Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/galaxy/tool_util/parser/output_objects.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 from galaxy.util.dictifiable import Dictifiable |
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2 from .output_actions import ToolOutputActionGroup |
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3 from .output_collection_def import dataset_collector_descriptions_from_output_dict |
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4 |
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5 |
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6 class ToolOutputBase(Dictifiable): |
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7 |
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8 def __init__(self, name, label=None, filters=None, hidden=False, from_expression=None): |
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9 super().__init__() |
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10 self.name = name |
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11 self.label = label |
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12 self.filters = filters or [] |
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13 self.hidden = hidden |
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14 self.collection = False |
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15 self.from_expression = from_expression |
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16 |
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17 def to_dict(self, view='collection', value_mapper=None, app=None): |
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18 return super().to_dict(view=view, value_mapper=value_mapper) |
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19 |
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20 |
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21 class ToolOutput(ToolOutputBase): |
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22 """ |
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23 Represents an output datasets produced by a tool. For backward |
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24 compatibility this behaves as if it were the tuple:: |
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25 |
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26 (format, metadata_source, parent) |
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27 """ |
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28 |
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29 dict_collection_visible_keys = ['name', 'format', 'label', 'hidden', 'output_type', 'format_source', |
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30 'default_identifier_source', 'metadata_source', 'parent', 'count', 'from_work_dir'] |
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31 |
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32 def __init__(self, name, format=None, format_source=None, metadata_source=None, |
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33 parent=None, label=None, filters=None, actions=None, hidden=False, |
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34 implicit=False, from_expression=None): |
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35 super().__init__(name, label=label, filters=filters, hidden=hidden, from_expression=from_expression) |
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36 self.output_type = "data" |
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37 self.format = format |
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38 self.format_source = format_source |
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39 self.metadata_source = metadata_source |
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40 self.parent = parent |
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41 self.actions = actions |
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42 |
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43 # Initialize default values |
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44 self.change_format = [] |
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45 self.implicit = implicit |
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46 self.from_work_dir = None |
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47 |
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48 # Tuple emulation |
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49 |
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50 def __len__(self): |
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51 return 3 |
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52 |
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53 def __getitem__(self, index): |
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54 if index == 0: |
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55 return self.format |
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56 elif index == 1: |
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57 return self.metadata_source |
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58 elif index == 2: |
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59 return self.parent |
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60 else: |
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61 raise IndexError(index) |
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62 |
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63 def __iter__(self): |
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64 return iter((self.format, self.metadata_source, self.parent)) |
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65 |
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66 def to_dict(self, view='collection', value_mapper=None, app=None): |
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67 as_dict = super().to_dict(view=view, value_mapper=value_mapper, app=app) |
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68 format = self.format |
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69 if format and format != "input" and app: |
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70 edam_format = app.datatypes_registry.edam_formats.get(self.format) |
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71 as_dict["edam_format"] = edam_format |
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72 edam_data = app.datatypes_registry.edam_data.get(self.format) |
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73 as_dict["edam_data"] = edam_data |
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74 as_dict['discover_datasets'] = list(map(lambda d: d.to_dict(), self.dataset_collector_descriptions)) |
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75 return as_dict |
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76 |
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77 @staticmethod |
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78 def from_dict(name, output_dict, tool=None): |
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79 output = ToolOutput(name) |
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80 output.format = output_dict.get("format", "data") |
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81 output.change_format = [] |
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82 output.format_source = output_dict.get("format_source", None) |
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83 output.default_identifier_source = output_dict.get("default_identifier_source", None) |
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84 output.metadata_source = output_dict.get("metadata_source", "") |
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85 output.parent = output_dict.get("parent", None) |
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86 output.label = output_dict.get("label", None) |
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87 output.count = output_dict.get("count", 1) |
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88 output.filters = [] |
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89 output.tool = tool |
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90 output.from_work_dir = output_dict.get("from_work_dir", None) |
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91 output.hidden = output_dict.get("hidden", "") |
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92 # TODO: implement tool output action group fixes |
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93 output.actions = ToolOutputActionGroup(output, None) |
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94 output.dataset_collector_descriptions = dataset_collector_descriptions_from_output_dict(output_dict) |
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95 return output |
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96 |
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97 |
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98 class ToolExpressionOutput(ToolOutputBase): |
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99 dict_collection_visible_keys = ('name', 'format', 'label', 'hidden', 'output_type') |
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100 |
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101 def __init__(self, name, output_type, from_expression, |
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102 label=None, filters=None, actions=None, hidden=False): |
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103 super().__init__(name, label=label, filters=filters, hidden=hidden) |
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104 self.output_type = output_type # JSON type... |
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105 self.from_expression = from_expression |
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106 self.format = "expression.json" # galaxy.datatypes.text.ExpressionJson.file_ext |
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107 |
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108 self.format_source = None |
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109 self.metadata_source = None |
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110 self.parent = None |
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111 self.actions = actions |
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112 |
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113 # Initialize default values |
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114 self.change_format = [] |
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115 self.implicit = False |
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116 self.from_work_dir = None |
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117 |
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118 |
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119 class ToolOutputCollection(ToolOutputBase): |
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120 """ |
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121 Represents a HistoryDatasetCollectionAssociation of output datasets produced |
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122 by a tool. |
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123 |
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124 .. code-block:: |
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125 |
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126 <outputs> |
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127 <collection type="list" label="${tool.name} on ${on_string} fasta"> |
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128 <discover_datasets pattern="__name__" ext="fasta" visible="True" directory="outputFiles" /> |
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129 </collection> |
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130 <collection type="paired" label="${tool.name} on ${on_string} paired reads"> |
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131 <data name="forward" format="fastqsanger" /> |
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132 <data name="reverse" format="fastqsanger"/> |
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133 </collection> |
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134 <outputs> |
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135 """ |
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136 dict_collection_visible_keys = ['name', 'format', 'label', 'hidden', 'output_type', 'default_format', |
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137 'default_format_source', 'default_metadata_source', 'inherit_format', 'inherit_metadata'] |
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138 |
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139 def __init__( |
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140 self, |
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141 name, |
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142 structure, |
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143 label=None, |
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144 filters=None, |
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145 hidden=False, |
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146 default_format="data", |
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147 default_format_source=None, |
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148 default_metadata_source=None, |
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149 inherit_format=False, |
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150 inherit_metadata=False |
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151 ): |
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152 super().__init__(name, label=label, filters=filters, hidden=hidden) |
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153 self.output_type = "collection" |
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154 self.collection = True |
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155 self.default_format = default_format |
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156 self.structure = structure |
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157 self.outputs = {} |
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158 |
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159 self.inherit_format = inherit_format |
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160 self.inherit_metadata = inherit_metadata |
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161 |
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162 self.metadata_source = default_metadata_source |
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163 self.format_source = default_format_source |
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164 self.change_format = [] # TODO |
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165 |
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166 def known_outputs(self, inputs, type_registry): |
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167 if self.dynamic_structure: |
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168 return [] |
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169 |
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170 # This line is probably not right - should verify structured_like |
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171 # or have outputs and all outputs have name. |
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172 if len(self.outputs) > 1: |
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173 output_parts = [ToolOutputCollectionPart(self, k, v) for k, v in self.outputs.items()] |
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174 else: |
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175 collection_prototype = self.structure.collection_prototype(inputs, type_registry) |
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176 |
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177 def prototype_dataset_element_to_output(element, parent_ids=None): |
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178 parent_ids = parent_ids or [] |
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179 name = element.element_identifier |
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180 format = self.default_format |
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181 if self.inherit_format: |
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182 format = element.dataset_instance.ext |
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183 output = ToolOutput( |
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184 name, |
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185 format=format, |
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186 format_source=self.format_source, |
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187 metadata_source=self.metadata_source, |
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188 implicit=True, |
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189 ) |
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190 if self.inherit_metadata: |
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191 output.metadata_source = element.dataset_instance |
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192 return ToolOutputCollectionPart( |
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193 self, |
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194 element.element_identifier, |
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195 output, |
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196 parent_ids=parent_ids, |
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197 ) |
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198 |
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199 def prototype_collection_to_output(collection_prototype, parent_ids=None): |
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200 parent_ids = parent_ids or [] |
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201 output_parts = [] |
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202 for element in collection_prototype.elements: |
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203 element_parts = [] |
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204 if not element.is_collection: |
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205 element_parts.append(prototype_dataset_element_to_output(element, parent_ids)) |
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206 else: |
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207 new_parent_ids = parent_ids[:] + [element.element_identifier] |
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208 element_parts.extend(prototype_collection_to_output(element.element_object, new_parent_ids)) |
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209 output_parts.extend(element_parts) |
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210 |
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211 return output_parts |
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212 |
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213 output_parts = prototype_collection_to_output(collection_prototype) |
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214 |
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215 return output_parts |
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216 |
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217 @property |
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218 def dynamic_structure(self): |
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219 return self.structure.dynamic |
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220 |
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221 @property |
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222 def dataset_collector_descriptions(self): |
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223 if not self.dynamic_structure: |
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224 raise Exception("dataset_collector_descriptions called for output collection with static structure") |
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225 return self.structure.dataset_collector_descriptions |
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226 |
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227 def to_dict(self, view='collection', value_mapper=None, app=None): |
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228 as_dict = super().to_dict(view=view, value_mapper=value_mapper, app=app) |
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229 as_dict['structure'] = self.structure.to_dict() |
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230 return as_dict |
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231 |
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232 @staticmethod |
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233 def from_dict(name, output_dict, tool=None): |
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234 structure = ToolOutputCollectionStructure.from_dict(output_dict["structure"]) |
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235 rval = ToolOutputCollection( |
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236 name, |
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237 structure=structure, |
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238 label=output_dict.get("label", None), |
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239 filters=None, |
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240 hidden=output_dict.get("hidden", False), |
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241 default_format=output_dict.get("default_format", "data"), |
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242 default_format_source=output_dict.get("default_format_source", None), |
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243 default_metadata_source=output_dict.get("default_metadata_source", None), |
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244 inherit_format=output_dict.get("inherit_format", False), |
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245 inherit_metadata=output_dict.get("inherit_metadata", False), |
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246 ) |
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247 return rval |
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248 |
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249 |
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250 class ToolOutputCollectionStructure: |
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251 |
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252 def __init__( |
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253 self, |
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254 collection_type, |
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255 collection_type_source=None, |
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256 collection_type_from_rules=None, |
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257 structured_like=None, |
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258 dataset_collector_descriptions=None, |
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259 ): |
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260 self.collection_type = collection_type |
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261 self.collection_type_source = collection_type_source |
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262 self.collection_type_from_rules = collection_type_from_rules |
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263 self.structured_like = structured_like |
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264 self.dataset_collector_descriptions = dataset_collector_descriptions or [] |
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265 if collection_type and collection_type_source: |
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266 raise ValueError("Cannot set both type and type_source on collection output.") |
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267 if collection_type is None and structured_like is None and dataset_collector_descriptions is None and collection_type_source is None and collection_type_from_rules is None: |
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268 raise ValueError("Output collection types must specify source of collection type information (e.g. structured_like or type_source).") |
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269 if dataset_collector_descriptions and (structured_like or collection_type_from_rules): |
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270 raise ValueError("Cannot specify dynamic structure (discovered_datasets) and collection type attributes structured_like or collection_type_from_rules.") |
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271 self.dynamic = bool(dataset_collector_descriptions) |
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272 |
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273 def collection_prototype(self, inputs, type_registry): |
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274 # either must have specified structured_like or something worse |
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275 if self.structured_like: |
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276 collection_prototype = inputs[self.structured_like].collection |
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277 else: |
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278 collection_type = self.collection_type |
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279 assert collection_type |
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280 collection_prototype = type_registry.prototype(collection_type) |
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281 collection_prototype.collection_type = collection_type |
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282 return collection_prototype |
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283 |
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284 def to_dict(self): |
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285 return { |
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286 'collection_type': self.collection_type, |
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287 'collection_type_source': self.collection_type_source, |
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288 'collection_type_from_rules': self.collection_type_from_rules, |
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289 'structured_like': self.structured_like, |
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290 'discover_datasets': [d.to_dict() for d in self.dataset_collector_descriptions], |
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291 } |
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292 |
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293 @staticmethod |
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294 def from_dict(as_dict): |
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295 structure = ToolOutputCollectionStructure( |
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296 collection_type=as_dict['collection_type'], |
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297 collection_type_source=as_dict['collection_type_source'], |
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298 collection_type_from_rules=as_dict['collection_type_from_rules'], |
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299 structured_like=as_dict['structured_like'], |
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300 dataset_collector_descriptions=dataset_collector_descriptions_from_output_dict(as_dict), |
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301 ) |
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302 return structure |
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303 |
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304 |
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305 class ToolOutputCollectionPart: |
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306 |
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307 def __init__(self, output_collection_def, element_identifier, output_def, parent_ids=None): |
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308 parent_ids = parent_ids or [] |
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309 self.output_collection_def = output_collection_def |
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310 self.element_identifier = element_identifier |
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311 self.output_def = output_def |
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312 self.parent_ids = parent_ids |
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313 |
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314 @property |
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315 def effective_output_name(self): |
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316 name = self.output_collection_def.name |
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317 part_name = self.element_identifier |
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318 effective_output_name = f"{name}|__part__|{part_name}" |
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319 return effective_output_name |
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320 |
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321 @staticmethod |
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322 def is_named_collection_part_name(name): |
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323 return "|__part__|" in name |
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324 |
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325 @staticmethod |
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326 def split_output_name(name): |
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327 assert ToolOutputCollectionPart.is_named_collection_part_name(name) |
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328 return name.split("|__part__|") |