Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/gxformat2/converter.py @ 4:79f47841a781 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:47:39 -0400
parents 26e78fe6e8c4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 """Functionality for converting a Format 2 workflow into a standard Galaxy workflow."""
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2 from __future__ import print_function
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3
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4 import copy
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5 import json
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6 import logging
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7 import os
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8 import sys
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9 import uuid
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10 from collections import OrderedDict
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11
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12 from ._labels import Labels
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13 from ._yaml import ordered_load
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14
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15 # source: step#output and $link: step#output instead of outputSource: step/output and $link: step/output
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16 SUPPORT_LEGACY_CONNECTIONS = os.environ.get("GXFORMAT2_SUPPORT_LEGACY_CONNECTIONS") == "1"
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17 STEP_TYPES = [
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18 "subworkflow",
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19 "data_input",
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20 "data_collection_input",
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21 "tool",
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22 "pause",
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23 "parameter_input",
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24 ]
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25
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26 STEP_TYPE_ALIASES = {
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27 'input': 'data_input',
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28 'input_collection': 'data_collection_input',
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29 'parameter': 'parameter_input',
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30 }
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31
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32 RUN_ACTIONS_TO_STEPS = {
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33 'GalaxyWorkflow': 'run_workflow_to_step',
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34 'GalaxyTool': 'run_tool_to_step',
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35 }
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36
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37 POST_JOB_ACTIONS = {
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38 'hide': {
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39 'action_class': "HideDatasetAction",
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40 'default': False,
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41 'arguments': lambda x: x,
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42 },
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43 'rename': {
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44 'action_class': 'RenameDatasetAction',
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45 'default': {},
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46 'arguments': lambda x: {'newname': x},
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47 },
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48 'delete_intermediate_datasets': {
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49 'action_class': 'DeleteIntermediatesAction',
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50 'default': False,
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51 'arguments': lambda x: x,
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52 },
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53 'change_datatype': {
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54 'action_class': 'ChangeDatatypeAction',
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55 'default': {},
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56 'arguments': lambda x: {'newtype': x},
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57 },
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58 'set_columns': {
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59 'action_class': 'ColumnSetAction',
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60 'default': {},
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61 'arguments': lambda x: x,
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62 },
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63 'add_tags': {
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64 'action_class': 'TagDatasetAction',
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65 'default': [],
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66 'arguments': lambda x: {'tags': ",".join(x)},
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67 },
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68 'remove_tags': {
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69 'action_class': 'RemoveTagDatasetAction',
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70 'default': [],
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71 'arguments': lambda x: {'tags': ",".join(x)},
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72 },
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73 }
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74
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75 log = logging.getLogger(__name__)
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76
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77
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78 def rename_arg(argument):
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79 return argument
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80
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81
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82 def clean_connection(value):
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83 if value and "#" in value and SUPPORT_LEGACY_CONNECTIONS:
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84 # Hope these are just used by Galaxy testing workflows and such, and not in production workflows.
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85 log.warn("Legacy workflow syntax for connections [%s] will not be supported in the future" % value)
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86 value = value.replace("#", "/", 1)
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87 else:
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88 return value
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89
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90
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91 class ImportOptions(object):
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92
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93 def __init__(self):
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94 self.deduplicate_subworkflows = False
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95
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96
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97 def yaml_to_workflow(has_yaml, galaxy_interface, workflow_directory, import_options=None):
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98 """Convert a Format 2 workflow into standard Galaxy format from supplied stream."""
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99 as_python = ordered_load(has_yaml)
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100 return python_to_workflow(as_python, galaxy_interface, workflow_directory, import_options=import_options)
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101
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102
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103 def python_to_workflow(as_python, galaxy_interface, workflow_directory=None, import_options=None):
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104 """Convert a Format 2 workflow into standard Galaxy format from supplied dictionary."""
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105 if "yaml_content" in as_python:
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106 as_python = ordered_load(as_python["yaml_content"])
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107
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108 if workflow_directory is None:
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109 workflow_directory = os.path.abspath(".")
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110
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111 conversion_context = ConversionContext(
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112 galaxy_interface,
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113 workflow_directory,
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114 import_options,
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115 )
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116 as_python = _preprocess_graphs(as_python, conversion_context)
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117 subworkflows = None
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118 if conversion_context.import_options.deduplicate_subworkflows:
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119 # TODO: import only required workflows...
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120 # TODO: dag sort these...
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121 subworkflows = OrderedDict()
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122 for graph_id, subworkflow_content in conversion_context.graph_ids.items():
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123 if graph_id == "main":
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124 continue
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125 subworkflow_conversion_context = conversion_context.get_subworkflow_conversion_context_graph("#" + graph_id)
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126 subworkflows[graph_id] = _python_to_workflow(copy.deepcopy(subworkflow_content), subworkflow_conversion_context)
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127 converted = _python_to_workflow(as_python, conversion_context)
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128 if subworkflows is not None:
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129 converted["subworkflows"] = subworkflows
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130 return converted
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131
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132
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133 # move to a utils file?
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134 def steps_as_list(format2_workflow, add_label=True):
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135 """Return steps as a list, converting ID map to list representation if needed."""
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136 steps = format2_workflow["steps"]
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137 steps = _convert_dict_to_id_list_if_needed(steps, add_label=True)
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138 return steps
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139
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140
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141 def ensure_step_position(step, order_index):
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142 """Ensure step contains a position definition."""
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143 if "position" not in step:
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144 step["position"] = {
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145 "left": 10 * order_index,
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146 "top": 10 * order_index
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147 }
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148
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149
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150 def _python_to_workflow(as_python, conversion_context):
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151
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152 if "class" not in as_python:
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153 raise Exception("This is not a not a valid Galaxy workflow definition, must define a class.")
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154
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155 if as_python["class"] != "GalaxyWorkflow":
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156 raise Exception("This is not a not a valid Galaxy workflow definition, 'class' must be 'GalaxyWorkflow'.")
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157
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158 # .ga files don't have this, drop it so it isn't interpreted as a format 2 workflow.
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159 as_python.pop("class")
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160
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161 _ensure_defaults(as_python, {
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162 "a_galaxy_workflow": "true",
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163 "format-version": "0.1",
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164 "name": "Workflow",
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165 "uuid": str(uuid.uuid4()),
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166 })
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167 _populate_annotation(as_python)
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168
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169 steps = steps_as_list(as_python)
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170
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171 convert_inputs_to_steps(as_python, steps)
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172
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173 if isinstance(steps, list):
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174 steps_as_dict = OrderedDict()
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175 for i, step in enumerate(steps):
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176 steps_as_dict[str(i)] = step
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177 if "id" not in step:
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178 step["id"] = i
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179
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180 if "label" in step:
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181 label = step["label"]
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182 conversion_context.labels[label] = i
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183
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184 # TODO: this really should be optional in Galaxy API.
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185 ensure_step_position(step, i)
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186
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187 as_python["steps"] = steps_as_dict
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188 steps = steps_as_dict
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189
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190 for step in steps.values():
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191 step_type = step.get("type", None)
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192 if "run" in step:
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193 if step_type is not None:
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194 raise Exception("Steps specified as run actions cannot specify a type.")
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195 run_action = step.get("run")
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196 run_action = conversion_context.get_runnable_description(run_action)
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197 if isinstance(run_action, dict):
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198 run_class = run_action["class"]
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199 run_to_step_function = eval(RUN_ACTIONS_TO_STEPS[run_class])
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200
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201 run_to_step_function(conversion_context, step, run_action)
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202 else:
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203 step["content_id"] = run_action
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204 step["type"] = "subworkflow"
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205 del step["run"]
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206
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207 for step in steps.values():
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208 step_type = step.get("type", "tool")
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209 step_type = STEP_TYPE_ALIASES.get(step_type, step_type)
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210 if step_type not in STEP_TYPES:
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211 raise Exception("Unknown step type encountered %s" % step_type)
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212 step["type"] = step_type
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213 eval("transform_%s" % step_type)(conversion_context, step)
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214
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215 outputs = as_python.get("outputs", [])
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216 outputs = _convert_dict_to_id_list_if_needed(outputs)
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217
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218 for output in outputs:
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219 assert isinstance(output, dict), "Output definition must be dictionary"
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220 assert "source" in output or "outputSource" in output, "Output definition must specify source"
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221
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222 if "label" in output and "id" in output:
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223 raise Exception("label and id are aliases for outputs, may only define one")
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224 if "label" not in output and "id" not in output:
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225 label = ""
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226
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227 raw_label = output.pop("label", None)
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228 raw_id = output.pop("id", None)
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229 label = raw_label or raw_id
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230 if Labels.is_anonymous_output_label(label):
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231 label = None
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232 source = clean_connection(output.get("outputSource"))
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233 if source is None and SUPPORT_LEGACY_CONNECTIONS:
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234 source = output.get("source").replace("#", "/", 1)
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235 id, output_name = conversion_context.step_output(source)
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236 step = steps[str(id)]
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237 workflow_output = {
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238 "output_name": output_name,
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239 "label": label,
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240 "uuid": output.get("uuid", None)
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241 }
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242 if "workflow_outputs" not in step:
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243 step["workflow_outputs"] = []
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244 step["workflow_outputs"].append(workflow_output)
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245
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246 return as_python
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247
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248
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249 def _preprocess_graphs(as_python, conversion_context):
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250 if not isinstance(as_python, dict):
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251 raise Exception("This is not a not a valid Galaxy workflow definition.")
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252
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253 format_version = as_python.get("format-version", "v2.0")
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254 assert format_version == "v2.0"
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255
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256 if "class" not in as_python and "$graph" in as_python:
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257 for subworkflow in as_python["$graph"]:
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258 if not isinstance(subworkflow, dict):
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259 raise Exception("Malformed workflow content in $graph")
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260 if "id" not in subworkflow:
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261 raise Exception("No subworkflow ID found for entry in $graph.")
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262 subworkflow_id = subworkflow["id"]
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263 if subworkflow_id == "main":
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264 as_python = subworkflow
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265
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266 conversion_context.register_runnable(subworkflow)
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267
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268 return as_python
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269
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270
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271 def convert_inputs_to_steps(workflow_dict, steps):
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272 """Convert workflow inputs to a steps in array - like in native Galaxy."""
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273 if "inputs" not in workflow_dict:
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274 return
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275
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276 inputs = workflow_dict["inputs"]
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277 new_steps = []
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278 inputs = _convert_dict_to_id_list_if_needed(inputs)
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279 for input_def_raw in inputs:
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280 input_def = input_def_raw.copy()
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281
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282 if "label" in input_def and "id" in input_def:
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283 raise Exception("label and id are aliases for inputs, may only define one")
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284 if "label" not in input_def and "id" not in input_def:
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285 raise Exception("Input must define a label.")
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286
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287 raw_label = input_def.pop("label", None)
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288 raw_id = input_def.pop("id", None)
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289 label = raw_label or raw_id
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290
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291 if not label:
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292 raise Exception("Input label must not be empty.")
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293
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294 input_type = input_def.pop("type", "data")
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295 if input_type in ["File", "data", "data_input"]:
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296 step_type = "data_input"
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297 elif input_type in ["collection", "data_collection", "data_collection_input"]:
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298 step_type = "data_collection_input"
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299 elif input_type in ["text", "integer", "float", "color", "boolean"]:
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300 step_type = "parameter_input"
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301 input_def["parameter_type"] = input_type
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302 else:
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303 raise Exception("Input type must be a data file or collection.")
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304
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305 step_def = input_def
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306 step_def.update({
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307 "type": step_type,
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308 "label": label,
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309 })
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310 new_steps.append(step_def)
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311
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312 for i, new_step in enumerate(new_steps):
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313 steps.insert(i, new_step)
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314
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315
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316 def run_workflow_to_step(conversion_context, step, run_action):
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317 step["type"] = "subworkflow"
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318 if conversion_context.import_options.deduplicate_subworkflows and _is_graph_id_reference(run_action):
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319 step["content_id"] = run_action
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320 else:
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321 subworkflow_conversion_context = conversion_context.get_subworkflow_conversion_context(step)
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322 step["subworkflow"] = _python_to_workflow(
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323 copy.deepcopy(run_action),
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324 subworkflow_conversion_context,
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325 )
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326
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327
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328 def _is_graph_id_reference(run_action):
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329 return run_action and not isinstance(run_action, dict)
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330
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331
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332 def transform_data_input(context, step):
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333 transform_input(context, step, default_name="Input dataset")
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334
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335
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336 def transform_data_collection_input(context, step):
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337 transform_input(context, step, default_name="Input dataset collection")
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338
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339
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340 def transform_parameter_input(context, step):
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341 transform_input(context, step, default_name="input_parameter")
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342
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343
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344 def transform_input(context, step, default_name):
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345 default_name = step.get("label", default_name)
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346 _populate_annotation(step)
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347 _ensure_inputs_connections(step)
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348
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349 if "inputs" not in step:
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350 step["inputs"] = [{}]
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351
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352 step_inputs = step["inputs"][0]
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353 if "name" in step_inputs:
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354 name = step_inputs["name"]
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355 else:
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356 name = default_name
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357
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358 _ensure_defaults(step_inputs, {
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359 "name": name,
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360 "description": "",
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361 })
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362 tool_state = {
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363 "name": name
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364 }
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365 for attrib in ["collection_type", "parameter_type", "optional", "default"]:
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366 if attrib in step:
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367 tool_state[attrib] = step[attrib]
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368
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369 _populate_tool_state(step, tool_state)
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370
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371
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372 def transform_pause(context, step, default_name="Pause for dataset review"):
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373 default_name = step.get("label", default_name)
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374 _populate_annotation(step)
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375
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376 _ensure_inputs_connections(step)
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377
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378 if "inputs" not in step:
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379 step["inputs"] = [{}]
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380
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381 step_inputs = step["inputs"][0]
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382 if "name" in step_inputs:
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383 name = step_inputs["name"]
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384 else:
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385 name = default_name
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386
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387 _ensure_defaults(step_inputs, {
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388 "name": name,
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389 })
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390 tool_state = {
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391 "name": name
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392 }
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393
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394 connect = _init_connect_dict(step)
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395 _populate_input_connections(context, step, connect)
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396 _populate_tool_state(step, tool_state)
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397
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398
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399 def transform_subworkflow(context, step):
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400 _populate_annotation(step)
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401
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402 _ensure_inputs_connections(step)
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403
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404 tool_state = {
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405 }
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406
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407 connect = _init_connect_dict(step)
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408 _populate_input_connections(context, step, connect)
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409 _populate_tool_state(step, tool_state)
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410
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411
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412 def _runtime_value():
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413 return {"__class__": "RuntimeValue"}
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414
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415
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416 def transform_tool(context, step):
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417 if "tool_id" not in step:
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418 raise Exception("Tool steps must define a tool_id.")
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419
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420 _ensure_defaults(step, {
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421 "name": step['tool_id'],
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422 "post_job_actions": {},
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423 "tool_version": None,
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424 })
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425 post_job_actions = step["post_job_actions"]
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426 _populate_annotation(step)
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427
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428 tool_state = {
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429 # TODO: Galaxy should not require tool state actually specify a __page__.
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430 "__page__": 0,
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431 }
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432
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433 connect = _init_connect_dict(step)
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434
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435 def append_link(key, value):
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436 if key not in connect:
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437 connect[key] = []
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438 assert "$link" in value
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439 link_value = value["$link"]
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440 connect[key].append(clean_connection(link_value))
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441
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442 def replace_links(value, key=""):
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443 if _is_link(value):
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444 append_link(key, value)
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445 # Filled in by the connection, so to force late
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446 # validation of the field just mark as RuntimeValue.
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447 # It would be better I guess if this were some other
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448 # value dedicated to this purpose (e.g. a ficitious
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449 # {"__class__": "ConnectedValue"}) that could be further
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450 # validated by Galaxy.
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451 return _runtime_value()
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452 if isinstance(value, dict):
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453 new_values = {}
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454 for k, v in value.items():
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455 new_key = _join_prefix(key, k)
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456 new_values[k] = replace_links(v, new_key)
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457 return new_values
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458 elif isinstance(value, list):
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459 new_values = []
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460 for i, v in enumerate(value):
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461 # If we are a repeat we need to modify the key
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462 # but not if values are actually $links.
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463 if _is_link(v):
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464 append_link(key, v)
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465 new_values.append(None)
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466 else:
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467 new_key = "%s_%d" % (key, i)
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468 new_values.append(replace_links(v, new_key))
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469 return new_values
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470 else:
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471 return value
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472
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473 # TODO: handle runtime inputs and state together.
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474 runtime_inputs = step.get("runtime_inputs", [])
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475 if "state" in step or runtime_inputs:
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476 step_state = step.pop("state", {})
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477 step_state = replace_links(step_state)
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478
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479 for key, value in step_state.items():
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480 tool_state[key] = json.dumps(value)
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481 for runtime_input in runtime_inputs:
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482 tool_state[runtime_input] = json.dumps(_runtime_value())
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483 elif "tool_state" in step:
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484 tool_state.update(step.get("tool_state"))
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485
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486 # Fill in input connections
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487 _populate_input_connections(context, step, connect)
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488
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489 _populate_tool_state(step, tool_state)
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490
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491 # Handle outputs.
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492 out = step.pop("out", None)
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493 if out is None:
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494 # Handle LEGACY 19.XX outputs key.
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495 out = step.pop("outputs", [])
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496 out = _convert_dict_to_id_list_if_needed(out)
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497 for output in out:
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498 name = output["id"]
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499 for action_key, action_dict in POST_JOB_ACTIONS.items():
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500 action_argument = output.get(action_key, action_dict['default'])
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501 if action_argument:
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502 action_class = action_dict['action_class']
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503 action_name = action_class + name
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504 action = _action(
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505 action_class,
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506 name,
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507 arguments=action_dict['arguments'](action_argument)
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508 )
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509 post_job_actions[action_name] = action
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510
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511
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512 def run_tool_to_step(conversion_context, step, run_action):
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513 tool_description = conversion_context.galaxy_interface.import_tool(
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514 run_action
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515 )
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516 step["type"] = "tool"
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517 step["tool_id"] = tool_description["tool_id"]
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518 step["tool_version"] = tool_description["tool_version"]
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519 step["tool_hash"] = tool_description.get("tool_hash")
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520 step["tool_uuid"] = tool_description.get("uuid")
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521
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522
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523 class BaseConversionContext(object):
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524
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525 def __init__(self):
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526 self.labels = {}
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527 self.subworkflow_conversion_contexts = {}
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528
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529 def step_id(self, label_or_id):
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530 if label_or_id in self.labels:
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531 id = self.labels[label_or_id]
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532 else:
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533 id = label_or_id
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534 return int(id)
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535
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536 def step_output(self, value):
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537 value_parts = str(value).split("/")
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538 if len(value_parts) == 1:
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539 value_parts.append("output")
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540 id = self.step_id(value_parts[0])
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541 return id, value_parts[1]
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542
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543 def get_subworkflow_conversion_context(self, step):
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544 # TODO: sometimes this method takes format2 steps and some times converted native ones
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545 # (for input connections) - redo this so the type signature is stronger.
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546 step_id = step.get("id")
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547 run_action = step.get("run")
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548 if self.import_options.deduplicate_subworkflows and _is_graph_id_reference(run_action):
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549 subworkflow_conversion_context = self.get_subworkflow_conversion_context_graph(run_action)
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550 return subworkflow_conversion_context
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551 if "content_id" in step:
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552 subworkflow_conversion_context = self.get_subworkflow_conversion_context_graph(step["content_id"])
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553 return subworkflow_conversion_context
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554
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555 if step_id not in self.subworkflow_conversion_contexts:
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556
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557 subworkflow_conversion_context = SubworkflowConversionContext(
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558 self
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559 )
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560 self.subworkflow_conversion_contexts[step_id] = subworkflow_conversion_context
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561 return self.subworkflow_conversion_contexts[step_id]
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562
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563 def get_runnable_description(self, run_action):
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564 if "@import" in run_action:
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565 if len(run_action) > 1:
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566 raise Exception("@import must be only key if present.")
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567
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568 run_action_path = run_action["@import"]
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569 runnable_path = os.path.join(self.workflow_directory, run_action_path)
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570 with open(runnable_path, "r") as f:
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571 runnable_description = ordered_load(f)
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572 run_action = runnable_description
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573
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574 if not self.import_options.deduplicate_subworkflows and _is_graph_id_reference(run_action):
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575 run_action = self.graph_ids[run_action[1:]]
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576
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577 return run_action
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578
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579
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580 class ConversionContext(BaseConversionContext):
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581
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582 def __init__(self, galaxy_interface, workflow_directory, import_options=None):
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583 super(ConversionContext, self).__init__()
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584 self.import_options = import_options or ImportOptions()
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585 self.graph_ids = OrderedDict()
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586 self.graph_id_subworkflow_conversion_contexts = {}
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587 self.workflow_directory = workflow_directory
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588 self.galaxy_interface = galaxy_interface
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589
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590 def register_runnable(self, run_action):
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591 assert "id" in run_action
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592 self.graph_ids[run_action["id"]] = run_action
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diff changeset
593
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diff changeset
594 def get_subworkflow_conversion_context_graph(self, graph_id):
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diff changeset
595 if graph_id not in self.graph_id_subworkflow_conversion_contexts:
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parents:
diff changeset
596 subworkflow_conversion_context = SubworkflowConversionContext(
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parents:
diff changeset
597 self
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diff changeset
598 )
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diff changeset
599 self.graph_id_subworkflow_conversion_contexts[graph_id] = subworkflow_conversion_context
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parents:
diff changeset
600 return self.graph_id_subworkflow_conversion_contexts[graph_id]
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601
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602
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parents:
diff changeset
603 class SubworkflowConversionContext(BaseConversionContext):
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604
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605 def __init__(self, parent_context):
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606 super(SubworkflowConversionContext, self).__init__()
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parents:
diff changeset
607 self.parent_context = parent_context
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608
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diff changeset
609 @property
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diff changeset
610 def graph_ids(self):
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diff changeset
611 return self.parent_context.graph_ids
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diff changeset
612
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diff changeset
613 @property
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diff changeset
614 def workflow_directory(self):
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diff changeset
615 return self.parent_context.workflow_directory
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616
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617 @property
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618 def import_options(self):
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diff changeset
619 return self.parent_context.import_options
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620
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621 @property
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622 def galaxy_interface(self):
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623 return self.parent_context.galaxy_interface
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diff changeset
624
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diff changeset
625 def get_subworkflow_conversion_context_graph(self, graph_id):
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626 return self.parent_context.get_subworkflow_conversion_context_graph(graph_id)
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627
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628
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629 def _action(type, name, arguments={}):
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630 return {
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631 "action_arguments": arguments,
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632 "action_type": type,
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633 "output_name": name,
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634 }
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635
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636
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637 def _is_link(value):
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638 return isinstance(value, dict) and "$link" in value
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639
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640
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641 def _join_prefix(prefix, key):
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642 if prefix:
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643 new_key = "%s|%s" % (prefix, key)
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parents:
diff changeset
644 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
645 new_key = key
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
646 return new_key
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
647
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
648
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
649 def _init_connect_dict(step):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
650 if "connect" not in step:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
651 step["connect"] = {}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
652
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
653 connect = step["connect"]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
654 del step["connect"]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
655
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
656 # handle CWL-style in dict connections.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
657 if "in" in step:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
658 step_in = step["in"]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
659 assert isinstance(step_in, dict)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
660 connection_keys = set()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
661 for key, value in step_in.items():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
662 # TODO: this can be a list right?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
663 if isinstance(value, dict) and 'source' in value:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
664 value = value["source"]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
665 elif isinstance(value, dict) and 'default' in value:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
666 continue
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
667 elif isinstance(value, dict):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
668 raise KeyError('step input must define either source or default %s' % value)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
669 connect[key] = [value]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
670 connection_keys.add(key)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
671
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
672 for key in connection_keys:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
673 del step_in[key]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
674
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
675 if len(step_in) == 0:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
676 del step['in']
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
677
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
678 return connect
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
679
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
680
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
681 def _populate_input_connections(context, step, connect):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
682 _ensure_inputs_connections(step)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
683 input_connections = step["input_connections"]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
684 is_subworkflow_step = step.get("type") == "subworkflow"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
685
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
686 for key, values in connect.items():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
687 input_connection_value = []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
688 if not isinstance(values, list):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
689 values = [values]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
690 for value in values:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
691 if not isinstance(value, dict):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
692 if key == "$step":
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
693 value += "/__NO_INPUT_OUTPUT_NAME__"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
694 id, output_name = context.step_output(value)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
695 value = {"id": id, "output_name": output_name}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
696 if is_subworkflow_step:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
697 subworkflow_conversion_context = context.get_subworkflow_conversion_context(step)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
698 input_subworkflow_step_id = subworkflow_conversion_context.step_id(key)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
699 value["input_subworkflow_step_id"] = input_subworkflow_step_id
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
700 input_connection_value.append(value)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
701 if key == "$step":
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
702 key = "__NO_INPUT_OUTPUT_NAME__"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
703 input_connections[key] = input_connection_value
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
704
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
705
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
706 def _populate_annotation(step):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
707 if "annotation" not in step and "doc" in step:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
708 annotation = step.pop("doc")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
709 step["annotation"] = annotation
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
710 elif "annotation" not in step:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
711 step["annotation"] = ""
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
712
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
713
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
714 def _ensure_inputs_connections(step):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
715 if "input_connections" not in step:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
716 step["input_connections"] = {}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
717
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
718
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
719 def _ensure_defaults(in_dict, defaults):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
720 for key, value in defaults.items():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
721 if key not in in_dict:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
722 in_dict[key] = value
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
723
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
724
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
725 def _populate_tool_state(step, tool_state):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
726 step["tool_state"] = json.dumps(tool_state)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
727
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
728
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
729 def _convert_dict_to_id_list_if_needed(dict_or_list, add_label=False):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
730 rval = dict_or_list
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
731 if isinstance(dict_or_list, dict):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
732 rval = []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
733 for key, value in dict_or_list.items():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
734 if not isinstance(value, dict):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
735 value = {"type": value}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
736 if add_label:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
737 value["label"] = key
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
738 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
739 value["id"] = key
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
740 rval.append(value)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
741 return rval
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
742
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
743
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
744 def main(argv):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
745 print(json.dumps(yaml_to_workflow(argv[0])))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
746
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
747
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
748 if __name__ == "__main__":
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
749 main(sys.argv)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
750
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
751 __all__ = (
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
752 'yaml_to_workflow',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
753 'python_to_workflow',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
754 )