Mercurial > repos > shellac > sam_consensus_v3

annotate env/lib/python3.9/site-packages/gxformat2/converter.py @ 0:4f3585e2f14b draft default tip

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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author shellac
date Mon, 22 Mar 2021 18:12:50 +0000 (2021-03-22)
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0
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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 argparse
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5 import copy
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6 import json
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7 import logging
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8 import os
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9 import sys
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10 import uuid
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11 from collections import OrderedDict
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12 from typing import Dict, Optional
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13
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14 from ._labels import Labels
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15 from .model import (
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16 convert_dict_to_id_list_if_needed,
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17 ensure_step_position,
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18 inputs_as_native_steps,
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19 with_step_ids,
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20 )
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21 from .yaml import ordered_load
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22
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23 SCRIPT_DESCRIPTION = """
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24 Convert a Format 2 Galaxy workflow description into a native format.
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25 """
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26
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27 # source: step#output and $link: step#output instead of outputSource: step/output and $link: step/output
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28 SUPPORT_LEGACY_CONNECTIONS = os.environ.get("GXFORMAT2_SUPPORT_LEGACY_CONNECTIONS") == "1"
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29 STEP_TYPES = [
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30 "subworkflow",
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31 "data_input",
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32 "data_collection_input",
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33 "tool",
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34 "pause",
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35 "parameter_input",
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36 ]
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37
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38 STEP_TYPE_ALIASES = {
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39 'input': 'data_input',
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40 'input_collection': 'data_collection_input',
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41 'parameter': 'parameter_input',
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42 }
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43
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44 RUN_ACTIONS_TO_STEPS = {
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45 'GalaxyWorkflow': 'run_workflow_to_step',
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46 'GalaxyTool': 'run_tool_to_step',
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47 }
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48
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49 POST_JOB_ACTIONS = {
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50 'hide': {
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51 'action_class': "HideDatasetAction",
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52 'default': False,
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53 'arguments': lambda x: x,
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54 },
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55 'rename': {
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56 'action_class': 'RenameDatasetAction',
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57 'default': {},
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58 'arguments': lambda x: {'newname': x},
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59 },
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60 'delete_intermediate_datasets': {
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61 'action_class': 'DeleteIntermediatesAction',
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62 'default': False,
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63 'arguments': lambda x: x,
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64 },
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65 'change_datatype': {
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66 'action_class': 'ChangeDatatypeAction',
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67 'default': {},
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68 'arguments': lambda x: {'newtype': x},
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69 },
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70 'set_columns': {
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71 'action_class': 'ColumnSetAction',
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72 'default': {},
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73 'arguments': lambda x: x,
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74 },
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75 'add_tags': {
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76 'action_class': 'TagDatasetAction',
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77 'default': [],
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78 'arguments': lambda x: {'tags': ",".join(x)},
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79 },
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80 'remove_tags': {
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81 'action_class': 'RemoveTagDatasetAction',
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82 'default': [],
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83 'arguments': lambda x: {'tags': ",".join(x)},
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84 },
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85 }
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86
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87 log = logging.getLogger(__name__)
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88
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89
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90 def rename_arg(argument):
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91 return argument
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92
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93
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94 def clean_connection(value):
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95 if value and "#" in value and SUPPORT_LEGACY_CONNECTIONS:
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96 # Hope these are just used by Galaxy testing workflows and such, and not in production workflows.
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97 log.warn("Legacy workflow syntax for connections [%s] will not be supported in the future" % value)
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98 value = value.replace("#", "/", 1)
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99 else:
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100 return value
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101
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102
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103 class ImportOptions(object):
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104
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105 def __init__(self):
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106 self.deduplicate_subworkflows = False
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107
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108
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109 def yaml_to_workflow(has_yaml, galaxy_interface, workflow_directory, import_options=None):
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110 """Convert a Format 2 workflow into standard Galaxy format from supplied stream."""
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111 as_python = ordered_load(has_yaml)
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112 return python_to_workflow(as_python, galaxy_interface, workflow_directory, import_options=import_options)
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113
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114
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115 def python_to_workflow(as_python, galaxy_interface, workflow_directory=None, import_options=None):
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116 """Convert a Format 2 workflow into standard Galaxy format from supplied dictionary."""
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117 if "yaml_content" in as_python:
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118 as_python = ordered_load(as_python["yaml_content"])
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119
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120 if workflow_directory is None:
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121 workflow_directory = os.path.abspath(".")
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122
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123 conversion_context = ConversionContext(
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124 galaxy_interface,
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125 workflow_directory,
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126 import_options,
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127 )
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128 as_python = _preprocess_graphs(as_python, conversion_context)
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129 subworkflows = None
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130 if conversion_context.import_options.deduplicate_subworkflows:
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131 # TODO: import only required workflows...
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132 # TODO: dag sort these...
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133 subworkflows = OrderedDict()
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134 for graph_id, subworkflow_content in conversion_context.graph_ids.items():
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135 if graph_id == "main":
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136 continue
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137 subworkflow_conversion_context = conversion_context.get_subworkflow_conversion_context_graph("#" + graph_id)
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138 subworkflows[graph_id] = _python_to_workflow(copy.deepcopy(subworkflow_content), subworkflow_conversion_context)
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139 converted = _python_to_workflow(as_python, conversion_context)
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140 if subworkflows is not None:
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141 converted["subworkflows"] = subworkflows
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142 return converted
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143
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144
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145 # move to a utils file?
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146 def steps_as_list(format2_workflow: dict, add_ids: bool = False, inputs_offset: int = 0, mutate: bool = False):
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147 """Return steps as a list, converting ID map to list representation if needed.
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148
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149 This method does mutate the supplied steps, try to make progress toward not doing this.
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150
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151 Add keys as labels instead of IDs. Why am I doing this?
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152 """
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153 if "steps" not in format2_workflow:
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154 raise Exception("No 'steps' key in dict, keys are %s" % format2_workflow.keys())
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155 steps = format2_workflow["steps"]
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156 steps = convert_dict_to_id_list_if_needed(steps, add_label=True, mutate=mutate)
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157 if add_ids:
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158 if mutate:
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159 _append_step_id_to_step_list_elements(steps, inputs_offset=inputs_offset)
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160 else:
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161 steps = with_step_ids(steps, inputs_offset=inputs_offset)
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162 return steps
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163
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164
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165 def _append_step_id_to_step_list_elements(steps: list, inputs_offset: int = 0):
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166 assert isinstance(steps, list)
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167 for i, step in enumerate(steps):
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168 if "id" not in step:
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169 step["id"] = i + inputs_offset
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170 assert step["id"] is not None
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171
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172
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173 def _python_to_workflow(as_python, conversion_context):
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174
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175 if "class" not in as_python:
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176 raise Exception("This is not a not a valid Galaxy workflow definition, must define a class.")
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177
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178 if as_python["class"] != "GalaxyWorkflow":
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179 raise Exception("This is not a not a valid Galaxy workflow definition, 'class' must be 'GalaxyWorkflow'.")
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180
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181 # .ga files don't have this, drop it so it isn't interpreted as a format 2 workflow.
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182 as_python.pop("class")
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183
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184 _ensure_defaults(as_python, {
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185 "a_galaxy_workflow": "true",
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186 "format-version": "0.1",
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187 "name": "Workflow",
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188 "uuid": str(uuid.uuid4()),
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189 })
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190 _populate_annotation(as_python)
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191
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192 steps = steps_as_list(as_python, mutate=True)
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193
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194 convert_inputs_to_steps(as_python, steps)
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195
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196 if isinstance(steps, list):
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197 _append_step_id_to_step_list_elements(steps)
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198 steps_as_dict = OrderedDict()
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199 for i, step in enumerate(steps):
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200 steps_as_dict[str(i)] = step
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201 if "label" in step:
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202 label = step["label"]
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203 conversion_context.labels[label] = i
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204
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205 # TODO: this really should be optional in Galaxy API.
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206 ensure_step_position(step, i)
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207
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208 as_python["steps"] = steps_as_dict
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209 steps = steps_as_dict
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210
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211 for step in steps.values():
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212 step_type = step.get("type", None)
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213 if "run" in step:
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214 if step_type is not None:
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215 raise Exception("Steps specified as run actions cannot specify a type.")
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216 run_action = step.get("run")
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217 run_action = conversion_context.get_runnable_description(run_action)
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218 if isinstance(run_action, dict):
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219 run_class = run_action["class"]
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220 run_to_step_function = eval(RUN_ACTIONS_TO_STEPS[run_class])
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221
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222 run_to_step_function(conversion_context, step, run_action)
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223 else:
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224 step["content_id"] = run_action
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225 step["type"] = "subworkflow"
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226 del step["run"]
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227
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228 for step in steps.values():
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229 step_type = step.get("type", "tool")
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230 step_type = STEP_TYPE_ALIASES.get(step_type, step_type)
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231 if step_type not in STEP_TYPES:
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232 raise Exception("Unknown step type encountered %s" % step_type)
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233 step["type"] = step_type
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234 eval("transform_%s" % step_type)(conversion_context, step)
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235
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236 outputs = as_python.pop("outputs", [])
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237 outputs = convert_dict_to_id_list_if_needed(outputs)
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238
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239 for output in outputs:
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240 assert isinstance(output, dict), "Output definition must be dictionary"
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241 assert "source" in output or "outputSource" in output, "Output definition must specify source"
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242
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243 if "label" in output and "id" in output:
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244 raise Exception("label and id are aliases for outputs, may only define one")
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245 if "label" not in output and "id" not in output:
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246 label = ""
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247
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248 raw_label = output.pop("label", None)
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249 raw_id = output.pop("id", None)
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250 label = raw_label or raw_id
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251 if Labels.is_anonymous_output_label(label):
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252 label = None
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253 source = clean_connection(output.get("outputSource"))
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254 if source is None and SUPPORT_LEGACY_CONNECTIONS:
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255 source = output.get("source").replace("#", "/", 1)
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256 id, output_name = conversion_context.step_output(source)
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257 step = steps[str(id)]
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258 workflow_output = {
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259 "output_name": output_name,
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260 "label": label,
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261 "uuid": output.get("uuid", None)
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262 }
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263 if "workflow_outputs" not in step:
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264 step["workflow_outputs"] = []
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265 step["workflow_outputs"].append(workflow_output)
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266
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267 return as_python
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268
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269
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270 def _preprocess_graphs(as_python, conversion_context):
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271 if not isinstance(as_python, dict):
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272 raise Exception("This is not a not a valid Galaxy workflow definition.")
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273
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274 format_version = as_python.get("format-version", "v2.0")
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275 assert format_version == "v2.0"
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276
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277 if "class" not in as_python and "$graph" in as_python:
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278 for subworkflow in as_python["$graph"]:
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279 if not isinstance(subworkflow, dict):
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280 raise Exception("Malformed workflow content in $graph")
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281 if "id" not in subworkflow:
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282 raise Exception("No subworkflow ID found for entry in $graph.")
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283 subworkflow_id = subworkflow["id"]
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284 if subworkflow_id == "main":
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285 as_python = subworkflow
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286
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287 conversion_context.register_runnable(subworkflow)
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288
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289 return as_python
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290
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291
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292 def convert_inputs_to_steps(workflow_dict: dict, steps: list):
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293 """Convert workflow inputs to a steps in array - like in native Galaxy.
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294
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295 workflow_dict is a Format 2 representation of a workflow and steps is a
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296 list of steps. This method will prepend all the inputs as as steps to the
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297 steps list. This method modifies both workflow_dict and steps.
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298 """
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299 if "inputs" not in workflow_dict:
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300 return
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301
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302 input_steps = inputs_as_native_steps(workflow_dict)
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303 workflow_dict.pop("inputs")
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304 for i, new_step in enumerate(input_steps):
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305 steps.insert(i, new_step)
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306
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307
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308 def run_workflow_to_step(conversion_context, step, run_action):
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309 step["type"] = "subworkflow"
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310 if conversion_context.import_options.deduplicate_subworkflows and _is_graph_id_reference(run_action):
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311 step["content_id"] = run_action
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312 else:
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313 subworkflow_conversion_context = conversion_context.get_subworkflow_conversion_context(step)
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314 step["subworkflow"] = _python_to_workflow(
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315 copy.deepcopy(run_action),
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316 subworkflow_conversion_context,
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317 )
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318
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319
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320 def _is_graph_id_reference(run_action):
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321 return run_action and not isinstance(run_action, dict)
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322
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323
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324 def transform_data_input(context, step):
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325 transform_input(context, step, default_name="Input dataset")
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326
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327
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328 def transform_data_collection_input(context, step):
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329 transform_input(context, step, default_name="Input dataset collection")
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330
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331
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332 def transform_parameter_input(context, step):
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333 transform_input(context, step, default_name="input_parameter")
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334
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335
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336 def transform_input(context, step, default_name):
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337 default_name = step.get("label", default_name)
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338 _populate_annotation(step)
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339 _ensure_inputs_connections(step)
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340
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341 if "inputs" not in step:
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342 step["inputs"] = [{}]
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343
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344 step_inputs = step["inputs"][0]
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345 if "name" in step_inputs:
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346 name = step_inputs["name"]
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347 else:
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348 name = default_name
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349
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350 _ensure_defaults(step_inputs, {
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351 "name": name,
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352 "description": "",
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353 })
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354 tool_state = {
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355 "name": name
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356 }
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357 for attrib in ["collection_type", "parameter_type", "optional", "default", "format", "restrictions", "restrictOnConnections", "suggestions"]:
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358 if attrib in step:
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359 tool_state[attrib] = step[attrib]
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360
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361 _populate_tool_state(step, tool_state)
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362
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363
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364 def transform_pause(context, step, default_name="Pause for dataset review"):
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365 default_name = step.get("label", default_name)
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366 _populate_annotation(step)
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367
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368 _ensure_inputs_connections(step)
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369
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370 if "inputs" not in step:
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371 step["inputs"] = [{}]
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372
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373 step_inputs = step["inputs"][0]
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374 if "name" in step_inputs:
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375 name = step_inputs["name"]
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376 else:
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377 name = default_name
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378
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379 _ensure_defaults(step_inputs, {
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380 "name": name,
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381 })
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382 tool_state = {
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383 "name": name
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384 }
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385
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386 connect = _init_connect_dict(step)
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387 _populate_input_connections(context, step, connect)
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388 _populate_tool_state(step, tool_state)
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389
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390
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391 def transform_subworkflow(context, step):
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392 _populate_annotation(step)
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393
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394 _ensure_inputs_connections(step)
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395
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396 tool_state = {
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397 }
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398
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399 connect = _init_connect_dict(step)
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400 _populate_input_connections(context, step, connect)
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401 _populate_tool_state(step, tool_state)
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402
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403
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404 def _runtime_value():
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405 return {"__class__": "RuntimeValue"}
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406
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407
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408 def transform_tool(context, step):
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409 if "tool_id" not in step:
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410 raise Exception("Tool steps must define a tool_id.")
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411
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412 _ensure_defaults(step, {
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413 "name": step['tool_id'],
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414 "post_job_actions": {},
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415 "tool_version": None,
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416 })
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417 post_job_actions = step["post_job_actions"]
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418 _populate_annotation(step)
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419
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420 tool_state = {
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421 # TODO: Galaxy should not require tool state actually specify a __page__.
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422 "__page__": 0,
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423 }
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424
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425 connect = _init_connect_dict(step)
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426
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427 def append_link(key, value):
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428 if key not in connect:
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429 connect[key] = []
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430 assert "$link" in value
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431 link_value = value["$link"]
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432 connect[key].append(clean_connection(link_value))
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433
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434 def replace_links(value, key=""):
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435 if _is_link(value):
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436 append_link(key, value)
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437 # Filled in by the connection, so to force late
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438 # validation of the field just mark as RuntimeValue.
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439 # It would be better I guess if this were some other
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440 # value dedicated to this purpose (e.g. a ficitious
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441 # {"__class__": "ConnectedValue"}) that could be further
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442 # validated by Galaxy.
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443 return _runtime_value()
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444 if isinstance(value, dict):
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445 new_values = {}
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446 for k, v in value.items():
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447 new_key = _join_prefix(key, k)
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448 new_values[k] = replace_links(v, new_key)
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449 return new_values
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450 elif isinstance(value, list):
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451 new_values = []
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452 for i, v in enumerate(value):
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453 # If we are a repeat we need to modify the key
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454 # but not if values are actually $links.
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455 if _is_link(v):
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456 append_link(key, v)
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457 new_values.append(None)
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458 else:
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459 new_key = "%s_%d" % (key, i)
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460 new_values.append(replace_links(v, new_key))
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461 return new_values
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462 else:
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463 return value
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464
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465 # TODO: handle runtime inputs and state together.
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466 runtime_inputs = step.get("runtime_inputs", [])
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467 if "state" in step or runtime_inputs:
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468 step_state = step.pop("state", {})
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469 step_state = replace_links(step_state)
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470
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471 for key, value in step_state.items():
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472 tool_state[key] = json.dumps(value)
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473 for runtime_input in runtime_inputs:
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474 tool_state[runtime_input] = json.dumps(_runtime_value())
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475 elif "tool_state" in step:
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476 tool_state.update(step.get("tool_state"))
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477
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478 # Fill in input connections
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479 _populate_input_connections(context, step, connect)
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480
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481 _populate_tool_state(step, tool_state)
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482
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483 # Handle outputs.
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484 out = step.pop("out", None)
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485 if out is None:
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486 # Handle LEGACY 19.XX outputs key.
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487 out = step.pop("outputs", [])
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488 out = convert_dict_to_id_list_if_needed(out)
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489 for output in out:
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490 name = output["id"]
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491 for action_key, action_dict in POST_JOB_ACTIONS.items():
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492 action_argument = output.get(action_key, action_dict['default'])
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493 if action_argument:
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494 action_class = action_dict['action_class']
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495 action_name = action_class + name
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496 action = _action(
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497 action_class,
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498 name,
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499 arguments=action_dict['arguments'](action_argument)
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500 )
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501 post_job_actions[action_name] = action
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502
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503
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504 def run_tool_to_step(conversion_context, step, run_action):
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505 tool_description = conversion_context.galaxy_interface.import_tool(
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506 run_action
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507 )
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508 step["type"] = "tool"
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509 step["tool_id"] = tool_description["tool_id"]
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510 step["tool_version"] = tool_description["tool_version"]
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511 step["tool_hash"] = tool_description.get("tool_hash")
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512 step["tool_uuid"] = tool_description.get("uuid")
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513
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514
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515 class BaseConversionContext(object):
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516
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517 def __init__(self):
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518 self.labels = {}
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519 self.subworkflow_conversion_contexts = {}
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520
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521 def step_id(self, label_or_id):
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522 if label_or_id in self.labels:
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523 id = self.labels[label_or_id]
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524 else:
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525 id = label_or_id
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526 return int(id)
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527
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528 def step_output(self, value):
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529 value_parts = str(value).split("/")
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530 if len(value_parts) == 1:
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531 value_parts.append("output")
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532 id = self.step_id(value_parts[0])
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533 return id, value_parts[1]
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534
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535 def get_subworkflow_conversion_context(self, step):
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536 # TODO: sometimes this method takes format2 steps and some times converted native ones
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537 # (for input connections) - redo this so the type signature is stronger.
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538 step_id = step.get("id")
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539 run_action = step.get("run")
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540 if self.import_options.deduplicate_subworkflows and _is_graph_id_reference(run_action):
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541 subworkflow_conversion_context = self.get_subworkflow_conversion_context_graph(run_action)
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542 return subworkflow_conversion_context
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543 if "content_id" in step:
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544 subworkflow_conversion_context = self.get_subworkflow_conversion_context_graph(step["content_id"])
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545 return subworkflow_conversion_context
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546
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547 if step_id not in self.subworkflow_conversion_contexts:
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548
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549 subworkflow_conversion_context = SubworkflowConversionContext(
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550 self
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551 )
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552 self.subworkflow_conversion_contexts[step_id] = subworkflow_conversion_context
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553 return self.subworkflow_conversion_contexts[step_id]
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554
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555 def get_runnable_description(self, run_action):
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556 if "@import" in run_action:
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557 if len(run_action) > 1:
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558 raise Exception("@import must be only key if present.")
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559
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560 run_action_path = run_action["@import"]
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561 runnable_path = os.path.join(self.workflow_directory, run_action_path)
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562 with open(runnable_path, "r") as f:
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563 runnable_description = ordered_load(f)
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564 run_action = runnable_description
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565
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566 if not self.import_options.deduplicate_subworkflows and _is_graph_id_reference(run_action):
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567 run_action = self.graph_ids[run_action[1:]]
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568
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569 return run_action
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570
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571
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572 class ConversionContext(BaseConversionContext):
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573
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574 def __init__(self, galaxy_interface, workflow_directory, import_options: Optional[ImportOptions] = None):
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575 super(ConversionContext, self).__init__()
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576 self.import_options = import_options or ImportOptions()
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577 self.graph_ids = OrderedDict() # type: Dict
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578 self.graph_id_subworkflow_conversion_contexts = {} # type: Dict
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579 self.workflow_directory = workflow_directory
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580 self.galaxy_interface = galaxy_interface
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581
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582 def register_runnable(self, run_action):
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583 assert "id" in run_action
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584 self.graph_ids[run_action["id"]] = run_action
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585
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586 def get_subworkflow_conversion_context_graph(self, graph_id):
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587 if graph_id not in self.graph_id_subworkflow_conversion_contexts:
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588 subworkflow_conversion_context = SubworkflowConversionContext(
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589 self
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590 )
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591 self.graph_id_subworkflow_conversion_contexts[graph_id] = subworkflow_conversion_context
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592 return self.graph_id_subworkflow_conversion_contexts[graph_id]
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593
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594
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595 class SubworkflowConversionContext(BaseConversionContext):
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596
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597 def __init__(self, parent_context):
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598 super(SubworkflowConversionContext, self).__init__()
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599 self.parent_context = parent_context
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600
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601 @property
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602 def graph_ids(self):
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603 return self.parent_context.graph_ids
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604
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605 @property
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606 def workflow_directory(self):
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607 return self.parent_context.workflow_directory
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608
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609 @property
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610 def import_options(self):
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611 return self.parent_context.import_options
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612
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613 @property
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614 def galaxy_interface(self):
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615 return self.parent_context.galaxy_interface
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616
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617 def get_subworkflow_conversion_context_graph(self, graph_id):
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618 return self.parent_context.get_subworkflow_conversion_context_graph(graph_id)
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619
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620
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621 def _action(type, name, arguments={}):
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622 return {
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623 "action_arguments": arguments,
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624 "action_type": type,
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625 "output_name": name,
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626 }
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627
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628
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629 def _is_link(value):
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630 return isinstance(value, dict) and "$link" in value
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631
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632
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shellac
parents:
diff changeset
633 def _join_prefix(prefix, key):
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shellac
parents:
diff changeset
634 if prefix:
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shellac
parents:
diff changeset
635 new_key = "%s|%s" % (prefix, key)
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shellac
parents:
diff changeset
636 else:
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shellac
parents:
diff changeset
637 new_key = key
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shellac
parents:
diff changeset
638 return new_key
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shellac
parents:
diff changeset
639
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shellac
parents:
diff changeset
640
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parents:
diff changeset
641 def _init_connect_dict(step):
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shellac
parents:
diff changeset
642 if "connect" not in step:
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parents:
diff changeset
643 step["connect"] = {}
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parents:
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644
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parents:
diff changeset
645 connect = step["connect"]
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shellac
parents:
diff changeset
646 del step["connect"]
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parents:
diff changeset
647
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parents:
diff changeset
648 # handle CWL-style in dict connections.
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shellac
parents:
diff changeset
649 if "in" in step:
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parents:
diff changeset
650 step_in = step["in"]
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parents:
diff changeset
651 assert isinstance(step_in, dict)
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parents:
diff changeset
652 connection_keys = set()
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shellac
parents:
diff changeset
653 for key, value in step_in.items():
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shellac
parents:
diff changeset
654 # TODO: this can be a list right?
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shellac
parents:
diff changeset
655 if isinstance(value, dict) and 'source' in value:
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shellac
parents:
diff changeset
656 value = value["source"]
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parents:
diff changeset
657 elif isinstance(value, dict) and 'default' in value:
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shellac
parents:
diff changeset
658 continue
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parents:
diff changeset
659 elif isinstance(value, dict):
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parents:
diff changeset
660 raise KeyError('step input must define either source or default %s' % value)
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parents:
diff changeset
661 connect[key] = [value]
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parents:
diff changeset
662 connection_keys.add(key)
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parents:
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663
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parents:
diff changeset
664 for key in connection_keys:
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shellac
parents:
diff changeset
665 del step_in[key]
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shellac
parents:
diff changeset
666
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shellac
parents:
diff changeset
667 if len(step_in) == 0:
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shellac
parents:
diff changeset
668 del step['in']
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parents:
diff changeset
669
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shellac
parents:
diff changeset
670 return connect
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shellac
parents:
diff changeset
671
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shellac
parents:
diff changeset
672
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shellac
parents:
diff changeset
673 def _populate_input_connections(context, step, connect):
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shellac
parents:
diff changeset
674 _ensure_inputs_connections(step)
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shellac
parents:
diff changeset
675 input_connections = step["input_connections"]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
676 is_subworkflow_step = step.get("type") == "subworkflow"
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shellac
parents:
diff changeset
677
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
678 for key, values in connect.items():
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shellac
parents:
diff changeset
679 input_connection_value = []
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
680 if not isinstance(values, list):
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shellac
parents:
diff changeset
681 values = [values]
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shellac
parents:
diff changeset
682 for value in values:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
683 if not isinstance(value, dict):
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shellac
parents:
diff changeset
684 if key == "$step":
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
685 value += "/__NO_INPUT_OUTPUT_NAME__"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
686 id, output_name = context.step_output(value)
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shellac
parents:
diff changeset
687 value = {"id": id, "output_name": output_name}
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
688 if is_subworkflow_step:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
689 subworkflow_conversion_context = context.get_subworkflow_conversion_context(step)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
690 input_subworkflow_step_id = subworkflow_conversion_context.step_id(key)
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shellac
parents:
diff changeset
691 value["input_subworkflow_step_id"] = input_subworkflow_step_id
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shellac
parents:
diff changeset
692 input_connection_value.append(value)
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shellac
parents:
diff changeset
693 if key == "$step":
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shellac
parents:
diff changeset
694 key = "__NO_INPUT_OUTPUT_NAME__"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
695 input_connections[key] = input_connection_value
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shellac
parents:
diff changeset
696
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
697
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
698 def _populate_annotation(step):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
699 if "annotation" not in step and "doc" in step:
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shellac
parents:
diff changeset
700 annotation = step.pop("doc")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
701 step["annotation"] = annotation
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
702 elif "annotation" not in step:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
703 step["annotation"] = ""
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
704
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
705
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
706 def _ensure_inputs_connections(step):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
707 if "input_connections" not in step:
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shellac
parents:
diff changeset
708 step["input_connections"] = {}
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shellac
parents:
diff changeset
709
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
710
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shellac
parents:
diff changeset
711 def _ensure_defaults(in_dict, defaults):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
712 for key, value in defaults.items():
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
713 if key not in in_dict:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
714 in_dict[key] = value
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
715
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
716
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
717 def _populate_tool_state(step, tool_state):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
718 step["tool_state"] = json.dumps(tool_state)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
719
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
720
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
721 def main(argv=None):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
722 """Entry point for script to conversion from Format 2 interface."""
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
723 if argv is None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
724 argv = sys.argv[1:]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
725
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
726 args = _parser().parse_args(argv)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
727
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
728 format2_path = args.input_path
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
729 output_path = args.output_path or (format2_path + ".gxwf.yml")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
730
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
731 workflow_directory = os.path.abspath(format2_path)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
732 galaxy_interface = None
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
733
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
734 with open(format2_path, "r") as f:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
735 has_workflow = ordered_load(f)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
736
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
737 output = python_to_workflow(has_workflow, galaxy_interface=galaxy_interface, workflow_directory=workflow_directory)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
738 with open(output_path, "w") as f:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
739 json.dump(output, f, indent=4)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
740
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
741
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
742 def _parser():
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
743 parser = argparse.ArgumentParser(description=SCRIPT_DESCRIPTION)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
744 parser.add_argument('input_path', metavar='INPUT', type=str,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
745 help='input workflow path (.ga)')
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
746 parser.add_argument('output_path', metavar='OUTPUT', type=str, nargs="?",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
747 help='output workflow path (.gxfw.yml)')
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
748 return parser
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
749
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
750
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
751 if __name__ == "__main__":
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
752 main(sys.argv)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
753
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
754
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
755 __all__ = (
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
756 'main',
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
757 'python_to_workflow',
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
758 'yaml_to_workflow',
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
759 )