Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/galaxy/util/rules_dsl.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 import abc |
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2 import itertools |
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3 import re |
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4 from typing import List, Type |
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5 |
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6 import yaml |
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7 from pkg_resources import resource_stream |
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8 |
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9 |
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10 def get_rules_specification(): |
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11 return yaml.safe_load(resource_stream(__name__, 'rules_dsl_spec.yml')) |
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12 |
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13 |
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14 def _ensure_rule_contains_keys(rule, keys): |
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15 for key, instance_class in keys.items(): |
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16 if key not in rule: |
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17 raise ValueError("Rule of type [{}] does not contain key [{}].".format(rule["type"], key)) |
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18 value = rule[key] |
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19 if not isinstance(value, instance_class): |
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20 raise ValueError("Rule of type [{}] does not contain correct value type for key [{}].".format(rule["type"], key)) |
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21 |
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22 |
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23 def _ensure_key_value_in(rule, key, values): |
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24 value = rule[key] |
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25 if value not in values: |
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26 raise ValueError(f"Invalid value [{value}] for [{key}] encountered.") |
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27 |
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28 |
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29 def _ensure_valid_pattern(expression): |
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30 re.compile(expression) |
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31 |
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32 |
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33 def apply_regex(regex, target, data, replacement=None, group_count=None): |
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34 pattern = re.compile(regex) |
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35 |
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36 def new_row(row): |
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37 source = row[target] |
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38 if replacement is None: |
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39 match = pattern.search(source) |
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40 if not match: |
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41 raise Exception(f"Problem applying regular expression [{regex}] to [{source}].") |
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42 |
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43 if group_count: |
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44 if len(match.groups()) != group_count: |
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45 raise Exception("Problem applying regular expression, wrong number of groups found.") |
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46 |
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47 result = row + list(match.groups()) |
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48 else: |
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49 result = row + [match.group(0)] |
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50 else: |
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51 result = row + [pattern.search(source).expand(replacement)] |
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52 |
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53 return result |
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54 |
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55 new_data = list(map(new_row, data)) |
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56 return new_data |
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57 |
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58 |
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59 class BaseRuleDefinition(metaclass=abc.ABCMeta): |
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60 |
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61 @abc.abstractproperty |
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62 def rule_type(self): |
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63 """Short string describing type of rule (plugin class) to use.""" |
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64 |
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65 @abc.abstractmethod |
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66 def validate_rule(self, rule): |
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67 """Validate dictified rule definition of this type.""" |
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68 |
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69 @abc.abstractmethod |
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70 def apply(self, rule, data, sources): |
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71 """Apply validated, dictified rule definition to supplied data.""" |
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72 |
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73 |
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74 class AddColumnMetadataRuleDefinition(BaseRuleDefinition): |
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75 rule_type = "add_column_metadata" |
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76 |
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77 def validate_rule(self, rule): |
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78 _ensure_rule_contains_keys(rule, {"value": str}) |
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79 |
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80 def apply(self, rule, data, sources): |
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81 rule_value = rule["value"] |
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82 if rule_value.startswith("identifier"): |
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83 identifier_index = int(rule_value[len("identifier"):]) |
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84 |
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85 new_rows = [] |
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86 for index, row in enumerate(data): |
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87 new_rows.append(row + [sources[index]["identifiers"][identifier_index]]) |
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88 |
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89 elif rule_value == "tags": |
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90 |
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91 def sorted_tags(index): |
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92 tags = sorted(sources[index]["tags"]) |
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93 return [",".join(tags)] |
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94 |
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95 new_rows = [] |
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96 for index, row in enumerate(data): |
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97 new_rows.append(row + sorted_tags(index)) |
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98 |
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99 return new_rows, sources |
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100 |
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101 |
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102 class AddColumnGroupTagValueRuleDefinition(BaseRuleDefinition): |
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103 rule_type = "add_column_group_tag_value" |
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104 |
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105 def validate_rule(self, rule): |
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106 _ensure_rule_contains_keys(rule, {"value": str}) |
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107 |
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108 def apply(self, rule, data, sources): |
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109 rule_value = rule["value"] |
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110 tag_prefix = "group:%s:" % rule_value |
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111 |
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112 new_rows = [] |
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113 for index, row in enumerate(data): |
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114 group_tag_value = None |
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115 source = sources[index] |
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116 tags = source["tags"] |
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117 for tag in sorted(tags): |
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118 if tag.startswith(tag_prefix): |
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119 group_tag_value = tag[len(tag_prefix):] |
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120 break |
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121 |
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122 if group_tag_value is None: |
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123 group_tag_value = rule.get("default_value", "") |
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124 |
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125 new_rows.append(row + [group_tag_value]) |
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126 |
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127 return new_rows, sources |
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128 |
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129 |
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130 class AddColumnConcatenateRuleDefinition(BaseRuleDefinition): |
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131 rule_type = "add_column_concatenate" |
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132 |
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133 def validate_rule(self, rule): |
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134 _ensure_rule_contains_keys(rule, {"target_column_0": int, "target_column_1": int}) |
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135 |
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136 def apply(self, rule, data, sources): |
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137 column_0 = rule["target_column_0"] |
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138 column_1 = rule["target_column_1"] |
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139 |
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140 new_rows = [] |
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141 for row in data: |
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142 new_rows.append(row + [row[column_0] + row[column_1]]) |
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143 |
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144 return new_rows, sources |
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145 |
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146 |
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147 class AddColumnBasenameRuleDefinition(BaseRuleDefinition): |
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148 rule_type = "add_column_basename" |
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149 |
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150 def validate_rule(self, rule): |
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151 _ensure_rule_contains_keys(rule, {"target_column": int}) |
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152 |
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153 def apply(self, rule, data, sources): |
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154 column = rule["target_column"] |
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155 re = r"[^/]*$" |
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156 return apply_regex(re, column, data), sources |
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157 |
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158 |
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159 class AddColumnRegexRuleDefinition(BaseRuleDefinition): |
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160 rule_type = "add_column_regex" |
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161 |
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162 def validate_rule(self, rule): |
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163 _ensure_rule_contains_keys(rule, {"target_column": int, "expression": str}) |
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164 _ensure_valid_pattern(rule["expression"]) |
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165 |
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166 def apply(self, rule, data, sources): |
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167 target = rule["target_column"] |
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168 expression = rule["expression"] |
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169 replacement = rule.get("replacement") |
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170 group_count = rule.get("group_count") |
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171 |
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172 return apply_regex(expression, target, data, replacement, group_count), sources |
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173 |
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174 |
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175 class AddColumnRownumRuleDefinition(BaseRuleDefinition): |
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176 rule_type = "add_column_rownum" |
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177 |
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178 def validate_rule(self, rule): |
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179 _ensure_rule_contains_keys(rule, {"start": int}) |
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180 |
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181 def apply(self, rule, data, sources): |
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182 start = rule["start"] |
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183 |
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184 new_rows = [] |
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185 for index, row in enumerate(data): |
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186 new_rows.append(row + ["%d" % (index + start)]) |
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187 |
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188 return new_rows, sources |
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189 |
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190 |
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191 class AddColumnValueRuleDefinition(BaseRuleDefinition): |
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192 rule_type = "add_column_value" |
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193 |
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194 def validate_rule(self, rule): |
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195 _ensure_rule_contains_keys(rule, {"value": str}) |
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196 |
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197 def apply(self, rule, data, sources): |
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198 value = rule["value"] |
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199 |
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200 new_rows = [] |
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201 for row in data: |
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202 new_rows.append(row + [str(value)]) |
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203 |
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204 return new_rows, sources |
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205 |
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206 |
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207 class AddColumnSubstrRuleDefinition(BaseRuleDefinition): |
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208 rule_type = "add_column_substr" |
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209 |
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210 def validate_rule(self, rule): |
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211 _ensure_rule_contains_keys(rule, { |
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212 "target_column": int, |
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213 "length": int, |
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214 "substr_type": str, |
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215 }) |
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216 _ensure_key_value_in(rule, "substr_type", ["keep_prefix", "drop_prefix", "keep_suffix", "drop_suffix"]) |
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217 |
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218 def apply(self, rule, data, sources): |
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219 target = rule["target_column"] |
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220 length = rule["length"] |
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221 substr_type = rule["substr_type"] |
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222 |
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223 def new_row(row): |
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224 original_value = row[target] |
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225 start = 0 |
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226 end = len(original_value) |
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227 |
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228 if substr_type == "keep_prefix": |
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229 end = length |
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230 elif substr_type == "drop_prefix": |
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231 start = length |
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232 elif substr_type == "keep_suffix": |
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233 start = end - length |
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234 if start < 0: |
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235 start = 0 |
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236 else: |
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237 end = end - length |
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238 if end < 0: |
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239 end = 0 |
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240 |
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241 return row + [original_value[start:end]] |
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242 |
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243 return list(map(new_row, data)), sources |
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244 |
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245 |
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246 class RemoveColumnsRuleDefinition(BaseRuleDefinition): |
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247 rule_type = "remove_columns" |
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248 |
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249 def validate_rule(self, rule): |
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250 _ensure_rule_contains_keys(rule, { |
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251 "target_columns": list, |
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252 }) |
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253 |
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254 def apply(self, rule, data, sources): |
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255 target_columns = rule["target_columns"] |
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256 |
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257 def new_row(row): |
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258 new = [] |
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259 for index, val in enumerate(row): |
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260 if index not in target_columns: |
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261 new.append(val) |
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262 return new |
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263 |
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264 return list(map(new_row, data)), sources |
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265 |
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266 |
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267 def _filter_index(func, iterable): |
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268 result = [] |
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269 for index, x in enumerate(iterable): |
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270 if func(index): |
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271 result.append(x) |
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272 |
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273 return result |
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274 |
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275 |
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276 class AddFilterRegexRuleDefinition(BaseRuleDefinition): |
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277 rule_type = "add_filter_regex" |
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278 |
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279 def validate_rule(self, rule): |
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280 _ensure_rule_contains_keys(rule, { |
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281 "target_column": int, |
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282 "invert": bool, |
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283 "expression": str, |
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284 }) |
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285 _ensure_valid_pattern(rule["expression"]) |
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286 |
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287 def apply(self, rule, data, sources): |
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288 target_column = rule["target_column"] |
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289 invert = rule["invert"] |
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290 regex = rule["expression"] |
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291 |
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292 def _filter(index): |
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293 row = data[index] |
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294 val = row[target_column] |
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295 pattern = re.compile(regex) |
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296 return not invert if pattern.search(val) else invert |
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297 |
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298 return _filter_index(_filter, data), _filter_index(_filter, sources) |
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299 |
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300 |
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301 class AddFilterCountRuleDefinition(BaseRuleDefinition): |
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302 rule_type = "add_filter_count" |
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303 |
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304 def validate_rule(self, rule): |
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305 _ensure_rule_contains_keys(rule, { |
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306 "count": int, |
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307 "invert": bool, |
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308 "which": str, |
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309 }) |
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310 _ensure_key_value_in(rule, "which", ["first", "last"]) |
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311 |
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312 def apply(self, rule, data, sources): |
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313 num_rows = len(data) |
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314 invert = rule["invert"] |
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315 n = rule["count"] |
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316 which = rule["which"] |
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317 |
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318 def _filter(index): |
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319 if which == "first": |
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320 matches = index >= n |
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321 else: |
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322 matches = index < (num_rows - n) |
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323 return not invert if matches else invert |
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324 |
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325 return _filter_index(_filter, data), _filter_index(_filter, sources) |
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326 |
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327 |
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328 class AddFilterEmptyRuleDefinition(BaseRuleDefinition): |
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329 rule_type = "add_filter_empty" |
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330 |
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331 def validate_rule(self, rule): |
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332 _ensure_rule_contains_keys(rule, { |
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333 "target_column": int, |
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334 "invert": bool |
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335 }) |
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336 |
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337 def apply(self, rule, data, sources): |
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338 invert = rule["invert"] |
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339 target_column = rule["target_column"] |
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340 |
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341 def _filter(index): |
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342 non_empty = len(data[index][target_column]) != 0 |
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343 return not invert if non_empty else invert |
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344 |
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345 return _filter_index(_filter, data), _filter_index(_filter, sources) |
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346 |
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347 |
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348 class AddFilterMatchesRuleDefinition(BaseRuleDefinition): |
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349 rule_type = "add_filter_matches" |
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350 |
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351 def validate_rule(self, rule): |
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352 _ensure_rule_contains_keys(rule, { |
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353 "target_column": int, |
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354 "invert": bool, |
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355 "value": str, |
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356 }) |
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357 |
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358 def apply(self, rule, data, sources): |
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359 invert = rule["invert"] |
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360 target_column = rule["target_column"] |
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361 value = rule["value"] |
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362 |
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363 def _filter(index): |
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364 row = data[index] |
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365 val = row[target_column] |
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366 return not invert if val == value else invert |
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367 |
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368 return _filter_index(_filter, data), _filter_index(_filter, sources) |
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369 |
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370 |
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371 class AddFilterCompareRuleDefinition(BaseRuleDefinition): |
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372 rule_type = "add_filter_compare" |
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373 |
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374 def validate_rule(self, rule): |
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375 _ensure_rule_contains_keys(rule, { |
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376 "target_column": int, |
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377 "value": int, |
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378 "compare_type": str, |
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379 }) |
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380 _ensure_key_value_in(rule, "compare_type", ["less_than", "less_than_equal", "greater_than", "greater_than_equal"]) |
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381 |
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382 def apply(self, rule, data, sources): |
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383 target_column = rule["target_column"] |
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384 value = rule["value"] |
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385 compare_type = rule["compare_type"] |
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386 |
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387 def _filter(index): |
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388 row = data[index] |
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389 target_value = float(row[target_column]) |
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390 if compare_type == "less_than": |
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391 matches = target_value < value |
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392 elif compare_type == "less_than_equal": |
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393 matches = target_value <= value |
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394 elif compare_type == "greater_than": |
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395 matches = target_value > value |
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396 elif compare_type == "greater_than_equal": |
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397 matches = target_value >= value |
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398 |
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399 return matches |
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400 |
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401 return _filter_index(_filter, data), _filter_index(_filter, sources) |
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402 |
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403 |
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404 class SortRuleDefinition(BaseRuleDefinition): |
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405 rule_type = "sort" |
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406 |
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407 def validate_rule(self, rule): |
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408 _ensure_rule_contains_keys(rule, { |
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409 "target_column": int, |
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410 "numeric": bool, |
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411 }) |
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412 |
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413 def apply(self, rule, data, sources): |
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414 target = rule["target_column"] |
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415 numeric = rule["numeric"] |
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416 |
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417 sortable = zip(data, sources) |
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418 |
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419 def sort_func(item): |
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420 a_val = item[0][target] |
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421 if numeric: |
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422 a_val = float(a_val) |
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423 return a_val |
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424 |
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425 sorted_data = sorted(sortable, key=sort_func) |
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426 |
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427 new_data = [] |
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428 new_sources = [] |
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429 |
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430 for (row, source) in sorted_data: |
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431 new_data.append(row) |
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432 new_sources.append(source) |
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433 |
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434 return new_data, new_sources |
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435 |
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436 |
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437 class SwapColumnsRuleDefinition(BaseRuleDefinition): |
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438 rule_type = "swap_columns" |
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439 |
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440 def validate_rule(self, rule): |
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441 _ensure_rule_contains_keys(rule, { |
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442 "target_column_0": int, |
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443 "target_column_1": int, |
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444 }) |
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445 |
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446 def apply(self, rule, data, sources): |
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447 target_column_0 = rule["target_column_0"] |
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448 target_column_1 = rule["target_column_1"] |
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449 |
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450 def new_row(row): |
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451 row_copy = row[:] |
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452 row_copy[target_column_0] = row[target_column_1] |
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453 row_copy[target_column_1] = row[target_column_0] |
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454 return row_copy |
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455 |
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456 return list(map(new_row, data)), sources |
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457 |
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458 |
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459 class SplitColumnsRuleDefinition(BaseRuleDefinition): |
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460 rule_type = "split_columns" |
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461 |
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462 def validate_rule(self, rule): |
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463 _ensure_rule_contains_keys(rule, { |
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464 "target_columns_0": list, |
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465 "target_columns_1": list, |
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466 }) |
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467 |
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468 def apply(self, rule, data, sources): |
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469 target_columns_0 = rule["target_columns_0"] |
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470 target_columns_1 = rule["target_columns_1"] |
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471 |
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472 def split_row(row): |
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473 new_row_0 = [] |
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474 new_row_1 = [] |
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475 for index, el in enumerate(row): |
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476 if index in target_columns_0: |
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477 new_row_0.append(el) |
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478 elif index in target_columns_1: |
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479 new_row_1.append(el) |
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480 else: |
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481 new_row_0.append(el) |
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482 new_row_1.append(el) |
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483 |
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484 return [new_row_0, new_row_1] |
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485 |
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486 data = flat_map(split_row, data) |
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487 sources = flat_map(lambda x: [x, x], sources) |
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488 |
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489 return data, sources |
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490 |
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491 |
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492 def flat_map(f, items): |
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493 return list(itertools.chain.from_iterable(map(f, items))) |
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494 |
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495 |
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496 class RuleSet: |
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497 |
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498 def __init__(self, rule_set_as_dict): |
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499 self.raw_rules = rule_set_as_dict["rules"] |
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500 self.raw_mapping = rule_set_as_dict.get("mapping", []) |
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501 |
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502 @property |
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503 def rules(self): |
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504 return self.raw_rules |
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505 |
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506 def _rules_with_definitions(self): |
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507 for rule in self.raw_rules: |
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508 yield (rule, RULES_DEFINITIONS[rule["type"]]) |
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509 |
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510 def apply(self, data, sources): |
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511 for rule, rule_definition in self._rules_with_definitions(): |
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512 rule_definition.validate_rule(rule) |
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513 data, sources = rule_definition.apply(rule, data, sources) |
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514 |
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515 return data, sources |
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516 |
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517 @property |
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518 def has_errors(self): |
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519 errored = False |
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520 try: |
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521 for rule, rule_definition in self._rules_with_definitions(): |
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522 rule_definition.validate_rule(rule) |
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523 except Exception: |
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524 errored = True |
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525 return errored |
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526 |
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527 @property |
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528 def mapping_as_dict(self): |
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529 as_dict = {} |
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530 for mapping in self.raw_mapping: |
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531 as_dict[mapping["type"]] = mapping |
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532 |
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533 return as_dict |
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534 |
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535 # Rest of this is generic, things here are Galaxy collection specific, think about about |
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536 # subclass of RuleSet for collection creation. |
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537 @property |
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538 def identifier_columns(self): |
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539 mapping_as_dict = self.mapping_as_dict |
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540 identifier_columns = [] |
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541 if "list_identifiers" in mapping_as_dict: |
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542 identifier_columns.extend(mapping_as_dict["list_identifiers"]["columns"]) |
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543 if "paired_identifier" in mapping_as_dict: |
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544 identifier_columns.append(mapping_as_dict["paired_identifier"]["columns"][0]) |
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545 |
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546 return identifier_columns |
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547 |
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548 @property |
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549 def collection_type(self): |
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550 mapping_as_dict = self.mapping_as_dict |
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551 list_columns = mapping_as_dict.get("list_identifiers", {"columns": []})["columns"] |
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552 collection_type = ":".join(map(lambda c: "list", list_columns)) |
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553 if "paired_identifier" in mapping_as_dict: |
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554 if collection_type: |
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555 collection_type += ":paired" |
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556 else: |
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557 collection_type = "paired" |
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558 return collection_type |
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559 |
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560 @property |
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561 def display(self): |
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562 message = "Rules:\n" |
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563 message += "".join("- %s\n" % r for r in self.raw_rules) |
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564 message += "Column Definitions:\n" |
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565 message += "".join("- %s\n" % m for m in self.raw_mapping) |
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566 return message |
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567 |
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568 |
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569 RULES_DEFINITION_CLASSES: List[Type[BaseRuleDefinition]] = [ |
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570 AddColumnMetadataRuleDefinition, |
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571 AddColumnGroupTagValueRuleDefinition, |
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572 AddColumnConcatenateRuleDefinition, |
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573 AddColumnBasenameRuleDefinition, |
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574 AddColumnRegexRuleDefinition, |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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575 AddColumnRownumRuleDefinition, |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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576 AddColumnValueRuleDefinition, |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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577 AddColumnSubstrRuleDefinition, |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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578 RemoveColumnsRuleDefinition, |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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579 AddFilterRegexRuleDefinition, |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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580 AddFilterCountRuleDefinition, |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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581 AddFilterEmptyRuleDefinition, |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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582 AddFilterMatchesRuleDefinition, |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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583 AddFilterCompareRuleDefinition, |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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584 SortRuleDefinition, |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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585 SwapColumnsRuleDefinition, |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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586 SplitColumnsRuleDefinition, |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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587 ] |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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588 RULES_DEFINITIONS = {} |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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589 for rule_class in RULES_DEFINITION_CLASSES: |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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590 RULES_DEFINITIONS[rule_class.rule_type] = rule_class() |