_key) |
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37 if value: |
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38 data[top_level_key] = value |
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39 |
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40 native_steps = format2_dict.get("steps") |
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41 |
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42 label_map = {} |
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43 all_labeled = True |
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44 for key, step in native_steps.items(): |
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45 label = step.get("label") |
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46 if not label: |
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47 all_labeled = False |
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48 label_map[str(key)] = label |
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49 |
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50 inputs = OrderedDict() |
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51 outputs = OrderedDict() |
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52 steps = [] |
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53 |
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54 labels = Labels() |
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55 |
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56 # For each step, rebuild the form and encode the state |
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57 for step in native_steps.values(): |
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58 for workflow_output in step.get("workflow_outputs", []): |
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59 source = _to_source(workflow_output, label_map, output_id=step["id"]) |
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60 output_id = labels.ensure_new_output_label(workflow_output.get("label")) |
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61 outputs[output_id] = {"outputSource": source} |
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62 |
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63 module_type = step.get("type") |
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64 if module_type in ['data_input', 'data_collection_input', 'parameter_input']: |
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65 step_id = step["label"] # TODO: auto-label |
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66 input_dict = {} |
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67 tool_state = _tool_state(step) |
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68 input_dict['type'] = native_input_to_format2_type(step, tool_state) |
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69 for tool_state_key in ['optional', 'format', 'default', 'restrictions', 'suggestions', 'restrictOnConnections']: |
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70 if tool_state_key in tool_state: |
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71 input_dict[tool_state_key] = tool_state[tool_state_key] |
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72 |
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73 _copy_common_properties(step, input_dict) |
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74 # If we are only copying property - use the CWL-style short-hand |
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75 if len(input_dict) == 1: |
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76 inputs[step_id] = input_dict["type"] |
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77 else: |
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78 inputs[step_id] = input_dict |
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79 continue |
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80 |
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81 if module_type == "pause": |
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82 step_dict = OrderedDict() |
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83 optional_props = ['label'] |
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84 _copy_common_properties(step, step_dict) |
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85 _copy_properties(step, step_dict, optional_props=optional_props) |
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86 _convert_input_connections(step, step_dict, label_map) |
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87 step_dict["type"] = "pause" |
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88 steps.append(step_dict) |
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89 continue |
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90 |
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91 if module_type == 'subworkflow': |
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92 step_dict = OrderedDict() |
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93 optional_props = ['label'] |
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94 _copy_common_properties(step, step_dict) |
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95 _copy_properties(step, step_dict, optional_props=optional_props) |
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96 _convert_input_connections(step, step_dict, label_map) |
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97 _convert_post_job_actions(step, step_dict) |
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98 subworkflow_native_dict = step["subworkflow"] |
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99 subworkflow = from_galaxy_native(subworkflow_native_dict, tool_interface=tool_interface, json_wrapper=False) |
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100 step_dict["run"] = subworkflow |
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101 steps.append(step_dict) |
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102 continue |
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103 |
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104 if module_type != 'tool': |
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105 raise NotImplementedError("Unhandled module type %s" % module_type) |
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106 |
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107 step_dict = OrderedDict() |
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108 optional_props = ['label', 'tool_shed_repository'] |
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109 required_props = ['tool_id', 'tool_version'] |
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110 _copy_properties(step, step_dict, optional_props, required_props) |
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111 _copy_common_properties(step, step_dict) |
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112 |
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113 tool_state = _tool_state(step) |
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114 tool_state.pop("__page__", None) |
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115 tool_state.pop("__rerun_remap_job_id__", None) |
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116 step_dict['tool_state'] = tool_state |
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117 |
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118 _convert_input_connections(step, step_dict, label_map) |
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119 _convert_post_job_actions(step, step_dict) |
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120 steps.append(step_dict) |
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121 |
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122 data['inputs'] = inputs |
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123 data['outputs'] = outputs |
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124 |
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125 if all_labeled: |
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126 steps_dict = OrderedDict() |
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127 for step in steps: |
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128 label = step.pop("label") |
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129 steps_dict[label] = step |
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130 data['steps'] = steps_dict |
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131 else: |
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132 data['steps'] = steps |
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133 |
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134 if json_wrapper: |
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135 return { |
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136 "yaml_content": ordered_dump(data) |
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137 } |
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138 |
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139 return data |
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140 |
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141 |
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142 def _tool_state(step): |
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143 tool_state = json.loads(step['tool_state']) |
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144 return tool_state |
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145 |
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146 |
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147 def _copy_properties(from_native_step, to_format2_step, optional_props=[], required_props=[]): |
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148 for prop in optional_props: |
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149 value = from_native_step.get(prop) |
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150 if value: |
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151 to_format2_step[prop] = value |
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152 for prop in required_props: |
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153 value = from_native_step.get(prop) |
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154 to_format2_step[prop] = value |
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155 |
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156 |
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157 def _convert_input_connections(from_native_step, to_format2_step, label_map): |
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158 in_dict = from_native_step.get("in", {}).copy() |
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159 input_connections = from_native_step['input_connections'] |
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160 for input_name, input_defs in input_connections.items(): |
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161 if not isinstance(input_defs, list): |
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162 input_defs = [input_defs] |
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163 for input_def in input_defs: |
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164 source = _to_source(input_def, label_map) |
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165 if input_name == "__NO_INPUT_OUTPUT_NAME__": |
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166 input_name = "$step" |
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167 assert source.endswith("/__NO_INPUT_OUTPUT_NAME__") |
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168 source = source[:-len("/__NO_INPUT_OUTPUT_NAME__")] |
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169 in_dict[input_name] = { |
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170 "source": source |
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171 } |
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172 to_format2_step["in"] = in_dict |
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173 |
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174 |
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175 def _convert_post_job_actions(from_native_step, to_format2_step): |
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176 |
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177 def _ensure_output_def(key): |
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178 if "outputs" in to_format2_step: |
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179 to_format2_step["out"] = to_format2_step.pop("outputs") |
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180 elif "out" not in to_format2_step: |
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181 to_format2_step["out"] = {} |
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182 |
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183 outputs_dict = to_format2_step["out"] |
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184 if key not in outputs_dict: |
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185 outputs_dict[key] = {} |
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186 return outputs_dict[key] |
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187 |
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188 if "post_job_actions" in from_native_step: |
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189 post_job_actions = from_native_step["post_job_actions"].copy() |
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190 to_remove_keys = [] |
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191 |
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192 for post_job_action_key, post_job_action_value in post_job_actions.items(): |
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193 action_type = post_job_action_value["action_type"] |
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194 output_name = post_job_action_value.get("output_name") |
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195 action_args = post_job_action_value.get("action_arguments", {}) |
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196 |
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197 handled = True |
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198 if action_type == "RenameDatasetAction": |
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199 output_dict = _ensure_output_def(output_name) |
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200 output_dict["rename"] = action_args["newname"] |
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201 handled = True |
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202 elif action_type == "HideDatasetAction": |
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203 output_dict = _ensure_output_def(output_name) |
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204 output_dict["hide"] = True |
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205 handled = True |
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206 elif action_type == "DeleteIntermediatesAction": |
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207 output_dict = _ensure_output_def(output_name) |
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208 output_dict["delete_intermediate_datasets"] = True |
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209 elif action_type == "ChangeDatatypeAction": |
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210 output_dict = _ensure_output_def(output_name) |
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211 output_dict['change_datatype'] = action_args |
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212 handled = True |
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213 elif action_type == "TagDatasetAction": |
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214 output_dict = _ensure_output_def(output_name) |
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215 output_dict["add_tags"] = action_args["tags"].split(",") |
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216 elif action_type == "RemoveTagDatasetAction": |
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217 output_dict = _ensure_output_def(output_name) |
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218 output_dict["remove_tags"] = action_args["tags"].split(",") |
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219 elif action_type == "ColumnSetAction": |
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220 output_dict = _ensure_output_def(output_name) |
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221 output_dict["set_columns"] = action_args |
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222 else: |
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223 handled = False |
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224 |
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225 if handled: |
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226 to_remove_keys.append(post_job_action_key) |
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227 |
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228 for to_remove in to_remove_keys: |
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229 del post_job_actions[to_remove] |
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230 |
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231 if post_job_actions: |
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232 to_format2_step["post_job_actions"] = post_job_actions |
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233 |
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234 |
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235 def _to_source(has_output_name, label_map, output_id=None): |
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236 output_id = output_id if output_id is not None else has_output_name['id'] |
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237 output_id = str(output_id) |
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238 output_name = has_output_name['output_name'] |
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239 output_label = label_map.get(output_id) or output_id |
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240 if output_name == "output": |
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241 source = output_label |
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242 else: |
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243 source = "%s/%s" % (output_label, output_name) |
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244 return source |
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245 |
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246 |
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247 def main(argv=None): |
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248 """Entry point for script to convert native workflows to Format 2.""" |
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249 if argv is None: |
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250 argv = sys.argv[1:] |
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251 |
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252 args = _parser().parse_args(argv) |
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253 |
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254 format2_path = args.input_path |
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255 output_path = args.output_path or (format2_path + ".gxwf.yml") |
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256 with open(format2_path, "r") as f: |
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257 native_workflow_dict = json.load(f) |
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258 |
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259 as_dict = from_galaxy_native(native_workflow_dict) |
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260 with open(output_path, "w") as f: |
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261 ordered_dump(as_dict, f) |
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262 |
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263 |
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264 def _parser(): |
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265 parser = argparse.ArgumentParser(description=SCRIPT_DESCRIPTION) |
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266 parser.add_argument('input_path', metavar='INPUT', type=str, |
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267 help='input workflow path (.ga)') |
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268 parser.add_argument('output_path', metavar='OUTPUT', type=str, nargs="?", |
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269 help='output workflow path (.gxfw.yml)') |
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270 return parser |
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271 |
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272 |
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273 __all__ = ( |
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274 'from_galaxy_native', |
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275 'main', |
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276 ) |