Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/galaxy/util/permutations.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 """ 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 |
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10 from galaxy.exceptions import MessageException |
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11 from galaxy.util.bunch import Bunch |
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12 |
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13 input_classification = Bunch( |
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14 SINGLE="single", |
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15 MATCHED="matched", |
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16 MULTIPLIED="multiplied", |
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17 ) |
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18 |
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19 |
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20 class InputMatchedException(MessageException): |
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21 """ Indicates problem matching inputs while building up inputs |
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22 permutations. """ |
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23 |
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24 |
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25 def expand_multi_inputs(inputs, classifier, key_filter=None): |
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26 key_filter = key_filter or (lambda x: True) |
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27 |
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28 single_inputs, matched_multi_inputs, multiplied_multi_inputs = __split_inputs( |
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29 inputs, |
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30 classifier, |
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31 key_filter |
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32 ) |
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33 |
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34 # Build up every combination of inputs to be run together. |
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35 input_combos = __extend_with_matched_combos(single_inputs, matched_multi_inputs) |
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36 input_combos = __extend_with_multiplied_combos(input_combos, multiplied_multi_inputs) |
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37 |
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38 return input_combos |
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39 |
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40 |
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41 def __split_inputs(inputs, classifier, key_filter): |
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42 key_filter = key_filter or (lambda x: True) |
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43 |
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44 single_inputs = {} |
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45 matched_multi_inputs = {} |
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46 multiplied_multi_inputs = {} |
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47 |
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48 for input_key in filter(key_filter, inputs): |
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49 input_type, expanded_val = classifier(input_key) |
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50 if input_type == input_classification.SINGLE: |
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51 single_inputs[input_key] = expanded_val |
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52 elif input_type == input_classification.MATCHED: |
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53 matched_multi_inputs[input_key] = expanded_val |
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54 elif input_type == input_classification.MULTIPLIED: |
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55 multiplied_multi_inputs[input_key] = expanded_val |
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56 |
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57 return (single_inputs, matched_multi_inputs, multiplied_multi_inputs) |
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58 |
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59 |
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60 def __extend_with_matched_combos(single_inputs, multi_inputs): |
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61 """ |
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62 |
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63 {a => 1, b => 2} and {c => {3, 4}, d => {5, 6}} |
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64 |
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65 Becomes |
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66 |
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67 [ {a => 1, b => 2, c => 3, d => 5}, {a => 1, b => 2, c => 4, d => 6}, ] |
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68 |
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69 """ |
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70 |
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71 if len(multi_inputs) == 0: |
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72 return [single_inputs] |
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73 |
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74 matched_multi_inputs = [] |
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75 |
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76 first_multi_input_key = next(iter(multi_inputs.keys())) |
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77 first_multi_value = multi_inputs.get(first_multi_input_key) |
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78 |
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79 for value in first_multi_value: |
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80 new_inputs = __copy_and_extend_inputs(single_inputs, first_multi_input_key, value) |
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81 matched_multi_inputs.append(new_inputs) |
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82 |
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83 for multi_input_key, multi_input_values in multi_inputs.items(): |
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84 if multi_input_key == first_multi_input_key: |
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85 continue |
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86 if len(multi_input_values) != len(first_multi_value): |
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87 raise InputMatchedException("Received %d inputs for '%s' and %d inputs for '%s', these should be of equal length" % |
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88 (len(multi_input_values), multi_input_key, len(first_multi_value), first_multi_input_key)) |
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89 |
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90 for index, value in enumerate(multi_input_values): |
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91 matched_multi_inputs[index][multi_input_key] = value |
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92 |
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93 return matched_multi_inputs |
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94 |
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95 |
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96 def __extend_with_multiplied_combos(input_combos, multi_inputs): |
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97 combos = input_combos |
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98 |
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99 for multi_input_key, multi_input_value in multi_inputs.items(): |
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100 iter_combos = [] |
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101 |
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102 for combo in combos: |
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103 for input_value in multi_input_value: |
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104 iter_combo = __copy_and_extend_inputs(combo, multi_input_key, input_value) |
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105 iter_combos.append(iter_combo) |
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106 |
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107 combos = iter_combos |
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108 |
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109 return combos |
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110 |
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111 |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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112 def __copy_and_extend_inputs(inputs, key, value): |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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113 new_inputs = dict(inputs) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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114 new_inputs[key] = value |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
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changeset
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115 return new_inputs |