Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/gxformat2/abstract.py @ 0:4f3585e2f14b draft default tip
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author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 (2021-03-22) |
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1 """Module for exporting Galaxy workflows to CWL abstract interface.""" |
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2 import argparse |
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3 import sys |
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4 from typing import Any, Dict |
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5 |
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6 from gxformat2._scripts import ensure_format2 |
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7 from gxformat2.converter import steps_as_list |
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8 from gxformat2.normalize import NormalizedWorkflow, walk_id_list_or_dict |
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9 from gxformat2.yaml import ordered_dump_to_path, ordered_load |
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10 |
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11 CWL_VERSION = "v1.2" |
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12 |
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13 SCRIPT_DESCRIPTION = """ |
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14 This script converts the an executable Galaxy workflow (in either format - |
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15 Format 2 or native .ga) into an abstract CWL representation. |
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16 |
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17 In order to represent Galaxy tool executions in the Common Workflow Language |
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18 workflow language, they are serialized as v1.2+ abstract 'Operation' classes. |
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19 Because abstract 'Operation' classes are used, the resulting CWL workflow is |
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20 not executable - either in Galaxy or by CWL implementations. The resulting CWL |
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21 file should be thought of more as a common metadata specification describing |
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22 the workflow structure. |
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23 """ |
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24 |
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25 |
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26 def from_dict(workflow_dict: dict, subworkflow=False): |
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27 """Convert dictified Galaxy workflow into abstract CWL representation.""" |
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28 # TODO: pass some sort of flag to ensure_format2 to make sure information |
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29 # about step outputs that may be present in native format is not lost when |
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30 # converting to Format2. |
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31 workflow_dict = ensure_format2(workflow_dict) |
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32 normalized_workflow = NormalizedWorkflow(workflow_dict) |
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33 workflow_dict = normalized_workflow.normalized_workflow_dict |
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34 |
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35 requirements = {} # type: Dict[str, Any] |
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36 abstract_dict = { |
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37 'class': 'Workflow', |
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38 } # type: Dict[str, Any] |
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39 if not subworkflow: |
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40 abstract_dict["cwlVersion"] = CWL_VERSION |
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41 # inputs and outputs already mostly in CWL format... |
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42 |
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43 # TODO: add test case where format2 input without inputs declaration is used |
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44 abstract_dict["inputs"] = _format2_inputs_to_abstract(workflow_dict.get("inputs", {})) |
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45 abstract_dict["outputs"] = _format2_outputs_to_abstract(workflow_dict.get("outputs", {})) |
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46 steps = {} |
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47 for format2_step in steps_as_list(workflow_dict, add_ids=True, inputs_offset=len(abstract_dict["inputs"]), mutate=False): |
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48 label = format2_step.get("label") or format2_step.get("id") |
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49 assert label is not None |
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50 label = str(label) |
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51 steps[label] = _format2_step_to_abstract(format2_step, requirements=requirements) |
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52 |
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53 abstract_dict["steps"] = steps |
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54 if requirements: |
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55 abstract_dict['requirements'] = requirements |
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56 return abstract_dict |
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57 |
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58 |
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59 def _format2_step_to_abstract(format2_step, requirements): |
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60 """Convert Format2 step CWL 1.2+ abstract operation.""" |
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61 abstract_step = {} |
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62 if "run" in format2_step: |
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63 # probably encountered in subworkflow. |
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64 format2_run = format2_step["run"] |
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65 format2_run_class = format2_run["class"] |
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66 requirements["SubworkflowFeatureRequirement"] = {} |
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67 if format2_run_class == "GalaxyWorkflow": |
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68 # preprocess to ensure it has outs - should the original call be recursive? |
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69 step_run = from_dict(format2_run, subworkflow=True) |
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70 abstract_step["run"] = step_run |
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71 else: |
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72 raise NotImplementedError("Unknown runnabled type encountered [%s]" % format2_run_class) |
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73 else: |
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74 step_run = { |
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75 "class": "Operation", |
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76 "doc": format2_step.get("doc", ""), |
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77 "inputs": {}, # TODO |
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78 "outputs": {}, # TODO |
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79 } |
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80 abstract_step["run"] = step_run |
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81 abstract_step["in"] = _format2_in_to_abstract(format2_step.get("in", [])) |
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82 abstract_step["out"] = _format2_out_to_abstract(format2_step) |
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83 return abstract_step |
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84 |
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85 |
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86 def _format2_in_to_abstract(in_dict): |
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87 """Convert Format2 'in' dict for step into CWL abstract 'in' dict.""" |
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88 return in_dict |
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89 |
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90 |
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91 def _format2_out_to_abstract(format2_step, run=None): |
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92 """Convert Format2 'out' list for step into CWL abstract 'out' list.""" |
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93 cwl_out = [] |
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94 if "out" in format2_step: |
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95 out = format2_step.get("out") |
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96 if isinstance(out, dict): |
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97 for out_name, out_def in out.items(): |
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98 # discard PJA info when converting to abstract CWL |
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99 cwl_out.append(out_name) |
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100 else: |
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101 cwl_out = out |
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102 |
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103 return cwl_out |
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104 |
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105 |
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106 def _format2_inputs_to_abstract(inputs): |
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107 """Strip Galaxy extensions or namespace them.""" |
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108 abstract_inputs = {} |
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109 |
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110 for input_name, input_def in walk_id_list_or_dict(inputs): |
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111 if isinstance(input_def, dict): |
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112 input_type = input_def.get("type") |
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113 else: |
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114 input_type = input_def |
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115 input_def = {"type": input_type} |
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116 |
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117 if input_type == "data": |
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118 input_def["type"] = "File" |
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119 |
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120 _format2_type_to_abstract(input_def) |
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121 |
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122 # Strip off Galaxy extensions |
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123 input_def.pop("position", None) |
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124 abstract_inputs[input_name] = input_def |
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125 |
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126 return abstract_inputs |
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127 |
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128 |
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129 def _format2_type_to_abstract(has_type): |
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130 format2_type = has_type.pop("type") |
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131 if format2_type == "data": |
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132 cwl_type = "File" |
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133 elif format2_type == "collection": |
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134 # TODO: handled nested collections, pairs, etc... |
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135 cwl_type = "File[]" |
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136 else: |
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137 cwl_type = format2_type |
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138 optional = has_type.pop("optional", False) |
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139 if optional: |
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140 cwl_type += "?" |
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141 has_type["type"] = cwl_type |
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142 |
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143 |
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144 def _format2_outputs_to_abstract(outputs): |
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145 """Strip Galaxy extensions or namespace them.""" |
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146 for output_name, output in walk_id_list_or_dict(outputs): |
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147 if "type" not in output: |
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148 output["type"] = "File" |
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149 return outputs |
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150 |
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151 |
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152 def main(argv=None): |
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153 """Entry point for script to export abstract interface.""" |
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154 if argv is None: |
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155 argv = sys.argv[1:] |
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156 |
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157 args = _parser().parse_args(argv) |
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158 |
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159 workflow_path = args.input_path |
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160 output_path = args.output_path or (workflow_path + ".abstract.cwl") |
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161 |
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162 if workflow_path == "-": |
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163 workflow_dict = ordered_load(sys.stdin) |
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164 else: |
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165 with open(workflow_path, "r") as f: |
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166 workflow_dict = ordered_load(f) |
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167 |
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168 abstract_dict = from_dict(workflow_dict) |
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169 ordered_dump_to_path(abstract_dict, output_path) |
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170 return 0 |
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171 |
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172 |
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173 def _parser(): |
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174 parser = argparse.ArgumentParser(description=SCRIPT_DESCRIPTION) |
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175 parser.add_argument('input_path', metavar='INPUT', type=str, |
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176 help='input workflow path (.ga/gxwf.yml)') |
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177 parser.add_argument('output_path', metavar='OUTPUT', type=str, nargs="?", |
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178 help='output workflow path (.cwl)') |
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179 return parser |
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180 |
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181 |
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182 if __name__ == "__main__": |
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183 sys.exit(main()) |
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184 |
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185 |
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186 __all__ = ('main', 'from_dict') |