Mercurial > repos > shellac > sam_consensus_v3

annotate env/lib/python3.9/site-packages/gxformat2/model.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
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1 """Abstractions for dealing with Format2 data."""
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2 from typing import cast, Dict, List, Union
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3
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4 DictOrList = Union[Dict, List]
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5
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6
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7 def convert_dict_to_id_list_if_needed(
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8 dict_or_list: DictOrList,
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9 add_label: bool = False,
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10 mutate: bool = False,
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11 ) -> list:
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12 """Convert a list or dict to a list with keys embedded.
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13
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14 If `add_label` is True, embed dict keys as 'label' attribute
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15 else 'id'.
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16 """
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17 if isinstance(dict_or_list, dict):
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18 rval = []
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19 for key, value in dict_or_list.items():
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20 if not isinstance(value, dict):
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21 value = {"type": value}
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22 if not mutate:
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23 value = value.copy()
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24 if add_label:
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25 if value.get("label") is None:
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26 value["label"] = key
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27 else:
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28 value["id"] = key
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29 rval.append(value)
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30 else:
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31 rval = cast(list, dict_or_list)
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32 return rval
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33
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34
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35 def with_step_ids(steps: list, inputs_offset: int = 0):
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36 """Walk over a list of steps and ensure the steps have a numeric id if otherwise missing."""
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37 assert isinstance(steps, list)
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38 new_steps = []
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39 for i, step in enumerate(steps):
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40 if "id" not in step:
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41 step = step.copy()
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42 step["id"] = i + inputs_offset
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43 assert step["id"] is not None
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44 new_steps.append(step)
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45 return new_steps
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46
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47
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48 def ensure_step_position(step: dict, order_index: int):
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49 """Ensure step contains a position definition.
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50
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51 Modifies the input step dictionary.
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52 """
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53 if "position" not in step:
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54 step["position"] = {
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55 "left": 10 * order_index,
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56 "top": 10 * order_index
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57 }
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58
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59
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60 def native_input_to_format2_type(step: dict, tool_state: dict) -> str:
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61 """Return a Format2 input type ('type') from a native input step dictionary."""
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62 module_type = step.get("type")
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63 if module_type == 'data_collection_input':
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64 format2_type = 'collection'
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65 elif module_type == 'data_input':
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66 format2_type = 'data'
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67 elif module_type == "parameter_input":
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68 native_type = cast(str, tool_state.get("parameter_type"))
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69 format2_type = native_type
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70 if native_type == "integer":
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71 format2_type = "int"
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72 elif native_type == "text":
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73 format2_type = "string"
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74 return format2_type
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75
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76
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77 def inputs_as_normalized_steps(workflow_dict):
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78 """Return workflow inputs to a steps in array.
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79
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80 Normalize Format2 inputs. `workflow_dict` is a Format 2 representation of
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81 a workflow. This method does not modify `workflow_dict`.
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82 """
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83 if "inputs" not in workflow_dict:
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84 return []
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85
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86 inputs = workflow_dict.get("inputs", [])
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87 new_steps = []
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88 inputs = convert_dict_to_id_list_if_needed(inputs)
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89 for input_def_raw in with_step_ids(inputs):
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90 input_def = input_def_raw.copy()
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91
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92 if "label" in input_def and "id" in input_def:
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93 raise Exception("label and id are aliases for inputs, may only define one")
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94 if "label" not in input_def and "id" not in input_def:
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95 raise Exception("Input must define a label.")
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96
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97 raw_label = input_def.pop("label", None)
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98 raw_id = input_def.pop("id", None)
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99 label = raw_label or raw_id
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100
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101 if label is None:
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102 raise Exception("Input label must not be empty.")
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103
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104 step_type = input_def.pop("type", "data")
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105 if step_type == "File":
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106 step_type = "data"
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107 elif step_type == "integer":
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108 step_type = "int"
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109 elif step_type == "text":
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110 step_type = "string"
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111
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112 step_def = input_def
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113 step_def.update({
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114 "type": step_type,
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115 "id": label,
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116 })
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117 new_steps.append(step_def)
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118
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119 return new_steps
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120
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121
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122 def inputs_as_native_steps(workflow_dict: dict):
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123 """Return workflow inputs to a steps in array - like in native Galaxy.
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124
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125 Convert Format2 types into native ones. `workflow_dict` is a Format 2
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126 representation of a workflow. This method does not modify `workflow_dict`.
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127 """
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128 if "inputs" not in workflow_dict:
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129 return []
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130
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131 inputs = workflow_dict.get("inputs", [])
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132 new_steps = []
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133 inputs = convert_dict_to_id_list_if_needed(inputs)
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134 for input_def_raw in inputs:
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135 input_def = input_def_raw.copy()
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136
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137 if "label" in input_def and "id" in input_def:
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138 raise Exception("label and id are aliases for inputs, may only define one")
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139 if "label" not in input_def and "id" not in input_def:
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140 raise Exception("Input must define a label.")
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141
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142 raw_label = input_def.pop("label", None)
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143 raw_id = input_def.pop("id", None)
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144 label = raw_label or raw_id
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145
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146 if label is None:
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147 raise Exception("Input label must not be empty.")
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148
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149 input_type = input_def.pop("type", "data")
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150 if input_type in ["File", "data", "data_input"]:
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151 step_type = "data_input"
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152 elif input_type in ["collection", "data_collection", "data_collection_input"]:
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153 step_type = "data_collection_input"
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154 elif input_type in ["text", "string", "integer", "int", "float", "color", "boolean"]:
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155 step_type = "parameter_input"
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156 format2_type = input_type
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157 if format2_type == "int":
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158 native_type = "integer"
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159 elif format2_type == "string":
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160 native_type = "text"
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161 else:
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162 native_type = format2_type
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163 input_def["parameter_type"] = native_type
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164 else:
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165 raise Exception("Unknown input type [%s] encountered." % input_type)
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166
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167 step_def = input_def
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168 step_def.update({
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169 "type": step_type,
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170 "label": label,
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171 })
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172 new_steps.append(step_def)
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173
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174 return new_steps
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175
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176
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177 def outputs_as_list(as_python: dict) -> list:
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178 """Extract outputs from Format2 rep as list."""
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179 outputs = as_python.get("outputs", [])
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180 outputs = convert_dict_to_id_list_if_needed(outputs)
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181 return outputs