Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/galaxy/util/permutations.py @ 0:26e78fe6e8c4 draft

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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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1 """ There is some shared logic between matching/multiplying inputs in workflows
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2 and tools. This module is meant to capture some general permutation logic that
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3 can be applicable for both cases but will only be used in the newer tools case
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4 first.
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5
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6 Maybe this doesn't make sense and maybe much of this stuff could be replaced
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7 with itertools product and permutations. These are open questions.
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8 """
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9 from collections import OrderedDict
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10
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11 from galaxy.exceptions import MessageException
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12 from galaxy.util.bunch import Bunch
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13
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14 input_classification = Bunch(
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15 SINGLE="single",
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16 MATCHED="matched",
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17 MULTIPLIED="multiplied",
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18 )
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21 class InputMatchedException(MessageException):
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22 """ Indicates problem matching inputs while building up inputs
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23 permutations. """
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26 def expand_multi_inputs(inputs, classifier, key_filter=None):
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27 key_filter = key_filter or (lambda x: True)
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28
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29 single_inputs, matched_multi_inputs, multiplied_multi_inputs = __split_inputs(
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30 inputs,
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31 classifier,
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32 key_filter
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33 )
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34
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35 # Build up every combination of inputs to be run together.
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36 input_combos = __extend_with_matched_combos(single_inputs, matched_multi_inputs)
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37 input_combos = __extend_with_multiplied_combos(input_combos, multiplied_multi_inputs)
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38
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39 return input_combos
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41
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42 def __split_inputs(inputs, classifier, key_filter):
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43 key_filter = key_filter or (lambda x: True)
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44
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45 single_inputs = OrderedDict()
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46 matched_multi_inputs = OrderedDict()
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47 multiplied_multi_inputs = OrderedDict()
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48
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49 for input_key in filter(key_filter, inputs):
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50 input_type, expanded_val = classifier(input_key)
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51 if input_type == input_classification.SINGLE:
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52 single_inputs[input_key] = expanded_val
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53 elif input_type == input_classification.MATCHED:
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54 matched_multi_inputs[input_key] = expanded_val
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55 elif input_type == input_classification.MULTIPLIED:
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56 multiplied_multi_inputs[input_key] = expanded_val
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57
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58 return (single_inputs, matched_multi_inputs, multiplied_multi_inputs)
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59
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60
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61 def __extend_with_matched_combos(single_inputs, multi_inputs):
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62 """
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63
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64 {a => 1, b => 2} and {c => {3, 4}, d => {5, 6}}
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65
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66 Becomes
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67
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68 [ {a => 1, b => 2, c => 3, d => 5}, {a => 1, b => 2, c => 4, d => 6}, ]
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69
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70 """
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71
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72 if len(multi_inputs) == 0:
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73 return [single_inputs]
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74
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75 matched_multi_inputs = []
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76
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77 first_multi_input_key = next(iter(multi_inputs.keys()))
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78 first_multi_value = multi_inputs.get(first_multi_input_key)
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79
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80 for value in first_multi_value:
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81 new_inputs = __copy_and_extend_inputs(single_inputs, first_multi_input_key, value)
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82 matched_multi_inputs.append(new_inputs)
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83
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84 for multi_input_key, multi_input_values in multi_inputs.items():
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85 if multi_input_key == first_multi_input_key:
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86 continue
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87 if len(multi_input_values) != len(first_multi_value):
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88 raise InputMatchedException("Received %d inputs for '%s' and %d inputs for '%s', these should be of equal length" %
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89 (len(multi_input_values), multi_input_key, len(first_multi_value), first_multi_input_key))
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90
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91 for index, value in enumerate(multi_input_values):
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92 matched_multi_inputs[index][multi_input_key] = value
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93
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94 return matched_multi_inputs
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95
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96
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97 def __extend_with_multiplied_combos(input_combos, multi_inputs):
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98 combos = input_combos
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99
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100 for multi_input_key, multi_input_value in multi_inputs.items():
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101 iter_combos = []
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102
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103 for combo in combos:
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104 for input_value in multi_input_value:
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105 iter_combo = __copy_and_extend_inputs(combo, multi_input_key, input_value)
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106 iter_combos.append(iter_combo)
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107
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108 combos = iter_combos
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109
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110 return combos
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111
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112
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113 def __copy_and_extend_inputs(inputs, key, value):
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114 new_inputs = dict(inputs)
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115 new_inputs[key] = value
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116 return new_inputs